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Sadiq S, Harvey E, Mifsud JCO, Minasny B, McBratney AB, Pozza LE, Mahar JE, Holmes EC. Australian terrestrial environments harbour extensive RNA virus diversity. Virology 2024; 593:110007. [PMID: 38346363 DOI: 10.1016/j.virol.2024.110007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 03/13/2024]
Abstract
Australia is home to a diverse range of unique native fauna and flora. To address whether Australian ecosystems also harbour unique viruses, we performed meta-transcriptomic sequencing of 16 farmland and sediment samples taken from the east and west coasts of Australia. We identified 2460 putatively novel RNA viruses across 18 orders, the vast majority of which belonged to the microbe-associated phylum Lenarviricota. In many orders, such as the Nodamuvirales and Ghabrivirales, the novel viruses identified here comprised entirely new clades. Novel viruses also fell between established genera or families, such as in the Cystoviridae and Picornavirales, while highly divergent lineages were identified in the Sobelivirales and Ghabrivirales. Viral read abundance and alpha diversity were influenced by sampling site, soil type and land use, but not by depth from the surface. In sum, Australian soils and sediments are home to remarkable viral diversity, reflecting the biodiversity of local fauna and flora.
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Affiliation(s)
- Sabrina Sadiq
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Erin Harvey
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jonathon C O Mifsud
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Budiman Minasny
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Alex B McBratney
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Liana E Pozza
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jackie E Mahar
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
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Abstract
The origin of SARS-CoV-2 has evoked heated debate and strong accusations, yet seemingly little resolution. I review the scientific evidence on the origin of SARS-CoV-2 and its subsequent spread through the human population. The available data clearly point to a natural zoonotic emergence within, or closely linked to, the Huanan Seafood Wholesale Market in Wuhan. There is no direct evidence linking the emergence of SARS-CoV-2 to laboratory work conducted at the Wuhan Institute of Virology. The subsequent global spread of SARS-CoV-2 was characterized by a gradual adaptation to humans, with dual increases in transmissibility and virulence until the emergence of the Omicron variant. Of note has been the frequent transmission of SARS-CoV-2 from humans to other animals, marking it as a strongly host generalist virus. Unless lessons from the origin of SARS-CoV-2 are learned, it is inevitable that more zoonotic events leading to more epidemics and pandemics will plague human populations.
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Affiliation(s)
- Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
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Waller SJ, Egan E, Crow S, Charsley A, Lokman PM, Williams EK, Holmes EC, Geoghegan JL. Host and geography impact virus diversity in New Zealand's longfin and shortfin eels. Arch Virol 2024; 169:85. [PMID: 38546898 PMCID: PMC10978610 DOI: 10.1007/s00705-024-06019-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/17/2024] [Indexed: 04/01/2024]
Abstract
The fishing and aquaculture industry is vital for global food security, yet viral diseases can result in mass fish die-off events. Determining the viromes of traditionally understudied species, such as fish, enhances our understanding of the global virosphere and the factors that influence virome composition and disease emergence. Very little is known about the viruses present in New Zealand's native fish species, including the shortfin eel (Anguilla australis) and the longfin eel (Anguilla dieffenbachii), both of which are fished culturally by Māori (the indigenous population of New Zealand) and commercially. Through a total RNA metatranscriptomic analysis of longfin and shortfin eels across three different geographic locations in the South Island of New Zealand, we aimed to determine whether viruses had jumped between the two eel species and whether eel virome composition was impacted by life stage, species, and geographic location. We identified nine viral species spanning eight different families, thereby enhancing our understanding of eel virus diversity in New Zealand and the host range of these viral families. Viruses of the family Flaviviridae (genus Hepacivirus) were widespread and found in both longfin and shortfin eels, indicative of cross-species transmission or virus-host co-divergence. Notably, both host specificity and geographic location appeared to influence eel virome composition, highlighting the complex interaction between viruses, hosts, and their ecosystems. This study broadens our understanding of viromes in aquatic hosts and highlights the importance of gaining baseline knowledge of fish viral abundance and diversity, particularly in aquatic species that are facing population declines.
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Affiliation(s)
- Stephanie J Waller
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Eimear Egan
- National Institute of Water and Atmospheric Research, Auckland, 1010, New Zealand
| | - Shannan Crow
- National Institute of Water and Atmospheric Research, Auckland, 1010, New Zealand
| | - Anthony Charsley
- National Institute of Water and Atmospheric Research, Auckland, 1010, New Zealand
| | - P Mark Lokman
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Erica K Williams
- National Institute of Water and Atmospheric Research, Auckland, 1010, New Zealand
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand.
- Institute of Environmental Science and Research, Wellington, New Zealand.
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Costa VA, Ronco F, Mifsud JCO, Harvey E, Salzburger W, Holmes EC. Host adaptive radiation is associated with rapid virus diversification and cross-species transmission in African cichlid fishes. Curr Biol 2024; 34:1247-1257.e3. [PMID: 38428417 DOI: 10.1016/j.cub.2024.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/18/2023] [Accepted: 02/06/2024] [Indexed: 03/03/2024]
Abstract
Adaptive radiations are generated through a complex interplay of biotic and abiotic factors. Although adaptive radiations have been widely studied in the context of animal and plant evolution, little is known about how they impact the evolution of the viruses that infect these hosts, which in turn may provide insights into the drivers of cross-species transmission and hence disease emergence. We examined how the rapid adaptive radiation of the cichlid fishes of African Lake Tanganyika over the last 10 million years has shaped the diversity and evolution of the viruses they carry. Through metatranscriptomic analysis of 2,242 RNA sequencing libraries, we identified 121 vertebrate-associated viruses among various tissue types that fell into 13 RNA and 4 DNA virus groups. Host-switching was commonplace, particularly within the Astroviridae, Metahepadnavirus, Nackednavirus, Picornaviridae, and Hepacivirus groups, occurring more frequently than in other fish communities. A time-calibrated phylogeny revealed that hepacivirus diversification was not constant throughout the cichlid radiation but accelerated 2-3 million years ago, coinciding with a period of rapid cichlid diversification and niche packing in Lake Tanganyika, thereby providing more closely related hosts for viral infection. These data depict a dynamic virus ecosystem within the cichlids of Lake Tanganyika, characterized by rapid virus diversification and frequent host jumping, and likely reflecting their close phylogenetic relationships that lower the barriers to cross-species virus transmission.
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Affiliation(s)
- Vincenzo A Costa
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Fabrizia Ronco
- Natural History Museum, University of Oslo, 0562 Oslo, Norway
| | - Jonathon C O Mifsud
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Erin Harvey
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Walter Salzburger
- Zoological Institute, Department of Environmental Sciences, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
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Pan YF, Zhao H, Gou QY, Shi PB, Tian JH, Feng Y, Li K, Yang WH, Wu D, Tang G, Zhang B, Ren Z, Peng S, Luo GY, Le SJ, Xin GY, Wang J, Hou X, Peng MW, Kong JB, Chen XX, Yang CH, Mei SQ, Liao YQ, Cheng JX, Wang J, Chaolemen, Wu YH, Wang JB, An T, Huang X, Eden JS, Li J, Guo D, Liang G, Jin X, Holmes EC, Li B, Wang D, Li J, Wu WC, Shi M. Metagenomic analysis of individual mosquito viromes reveals the geographical patterns and drivers of viral diversity. Nat Ecol Evol 2024:10.1038/s41559-024-02365-0. [PMID: 38519631 DOI: 10.1038/s41559-024-02365-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 02/11/2024] [Indexed: 03/25/2024]
Abstract
Mosquito transmitted viruses are responsible for an increasing burden of human disease. Despite this, little is known about the diversity and ecology of viruses within individual mosquito hosts. Here, using a meta-transcriptomic approach, we determined the viromes of 2,438 individual mosquitoes (81 species), spanning ~4,000 km along latitudes and longitudes in China. From these data we identified 393 viral species associated with mosquitoes, including 7 (putative) species of arthropod-borne viruses (that is, arboviruses). We identified potential mosquito species and geographic hotspots of viral diversity and arbovirus occurrence, and demonstrated that the composition of individual mosquito viromes was strongly associated with host phylogeny. Our data revealed a large number of viruses shared among mosquito species or genera, enhancing our understanding of the host specificity of insect-associated viruses. We also detected multiple virus species that were widespread throughout the country, perhaps reflecting long-distance mosquito dispersal. Together, these results greatly expand the known mosquito virome, linked viral diversity at the scale of individual insects to that at a country-wide scale, and offered unique insights into the biogeography and diversity of viruses in insect vectors.
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Affiliation(s)
- Yuan-Fei Pan
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Hailong Zhao
- BGI Research, Shenzhen, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, China
| | - Qin-Yu Gou
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Pei-Bo Shi
- BGI Research, Shenzhen, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jun-Hua Tian
- Wuhan Center for Disease Control and Prevention, Wuhan, China
| | - Yun Feng
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, China
| | - Kun Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wei-Hong Yang
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, China
| | - De Wu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Guangpeng Tang
- Guizhou Center for Disease Control and Prevention, Guiyang, China
| | - Bing Zhang
- Xinjiang Key Laboratory of Molecular Biology for Endemic Diseases, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
| | - Zirui Ren
- BGI Research, Shenzhen, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, China
| | - Shiqin Peng
- BGI Research, Shenzhen, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, China
| | - Geng-Yan Luo
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Shi-Jia Le
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Gen-Yang Xin
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Jing Wang
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Xin Hou
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Min-Wu Peng
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Jian-Bin Kong
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Xin-Xin Chen
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Chun-Hui Yang
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Shi-Qiang Mei
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Yu-Qi Liao
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Jing-Xia Cheng
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Juan Wang
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, China
| | - Chaolemen
- Old Barag Banner Center for Disease Control and Prevention, Hulunbuir, China
| | - Yu-Hui Wu
- Old Barag Banner Center for Disease Control and Prevention, Hulunbuir, China
| | - Jian-Bo Wang
- Hulunbuir Center for Disease Control and Prevention, Hulunbuir, China
| | - Tongqing An
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xinyi Huang
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - John-Sebastian Eden
- Centre for Virus Research, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Deyin Guo
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, China
| | - Guodong Liang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xin Jin
- BGI Research, Shenzhen, China
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Bo Li
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China.
- Ministry of Education Key Laboratory for Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China.
| | - Daxi Wang
- BGI Research, Shenzhen, China.
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, China.
| | - Junhua Li
- BGI Research, Shenzhen, China.
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, China.
| | - Wei-Chen Wu
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
| | - Mang Shi
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
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Zhou H, Tian RR, Wang XR, Yang JX, Wang YX, Zhao ML, Zhang XD, Ma YH, Lv LB, Holmes EC, Zheng YT, Shi WF. Identification of novel mammalian viruses in tree shrews ( Tupaia belangeri chinensis). Zool Res 2024; 45:429-438. [PMID: 38485510 PMCID: PMC11017089 DOI: 10.24272/j.issn.2095-8137.2023.306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 12/25/2023] [Indexed: 03/19/2024] Open
Abstract
The Chinese tree shrew ( Tupaia belangeri chinensis), a member of the mammalian order Scandentia, exhibits considerable similarities with primates, including humans, in aspects of its nervous, immune, and metabolic systems. These similarities have established the tree shrew as a promising experimental model for biomedical research on cancer, infectious diseases, metabolic disorders, and mental health conditions. Herein, we used meta-transcriptomic sequencing to analyze plasma, as well as oral and anal swab samples, from 105 healthy asymptomatic tree shrews to identify the presence of potential zoonotic viruses. In total, eight mammalian viruses with complete genomes were identified, belonging to six viral families, including Flaviviridae, Hepeviridae, Parvovirinae, Picornaviridae, Sedoreoviridae, and Spinareoviridae. Notably, the presence of rotavirus was recorded in tree shrews for the first time. Three viruses - hepacivirus 1, parvovirus, and picornavirus - exhibited low genetic similarity (<70%) with previously reported viruses at the whole-genome scale, indicating novelty. Conversely, three other viruses - hepacivirus 2, hepatovirus A and hepevirus - exhibited high similarity (>94%) to known viral strains. Phylogenetic analyses also revealed that the rotavirus and mammalian orthoreovirus identified in this study may be novel reassortants. These findings provide insights into the diverse viral spectrum present in captive Chinese tree shrews, highlighting the necessity for further research into their potential for cross-species transmission.
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Affiliation(s)
- Hong Zhou
- School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong 250117, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, Shandong 271000, China
| | - Ren-Rong Tian
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Xiu-Rong Wang
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong 250117, China
| | - Jin-Xuan Yang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Yun-Xiao Wang
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong 250117, China
| | - Ming-Liang Zhao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Xu-Dong Zhang
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong 250117, China
| | - Yu-Hua Ma
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Long-Bao Lv
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China. E-mail:
| | - Wei-Feng Shi
- Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai Institute of Virology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China. E-mail:
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Xie L, Luo G, Yang Z, Wu WC, Chen J, Ren Y, Zeng Z, Ye G, Pan Y, Zhao WJ, Chen YQ, Hou W, Sun Y, Guo D, Yang Z, Li J, Holmes EC, Li Y, Chen L, Shi M. The clinical outcome of COVID-19 is strongly associated with microbiome dynamics in the upper respiratory tract. J Infect 2024; 88:106118. [PMID: 38342382 DOI: 10.1016/j.jinf.2024.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 02/13/2024]
Abstract
OBJECTIVES The respiratory tract is the portal of entry for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although a variety of respiratory pathogens other than SARS-CoV-2 have been associated with severe cases of COVID-19 disease, the dynamics of the upper respiratory microbiota during disease the course of disease, and how they impact disease manifestation, remain uncertain. METHODS We collected 349 longitudinal upper respiratory samples from a cohort of 65 COVID-19 patients (cohort 1), 28 samples from 28 recovered COVID-19 patients (cohort 2), and 59 samples from 59 healthy controls (cohort 3). All COVID-19 patients originated from the earliest stage of the epidemic in Wuhan. Based on a modified clinical scale, the disease course was divided into five clinical disease phases (pseudotimes): "Healthy" (pseudotime 0), "Incremental" (pseudotime 1), "Critical" (pseudotime 2), "Complicated" (pseudotime 3), "Convalescent" (pseudotime 4), and "Long-term follow-up" (pseudotime 5). Using meta-transcriptomics, we investigated the features and dynamics of transcriptionally active microbes in the upper respiratory tract (URT) over the course of COVID-19 disease, as well as its association with disease progression and clinical outcomes. RESULTS Our results revealed that the URT microbiome exhibits substantial heterogeneity during disease course. Two clusters of microbial communities characterized by low alpha diversity and enrichment for multiple pathogens or potential pathobionts (including Acinetobacter and Candida) were associated with disease progression and a worse clinical outcome. We also identified a series of microbial indicators that classified disease progression into more severe stages. Longitudinal analysis revealed that although the microbiome exhibited complex and changing patterns during COVID-19, a restoration of URT microbiomes from early dysbiosis toward more diverse status in later disease stages was observed in most patients. In addition, a group of potential pathobionts were strongly associated with the concentration of inflammatory indicators and mortality. CONCLUSION This study revealed strong links between URT microbiome dynamics and disease progression and clinical outcomes in COVID-19, implying that the treatment of severe disease should consider the full spectrum of microbial pathogens present.
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Affiliation(s)
- Linlin Xie
- Wuhan Research Center for Infectious Diseases and Tumors of the Chinese Academy of Medical Sciences/Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment/Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Gengyan Luo
- State key laboratory for biocontrol, Shenzhen Key Laboratory of Systems Medicine for inflammatory diseases, School of Medicine, Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Zhongzhou Yang
- State key laboratory for biocontrol, Shenzhen Key Laboratory of Systems Medicine for inflammatory diseases, School of Medicine, Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Wei-Chen Wu
- State key laboratory for biocontrol, Shenzhen Key Laboratory of Systems Medicine for inflammatory diseases, School of Medicine, Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Jintao Chen
- State Key Laboratory of Virology/Department of Laboratory Medicine/Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences/Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Yuting Ren
- State Key Laboratory of Virology/Department of Laboratory Medicine/Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences/Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Zhikun Zeng
- Wuhan Research Center for Infectious Diseases and Tumors of the Chinese Academy of Medical Sciences/Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment/Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Guangming Ye
- Wuhan Research Center for Infectious Diseases and Tumors of the Chinese Academy of Medical Sciences/Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment/Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yunbao Pan
- Wuhan Research Center for Infectious Diseases and Tumors of the Chinese Academy of Medical Sciences/Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment/Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Wen-Jing Zhao
- State key laboratory for biocontrol, Shenzhen Key Laboratory of Systems Medicine for inflammatory diseases, School of Medicine, Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Yao-Qing Chen
- School of Public Health (Shenzhen), Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Wei Hou
- State Key Laboratory of Virology/Department of Laboratory Medicine/Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences/Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Yanni Sun
- Department of Electrical Engineering, City University of Hong Kong, Hong Kong, China
| | - Deying Guo
- State key laboratory for biocontrol, Shenzhen Key Laboratory of Systems Medicine for inflammatory diseases, School of Medicine, Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Zifeng Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, Australia
| | - Yirong Li
- Wuhan Research Center for Infectious Diseases and Tumors of the Chinese Academy of Medical Sciences/Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment/Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China.
| | - Liangjun Chen
- Wuhan Research Center for Infectious Diseases and Tumors of the Chinese Academy of Medical Sciences/Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment/Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China.
| | - Mang Shi
- State key laboratory for biocontrol, Shenzhen Key Laboratory of Systems Medicine for inflammatory diseases, School of Medicine, Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
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8
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Waller SJ, Tortosa P, Thurley T, O’Donnell CFJ, Jackson R, Dennis G, Grimwood RM, Holmes EC, McInnes K, Geoghegan JL. Virome analysis of New Zealand's bats reveals cross-species viral transmission among the Coronaviridae. Virus Evol 2024; 10:veae008. [PMID: 38379777 PMCID: PMC10878368 DOI: 10.1093/ve/veae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 11/02/2023] [Accepted: 01/21/2024] [Indexed: 02/22/2024] Open
Abstract
The lesser short-tailed bat (Mystacina tuberculata) and the long-tailed bat (Chalinolobus tuberculatus) are Aotearoa New Zealand's only native extant terrestrial mammals and are believed to have migrated from Australia. Long-tailed bats arrived in New Zealand an estimated two million years ago and are closely related to other Australian bat species. Lesser short-tailed bats, in contrast, are the only extant species within the Mystacinidae and are estimated to have been living in isolation in New Zealand for the past 16-18 million years. Throughout this period of isolation, lesser short-tailed bats have become one of the most terrestrial bats in the world. Through a metatranscriptomic analysis of guano samples from eight locations across New Zealand, we aimed to characterise the viromes of New Zealand's bats and determine whether viruses have jumped between these species over the past two million years. High viral richness was observed among long-tailed bats with viruses spanning seven different viral families. In contrast, no bat-specific viruses were identified in lesser short-tailed bats. Both bat species harboured an abundance of likely dietary- and environment-associated viruses. We also identified alphacoronaviruses in long-tailed bat guano that had previously been identified in lesser short-tailed bats, suggesting that these viruses had jumped the species barrier after long-tailed bats migrated to New Zealand. Of note, an alphacoronavirus species discovered here possessed a complete genome of only 22,416 nucleotides with entire deletions or truncations of several non-structural proteins, thereby representing what may be the shortest genome within the Coronaviridae identified to date. Overall, this study has revealed a diverse range of novel viruses harboured by New Zealand's only native terrestrial mammals, in turn expanding our understanding of bat viral dynamics and evolution globally.
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Affiliation(s)
- Stephanie J Waller
- Department of Microbiology and Immunology, University of Otago, 720 Cumberland Street, Dunedin 9016, New Zealand
| | - Pablo Tortosa
- UMR PIMIT Processus Infectieux en Milieu Insulaire Tropical, Université de La Réunion, CNRS 9192, INSERM 1187, IRD 249, Plateforme de recherche CYROI, 2 rue Maxime Rivière, Ste Clotilde 97490, France
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Tertia Thurley
- Department of Conservation, New Zealand Government, P.O. Box 10420, Wellington 6143, New Zealand
| | - Colin F J O’Donnell
- Department of Conservation, New Zealand Government, P.O. Box 10420, Wellington 6143, New Zealand
| | - Rebecca Jackson
- Department of Conservation, New Zealand Government, P.O. Box 10420, Wellington 6143, New Zealand
| | - Gillian Dennis
- Department of Conservation, New Zealand Government, P.O. Box 10420, Wellington 6143, New Zealand
| | - Rebecca M Grimwood
- Department of Microbiology and Immunology, University of Otago, 720 Cumberland Street, Dunedin 9016, New Zealand
| | | | - Kate McInnes
- Department of Conservation, New Zealand Government, P.O. Box 10420, Wellington 6143, New Zealand
| | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, 720 Cumberland Street, Dunedin 9016, New Zealand
- Institute of Environmental Science and Research, 34 Kenepuru Drive, Kenepuru, Porirua, Wellington 5022, New Zealand
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Westmead Hospital, Level 5, Block K, Westmead, Sydney, NSW 2006, Australia
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9
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Dong X, Li C, Wang Y, Hu T, Zhang F, Meng F, Gao M, Han X, Wang G, Qin J, Nauwynck H, Holmes EC, Sorgeloos P, Sui L, Huang J, Shi W. Diversity and connectedness of brine shrimp viruses in global hypersaline ecosystems. Sci China Life Sci 2024; 67:188-203. [PMID: 37922067 DOI: 10.1007/s11427-022-2366-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 05/26/2023] [Indexed: 11/05/2023]
Abstract
Brine shrimp (Artemia) has existed on Earth for 400 million years and has major ecological importance in hypersaline ecosystems. As a crucial live food in aquaculture, brine shrimp cysts have become one of the most important aquatic products traded worldwide. However, our understanding of the biodiversity, prevalence and global connectedness of viruses in brine shrimp is still very limited. A total of 143 batches of brine shrimp (belonging to seven species) cysts were collected from six continents including 21 countries and more than 100 geographic locations worldwide during 1977-2019. In total, 55 novel RNA viruses were identified, which could be assigned to 18 different viral families and related clades. Eleven viruses were dsRNA viruses, 16 were +ssRNA viruses, and 28 were-ssRNA viruses. Phylogenetic analyses of the RNA-directed RNA polymerase (RdRp) showed that brine shrimp viruses were often grouped with viruses isolated from other invertebrates and fungi. Remarkably, most brine shrimp viruses were related to those from different hosts that might feed on brine shrimp or share the same ecological niche. A notable case was the novel brine shrimp noda-like virus 3, which shared 79.25% (RdRp) and 63.88% (capsid proteins) amino acid identity with covert mortality nodavirus (CMNV) that may cause losses in aquaculture. In addition, both virome composition and phylogenetic analyses revealed global connectedness in certain brine shrimp viruses, particularly among Asia and Northern America. This highlights the incredible species diversity of viruses in these ancient species and provides essential data for the prevalence of RNA viruses in the global aquaculture industry. More broadly, these findings provide novel insights into the previously unrecognized RNA virosphere in hypersaline ecosystems worldwide and demonstrate that human activity might have driven the global connectedness of brine shrimp viruses.
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Affiliation(s)
- Xuan Dong
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory; Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao, 266071, China
| | - Cixiu Li
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China
| | - Yiting Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory; Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao, 266071, China
- Dalian Ocean University, Dalian, 116023, China
| | - Tao Hu
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China
| | - Fan Zhang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory; Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao, 266071, China
| | - Fanzeng Meng
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory; Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao, 266071, China
| | - Meirong Gao
- Asian Regional Artemia Reference Center, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Xuekai Han
- Asian Regional Artemia Reference Center, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Guohao Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory; Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao, 266071, China
| | - Jiahao Qin
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory; Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao, 266071, China
| | | | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, 2006, Australia
| | | | - Liying Sui
- Asian Regional Artemia Reference Center, Tianjin University of Science & Technology, Tianjin, 300457, China.
| | - Jie Huang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory; Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao, 266071, China.
- Network of Aquaculture Centres in Asia-Pacific, Bangkok, 10900, Thailand.
| | - Weifeng Shi
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China.
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117, China.
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10
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Petrone ME, Parry R, Mifsud JCO, Van Brussel K, Vorhees I, Richards ZT, Holmes EC. Evidence for an ancient aquatic origin of the RNA viral order Articulavirales. Proc Natl Acad Sci U S A 2023; 120:e2310529120. [PMID: 37906647 PMCID: PMC10636315 DOI: 10.1073/pnas.2310529120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/03/2023] [Indexed: 11/02/2023] Open
Abstract
The emergence of previously unknown disease-causing viruses in mammals is in part the result of a long-term evolutionary process. Reconstructing the deep phylogenetic histories of viruses helps identify major evolutionary transitions and contextualizes the emergence of viruses in new hosts. We used a combination of total RNA sequencing and transcriptome data mining to extend the diversity and evolutionary history of the RNA virus order Articulavirales, which includes the influenza viruses. We identified instances of Articulavirales in the invertebrate phylum Cnidaria (including corals), constituting a novel and divergent family that we provisionally named the "Cnidenomoviridae." We further extended the evolutionary history of the influenza virus lineage by identifying four divergent, fish-associated influenza-like viruses, thereby supporting the hypothesis that fish were among the first hosts of influenza viruses. In addition, we substantially expanded the phylogenetic diversity of quaranjaviruses and proposed that this genus be reclassified as a family-the "Quaranjaviridae." Within this putative family, we identified a novel arachnid-infecting genus, provisionally named "Cheliceravirus." Notably, we observed a close phylogenetic relationship between the Crustacea- and Chelicerata-infecting "Quaranjaviridae" that is inconsistent with virus-host codivergence. Together, these data suggest that the Articulavirales has evolved over at least 600 million years, first emerging in aquatic animals. Importantly, the evolution of the Articulavirales was likely shaped by multiple aquatic-terrestrial transitions and substantial host jumps, some of which are still observable today.
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Affiliation(s)
- Mary E. Petrone
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW2006, Australia
- Laboratory of Data Discovery for Health Limited, Hong Kong Special Administrative Region, China
| | - Rhys Parry
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD4067, Australia
| | - Jonathon C. O. Mifsud
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW2006, Australia
| | - Kate Van Brussel
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW2006, Australia
| | - Ian Vorhees
- James A. Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY14850
| | - Zoe T. Richards
- Coral Conservation and Research Group, Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA6102, Australia
- Collections and Research, Western Australian Museum, Welshpool, WA6106, Australia
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW2006, Australia
- Laboratory of Data Discovery for Health Limited, Hong Kong Special Administrative Region, China
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11
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French RK, Anderson SH, Cain KE, Greene TC, Minor M, Miskelly CM, Montoya JM, Wille M, Muller CG, Taylor MW, Digby A, Holmes EC. Host phylogeny shapes viral transmission networks in an island ecosystem. Nat Ecol Evol 2023; 7:1834-1843. [PMID: 37679456 PMCID: PMC10627826 DOI: 10.1038/s41559-023-02192-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 08/04/2023] [Indexed: 09/09/2023]
Abstract
Virus transmission between host species underpins disease emergence. Both host phylogenetic relatedness and aspects of their ecology, such as species interactions and predator-prey relationships, may govern rates and patterns of cross-species virus transmission and hence zoonotic risk. To address the impact of host phylogeny and ecology on virus diversity and evolution, we characterized the virome structure of a relatively isolated island ecological community in Fiordland, New Zealand, that are linked through a food web. We show that phylogenetic barriers that inhibited cross-species virus transmission occurred at the level of host phyla (between the Chordata, Arthropoda and Streptophyta) as well as at lower taxonomic levels. By contrast, host ecology, manifest as predator-prey interactions and diet, had a smaller influence on virome composition, especially at higher taxonomic levels. The virus-host community comprised a 'small world' network, in which hosts with a high diversity of viruses were more likely to acquire new viruses, and generalist viruses that infect multiple hosts were more likely to infect additional species compared to host specialist viruses. Such a highly connected ecological community increases the likelihood of cross-species virus transmission, particularly among closely related species, and suggests that host generalist viruses present the greatest risk of disease emergence.
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Affiliation(s)
- Rebecca K French
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia.
| | - Sandra H Anderson
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Kristal E Cain
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Terry C Greene
- Biodiversity Group, Department of Conservation, Christchurch, New Zealand
| | - Maria Minor
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Colin M Miskelly
- Te Papa Tongarewa Museum of New Zealand, Wellington, New Zealand
| | - Jose M Montoya
- Theoretical and Experimental Ecology Station, National Centre for Scientific Research (CNRS), Moulis, France
| | - Michelle Wille
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Chris G Muller
- Wildbase, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Michael W Taylor
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Andrew Digby
- Kākāpō Recovery Team, Department of Conservation, Invercargill, New Zealand
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia.
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12
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Wierenga JR, Grimwood RM, Taylor HS, Hunter S, Argilla LS, Webster T, Lim L, French R, Schultz H, Jorge F, Bostina M, Burga L, Swindells-Wallace P, Holmes EC, McInnes K, Morgan KJ, Geoghegan JL. Total infectome investigation of diphtheritic stomatitis in yellow-eyed penguins (Megadyptes antipodes) reveals a novel and abundant megrivirus. Vet Microbiol 2023; 286:109895. [PMID: 37890432 DOI: 10.1016/j.vetmic.2023.109895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/15/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023]
Abstract
First identified in 2002, diphtheritic stomatitis (DS) is a devastating disease affecting yellow-eyed penguins (Megadyptes antipodes, or hoiho in te reo Māori). The disease is associated with oral lesions in chicks and has caused significant morbidity and mortality. DS is widespread among yellow-eyed penguin chicks on mainland New Zealand yet appears to be absent from the subantarctic population. Corynebacterium spp. have previously been suspected as causative agents yet, due to inconsistent cultures and inconclusive pathogenicity, their role in DS is unclear. Herein, we used a metatranscriptomic approach to identify potential causative agents of DS by revealing the presence and abundance of all viruses, bacteria, fungi and protozoa - together, the infectome. Oral and cloacal swab samples were collected from presymptomatic, symptomatic and recovered chicks along with a control group of healthy adults. Two novel viruses from the Picornaviridae were identified, one of which - yellow-eyed penguin megrivirus - was highly abundant in chicks irrespective of health status but not detected in healthy adults. Tissue from biopsied oral lesions also tested positive for the novel megrivirus upon PCR. We found no overall clustering among bacteria, protozoa and fungi communities at the genus level across samples, although Paraclostridium bifermentans was significantly more abundant in oral microbiota of symptomatic chicks compared to other groups. The detection of a novel and highly abundant megrivirus has sparked a new line of inquiry to investigate its potential association with DS.
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Affiliation(s)
- Janelle R Wierenga
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand; Wildbase, School of Veterinary Science, Massey University, New Zealand
| | - Rebecca M Grimwood
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Harry S Taylor
- Biodiversity Group, Department of Conservation/Te Papa Atawhai, New Zealand; Diagnostic and Surveillance Services, Biosecurity New Zealand, Ministry for Primary Industries, New Zealand
| | - Stuart Hunter
- Wildbase, School of Veterinary Science, Massey University, New Zealand
| | - Lisa S Argilla
- Wildlife Hospital, Dunedin, Otago Polytechnic School of Veterinary Nursing, New Zealand
| | | | - Lauren Lim
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Rebecca French
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Hendrik Schultz
- Biodiversity Group, Department of Conservation/Te Papa Atawhai, New Zealand
| | - Fátima Jorge
- Otago Micro and Nano Imaging, University of Otago, Dunedin, New Zealand
| | - Mihnea Bostina
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Laura Burga
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | | | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Australia
| | - Kate McInnes
- Biodiversity Group, Department of Conservation/Te Papa Atawhai, New Zealand
| | - Kerri J Morgan
- Wildbase, School of Veterinary Science, Massey University, New Zealand
| | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand; Institute of Environmental Science and Research, Wellington, New Zealand.
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13
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Harvey E, Mifsud JCO, Holmes EC, Mahar JE. Divergent hepaciviruses, delta-like viruses, and a chu-like virus in Australian marsupial carnivores (dasyurids). Virus Evol 2023; 9:vead061. [PMID: 37941997 PMCID: PMC10630069 DOI: 10.1093/ve/vead061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/05/2023] [Accepted: 10/12/2023] [Indexed: 11/10/2023] Open
Abstract
Although Australian marsupials are characterised by unique biology and geographic isolation, little is known about the viruses present in these iconic wildlife species. The Dasyuromorphia are an order of marsupial carnivores found only in Australia that include both the extinct Tasmanian tiger (thylacine) and the highly threatened Tasmanian devil. Several other members of the order are similarly under threat of extinction due to habitat loss, hunting, disease, and competition and predation by introduced species such as feral cats. We utilised publicly available RNA-seq data from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database to document the viral diversity within four Dasyuromorph species. Accordingly, we identified fifteen novel virus sequences from five DNA virus families (Adenoviridae, Anelloviridae, Gammaherpesvirinae, Papillomaviridae, and Polyomaviridae) and three RNA virus taxa: the order Jingchuvirales, the genus Hepacivirus, and the delta-like virus group. Of particular note was the identification of a marsupial-specific clade of delta-like viruses that may indicate an association of deltaviruses with marsupial species. In addition, we identified a highly divergent hepacivirus in a numbat liver transcriptome that falls outside of the larger mammalian clade. We also detect what may be the first Jingchuvirales virus in a mammalian host-a chu-like virus in Tasmanian devils-thereby expanding the host range beyond invertebrates and ectothermic vertebrates. As many of these Dasyuromorphia species are currently being used in translocation efforts to reseed populations across Australia, understanding their virome is of key importance to prevent the spread of viruses to naive populations.
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Affiliation(s)
- Erin Harvey
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jonathon C O Mifsud
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jackie E Mahar
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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14
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Chen YM, Hu SJ, Lin XD, Tian JH, Lv JX, Wang MR, Luo XQ, Pei YY, Hu RX, Song ZG, Holmes EC, Zhang YZ. Host traits shape virome composition and virus transmission in wild small mammals. Cell 2023; 186:4662-4675.e12. [PMID: 37734372 DOI: 10.1016/j.cell.2023.08.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 07/13/2023] [Accepted: 08/22/2023] [Indexed: 09/23/2023]
Abstract
Bats, rodents, and shrews are the most important animal sources of human infectious diseases. However, the evolution and transmission of viruses among them remain largely unexplored. Through the meta-transcriptomic sequencing of internal organ and fecal samples from 2,443 wild bats, rodents, and shrews sampled from four Chinese habitats, we identified 669 viruses, including 534 novel viruses, thereby greatly expanding the mammalian virome. Our analysis revealed high levels of phylogenetic diversity, identified cross-species virus transmission events, elucidated virus origins, and identified cases of invertebrate viruses in mammalian hosts. Host order and sample size were the most important factors impacting virome composition and patterns of virus spillover. Shrews harbored a high richness of viruses, including many invertebrate-associated viruses with multi-organ distributions, whereas rodents carried viruses with a greater capacity for host jumping. These data highlight the remarkable diversity of mammalian viruses in local habitats and their ability to emerge in new hosts.
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Affiliation(s)
- Yan-Mei Chen
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Shu-Jian Hu
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Xian-Dan Lin
- Wenzhou Center for Disease Control and Prevention, Wenzhou, Zhejiang 325002, China
| | - Jun-Hua Tian
- Wuhan Center for Disease Control and Prevention, Wuhan, Hubei 430022, China
| | - Jia-Xin Lv
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Miao-Ruo Wang
- Longquan Center for Disease Control and Prevention, Longquan, Zhejiang 323799, China
| | - Xiu-Qi Luo
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Yuan-Yuan Pei
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Rui-Xue Hu
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Zhi-Gang Song
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia; Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
| | - Yong-Zhen Zhang
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200438, China.
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15
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Le Lay C, Stott MB, Shi M, Sadiq S, Holmes EC. A metatranscriptomic analysis of geothermal hot springs reveals diverse RNA viruses including the phylum Lenarviricota. Virology 2023; 587:109873. [PMID: 37647722 DOI: 10.1016/j.virol.2023.109873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 08/08/2023] [Accepted: 08/21/2023] [Indexed: 09/01/2023]
Abstract
Little is known about the diversity of RNA viruses in geothermal systems. We generated total RNA sequencing data from two hot springs in Kuirau Park, Rotorua, New Zealand. In one data set, from a 71.8 °C pool, we observed a microbial community that was 98.5% archaea. The second data set, representing a cooler 36.8 °C geothermal hot spring, had a more diverse microbial profile: 58% bacteria, 34.5% eukaryotes and 7.5% archaea. Within this latter pool, we detected sequences likely representing 23 RNA viruses from the families Astroviridae, Tombusviridae, Polycipiviridae, Discistroviridae, Partitiviridae, and Mitoviridae, as well as from unclassified clades of the orders Tolivirales, Picornavirales, and Ghabrivirales. Most viruses had uncertain host associations. Of particular note, we identified four novel RNA viruses from the phylum Lenarviricota, commonly associated with bacteria and fungi, that occupied a divergent phylogenetic position within unclassified clades and may represent an ancient order-level taxon of unknown host association.
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Affiliation(s)
- Callum Le Lay
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Mang Shi
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Sabrina Sadiq
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia.
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16
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Grimwood RM, Fortune-Kelly G, Holmes EC, Ingram T, Geoghegan JL. Host specificity shapes fish viromes across lakes on an isolated remote island. Virology 2023; 587:109884. [PMID: 37757732 DOI: 10.1016/j.virol.2023.109884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/03/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023]
Abstract
Fish viromes often provide insights into the origin and evolution of viruses affecting tetrapods, including those associated with imporant human diseases. However, despite fish being the most diverse vertebrate group, their viruses are still understudied. We investigated the viromes of fish on Chatham Island (Rēkohu), a geographically isolated island housing 9% of New Zealand's threatened endemic fish species. Using metatranscriptomics, we analyzed samples from seven host species across 16 waterbodies. We identified 19 fish viruses, including 16 potentially novel species, expanding families such as the Coronaviridae, Hantaviridae, Poxviridae, and the recently proposed Tosoviridae. Surprisingly, virome composition was not influenced by the ecological factors measured and smelt (Retropinna retropinna) viromes were consistent across lakes despite differences in host life history, seawater influence, and community richness. Overall, fish viromes across Rēkohu were highly diverse and revealed a long history of co-divergence between host and virus despite their unique and geographically isolated ecosystem.
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Affiliation(s)
- Rebecca M Grimwood
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | | | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Travis Ingram
- Department of Zoology, University of Otago, Dunedin, 9016, New Zealand
| | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand; Institute of Environmental Science and Research, Wellington, 5018, New Zealand.
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17
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Crits-Christoph A, Levy JI, Pekar JE, Goldstein SA, Singh R, Hensel Z, Gangavarapu K, Rogers MB, Moshiri N, Garry RF, Holmes EC, Koopmans MPG, Lemey P, Popescu S, Rambaut A, Robertson DL, Suchard MA, Wertheim JO, Rasmussen AL, Andersen KG, Worobey M, Débarre F. Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic. bioRxiv 2023:2023.09.13.557637. [PMID: 37745602 PMCID: PMC10515900 DOI: 10.1101/2023.09.13.557637] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Wholesale Seafood Market, the site with the most reported wildlife vendors in the city of Wuhan, China. Here, we analyze publicly available qPCR and sequencing data from environmental samples collected in the Huanan market in early 2020. We demonstrate that the SARS-CoV-2 genetic diversity linked to this market is consistent with market emergence, and find increased SARS-CoV-2 positivity near and within a particular wildlife stall. We identify wildlife DNA in all SARS-CoV-2 positive samples from this stall. This includes species such as civets, bamboo rats, porcupines, hedgehogs, and one species, raccoon dogs, known to be capable of SARS-CoV-2 transmission. We also detect other animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them to those from other markets. This analysis provides the genetic basis for a short list of potential intermediate hosts of SARS-CoV-2 to prioritize for retrospective serological testing and viral sampling.
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Affiliation(s)
| | - Joshua I. Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan E. Pekar
- Department of Biomedical Informatics, University of California San Diego, La Jolla, CA, USA
| | - Stephen A. Goldstein
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Reema Singh
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Zach Hensel
- ITQB NOVA, Universidade NOVA de Lisboa, Lisbon, Av. da Republica, 2780-157, Oeiras, Portugal
| | - Karthik Gangavarapu
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Matthew B. Rogers
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Niema Moshiri
- Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA
| | - Robert F. Garry
- Tulane University, School of Medicine, Department of Microbiology and Immunology, New Orleans, LA 70112, USA; Zalgen Labs, Frederick, MD 21703, USA; Global Virus Network (GVN), Baltimore, MD 21201, USA
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Marion P. G. Koopmans
- Department of Viroscience, and Pandemic and Disaster Preparedness Centre., Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Saskia Popescu
- University of Maryland, School of Medicine, Department of Epidemiology & Public Health, Baltimore, MD 21201, USA
| | - Andrew Rambaut
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - David L. Robertson
- MRC-University of Glasgow Center for Virus Research, Glasgow, G61 1QH, UK
| | - Marc A. Suchard
- Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Joel O. Wertheim
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Angela L. Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kristian G. Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Florence Débarre
- Institut d’Écologie et des Sciences de l’Environnement (IEES-Paris, UMR 7618), CNRS, Sorbonne Université, UPEC, IRD, INRAE, Paris, France
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18
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Pan YF, Zhao H, Gou QY, Shi PB, Tian JH, Feng Y, Li K, Yang WH, Wu D, Tang G, Zhang B, Ren Z, Peng S, Luo GY, Le SJ, Xin GY, Wang J, Hou X, Peng MW, Kong JB, Chen XX, Yang CH, Mei SQ, Liao YQ, Cheng JX, Wang J, Chaolemen, Wu YH, Wang JB, An T, Huang X, Eden JS, Li J, Guo D, Liang G, Jin X, Holmes EC, Li B, Wang D, Li J, Wu WC, Shi M. Metagenomic analysis of individual mosquitos reveals the ecology of insect viruses. bioRxiv 2023:2023.08.28.555221. [PMID: 37732272 PMCID: PMC10508733 DOI: 10.1101/2023.08.28.555221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Mosquito transmitted viruses are responsible for an increasing burden of human disease. Despite this, little is known about the diversity and ecology of viruses within individual mosquito hosts. Using a meta-transcriptomic approach, we analysed the virome of 2,438 individual mosquitos (79 species), spanning ~4000 km along latitudes and longitudes in China. From these data we identified 393 core viral species associated with mosquitos, including seven (putative) arbovirus species. We identified potential species and geographic hotspots of viral richness and arbovirus occurrence, and demonstrated that host phylogeny had a strong impact on the composition of individual mosquito viromes. Our data revealed a large number of viruses shared among mosquito species or genera, expanding our knowledge of host specificity of insect-associated viruses. We also detected multiple virus species that were widespread throughout the country, possibly facilitated by long-distance mosquito migrations. Together, our results greatly expand the known mosquito virome, linked the viral diversity at the scale of individual insects to that at a country-wide scale, and offered unique insights into the ecology of viruses of insect vectors.
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Affiliation(s)
- Yuan-fei Pan
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Hailong Zhao
- BGI Research, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen 518083, China
| | - Qin-yu Gou
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Pei-bo Shi
- BGI Research, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Jun-hua Tian
- Wuhan Center for Disease Control and Prevention, Wuhan 430024, China
| | - Yun Feng
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali 671099, China
| | - Kun Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Wei-hong Yang
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali 671099, China
| | - De Wu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou 511430, China
| | - Guangpeng Tang
- Guizhou Center for Disease Control and Prevention, Guiyang 550004, China
| | - Bing Zhang
- Xinjiang Key Laboratory of Molecular Biology for Endemic Diseases, School of Basic Medical Sciences Xinjiang Medical University, Urumqi 830011, China
| | - Zirui Ren
- BGI Research, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen 518083, China
| | - Shiqin Peng
- BGI Research, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen 518083, China
| | - Geng-yan Luo
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Shi-jia Le
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Gen-yang Xin
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Jing Wang
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Xin Hou
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Min-wu Peng
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Jian-bin Kong
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Xin-xin Chen
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Chun-hui Yang
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Shi-qiang Mei
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Yu-qi Liao
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Jing-xia Cheng
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Juan Wang
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali 671099, China
| | - Chaolemen
- Old Barag Banner Center for Disease Control and Prevention, Hulunbuir 021500, China
| | - Yu-hui Wu
- Old Barag Banner Center for Disease Control and Prevention, Hulunbuir 021500, China
| | - Jian-bo Wang
- Hulunbuir Center for Disease Control and Prevention, Hulunbuir 021008, China
| | - Tongqing An
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Xinyi Huang
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - John-Sebastian Eden
- Centre for Virus Research, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Deyin Guo
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou 510000, China
| | - Guodong Liang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xin Jin
- BGI Research, Shenzhen 518083, China
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Bo Li
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Daxi Wang
- BGI Research, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen 518083, China
| | - Junhua Li
- BGI Research, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen 518083, China
| | - Wei-chen Wu
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Mang Shi
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
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19
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Van Brussel K, Mahar JE, Hall J, Bender H, Ortiz-Baez AS, Chang WS, Holmes EC, Rose K. Gammaretroviruses, novel viruses and pathogenic bacteria in Australian bats with neurological signs, pneumonia and skin lesions. Virology 2023; 586:43-55. [PMID: 37487325 DOI: 10.1016/j.virol.2023.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/25/2023] [Accepted: 07/12/2023] [Indexed: 07/26/2023]
Abstract
More than 70 bat species are found in mainland Australia. While most studies of bat viromes focus on sampling seemingly healthy individuals, little is known about the viruses and bacteria associated with diseased bats. We performed traditional diagnostic techniques and metatranscriptomic sequencing on tissue samples from 43 Australian bats, comprising three flying fox (Pteropodidae) and two microbat species experiencing a range of disease syndromes, including mass mortality, neurological signs, pneumonia and skin lesions. Of note, we identified the recently discovered Hervey pteropid gammaretrovirus in a bat with lymphoid leukemia, with evidence of replication consistent with an exogenous virus. The possible association of Hervey pteropid gammaretrovirus with lymphoid leukemia clearly merits additional investigation. One novel picornavirus and at least three new astroviruses and bat pegiviruses were also identified in a variety of tissue types, as well as a number of likely bacterial pathogens or opportunistic infections, most notably Pseudomonas aeruginosa.
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Affiliation(s)
- Kate Van Brussel
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, NSW, 2006, Australia
| | - Jackie E Mahar
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, NSW, 2006, Australia
| | - Jane Hall
- Australian Registry of Wildlife Health, Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | - Hannah Bender
- Australian Registry of Wildlife Health, Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | - Ayda Susana Ortiz-Baez
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, NSW, 2006, Australia
| | - Wei-Shan Chang
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, NSW, 2006, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, NSW, 2006, Australia.
| | - Karrie Rose
- Australian Registry of Wildlife Health, Taronga Conservation Society Australia, Mosman, New South Wales, Australia.
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20
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Giovanetti M, Pinotti F, Zanluca C, Fonseca V, Nakase T, Koishi AC, Tscha M, Soares G, Dorl GG, Marques AEM, Sousa R, Adelino TER, Xavier J, de Oliveira C, Patroca S, Guimaraes NR, Fritsch H, Mares-Guia MA, Levy F, Passos PH, da Silva VL, Pereira LA, Mendonça AF, de Macêdo IL, Ribeiro de Sousa DE, Rodrigues de Toledo Costa G, Botelho de Castro M, de Souza Andrade M, de Abreu FVS, Campos FS, Iani FCDM, Pereira MA, Cavalcante KRLJ, de Freitas ARR, Campelo de Albuquerque CF, Macário EM, dos Anjos MPD, Ramos RC, Campos AAS, Pinter A, Chame M, Abdalla L, Riediger IN, Ribeiro SP, Bento AI, de Oliveira T, Freitas C, Oliveira de Moura NF, Fabri A, dos Santos Rodrigues CD, Dos Santos CC, Barreto de Almeida MA, dos Santos E, Cardoso J, Augusto DA, Krempser E, Mucci LF, Gatti RR, Cardoso SF, Fuck JAB, Lopes MGD, Belmonte IL, Mayoral Pedroso da Silva G, Soares MRF, de Castilhos MDMS, de Souza e Silva JC, Bisetto Junior A, Pouzato EG, Tanabe LS, Arita DA, Matsuo R, dos Santos Raymundo J, Silva PCL, Santana Araújo Ferreira Silva A, Samila S, Carvalho G, Stabeli R, Navegantes W, Moreira LA, Ferreira AGA, Pinheiro GG, Nunes BTD, de Almeida Medeiros DB, Cruz ACR, Venâncio da Cunha R, Van Voorhis W, Bispo de Filippis AM, Almiron M, Holmes EC, Ramos DG, Romano A, Lourenço J, Alcantara LCJ, Duarte dos Santos CN. Genomic epidemiology unveils the dynamics and spatial corridor behind the Yellow Fever virus outbreak in Southern Brazil. Sci Adv 2023; 9:eadg9204. [PMID: 37656782 PMCID: PMC10854437 DOI: 10.1126/sciadv.adg9204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 07/26/2023] [Indexed: 09/03/2023]
Abstract
Despite the considerable morbidity and mortality of yellow fever virus (YFV) infections in Brazil, our understanding of disease outbreaks is hampered by limited viral genomic data. Here, through a combination of phylogenetic and epidemiological models, we reconstructed the recent transmission history of YFV within different epidemic seasons in Brazil. A suitability index based on the highly domesticated Aedes aegypti was able to capture the seasonality of reported human infections. Spatial modeling revealed spatial hotspots with both past reporting and low vaccination coverage, which coincided with many of the largest urban centers in the Southeast. Phylodynamic analysis unraveled the circulation of three distinct lineages and provided proof of the directionality of a known spatial corridor that connects the endemic North with the extra-Amazonian basin. This study illustrates that genomics linked with eco-epidemiology can provide new insights into the landscape of YFV transmission, augmenting traditional approaches to infectious disease surveillance and control.
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Affiliation(s)
- Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
- Department of Science and Technology for Humans and the Environment, Università of Campus Bio-Medico di Roma, Italy
| | | | - Camila Zanluca
- Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Paraná, Brazil
| | - Vagner Fonseca
- Organização Pan-Americana da Saúde/Organização Mundial da Saúde, Brasília, Distrito Federal, Brazil
| | - Taishi Nakase
- Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Andrea C. Koishi
- Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Paraná, Brazil
| | - Marcel Tscha
- Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Paraná, Brazil
| | - Guilherme Soares
- Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Paraná, Brazil
| | - Gisiane Gruber Dorl
- Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Paraná, Brazil
| | | | - Renato Sousa
- Laboratório de Patologia Veterinária, Hospital Veterinário UFPR, PR Brazil
| | - Talita Emile Ribeiro Adelino
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Joilson Xavier
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
- Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Carla de Oliveira
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | | | - Natalia Rocha Guimaraes
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Hegger Fritsch
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
- Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Flavia Levy
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Pedro Henrique Passos
- Coordenação Geral das Arboviroses, Secretaria de Vigilância em Saúde/Ministério da Saúde (CGARB/SVS-MS), Brasília, Distrito Federal, Brazil
| | | | - Luiz Augusto Pereira
- Laboratório Central de Saúde Pública Dr Giovanni Cysneiros, Goiânia, Goiás, Brazil
| | - Ana Flávia Mendonça
- Laboratório Central de Saúde Pública Dr Giovanni Cysneiros, Goiânia, Goiás, Brazil
| | - Isabel Luana de Macêdo
- Veterinary Pathology Laboratory, Campus Darcy Ribeiro, University of Brasília, Brasília, DF 70636- 200, Brazil
| | | | | | - Marcio Botelho de Castro
- Veterinary Pathology Laboratory, Campus Darcy Ribeiro, University of Brasília, Brasília, DF 70636- 200, Brazil
- Graduate Program in Animal Sciences, College of Agronomy and Veterinary Medicine, University of Brasília, Brasília, DF 70910-900, Brazil
| | - Miguel de Souza Andrade
- Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília 70910-900, DF, Brazil
| | | | - Fabrício Souza Campos
- Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre 90035-003, RS, Brazil
| | - Felipe Campos de Melo Iani
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Maira Alves Pereira
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | | | | | | | | | - Marlei Pickler Debiasi dos Anjos
- Laboratorio central de Saude Publica de Santa Catarina, Superintendência de Vigilância em Saúde – SES – Santa Catarina, South Brazil
| | - Rosane Campanher Ramos
- Laboratório Central de Saúde Pública do Estado do Rio Grande do Sul, Superintendência de Vigilância em Saúde – SES – Santa Catarina, South Brazil
| | | | - Adriano Pinter
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, 05508-000, Brazil
| | - Marcia Chame
- Oswaldo Cruz Foundation, Biodiversity, Wildlife Health Institutional Platform (PIBSS/Fiocruz), Rio de Janeiro, Brazil
| | - Livia Abdalla
- Oswaldo Cruz Foundation, Biodiversity, Wildlife Health Institutional Platform (PIBSS/Fiocruz), Rio de Janeiro, Brazil
| | | | - Sérvio Pontes Ribeiro
- Laboratory of Ecology of Diseases & Forests, NUPEB/ICEB, Federal University of Ouro Preto, Minas Gerais, Brazil
| | - Ana I. Bento
- Pandemic Prevention Initiative, The Rockefeller Foundation, Washington DC, USA
| | - Tulio de Oliveira
- School for Data Science and Computational Thinking, Faculty of Science and Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | - Carla Freitas
- Secretaria de Vigilância em Saúde, SVS, Brazilian Ministry of Health, Brasilia, Federal District, Brazil
| | | | - Allison Fabri
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | | | | | - Edmilson dos Santos
- Secretaria Estadual de Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Porto Alegre, RS, Brazil
| | - Jader Cardoso
- Secretaria Estadual de Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Porto Alegre, RS, Brazil
| | - Douglas Adriano Augusto
- Plataforma Institucional Biodiversidade e Saúde Silvestre - Centro de Informação em Saúde Silvestre (CISS) - Fiocruz/RJ, Avenida Brasil, 4365. Manguinhos - Rio de Janeiro - RJ Cep: 21.040-360
| | - Eduardo Krempser
- Plataforma Institucional Biodiversidade e Saúde Silvestre - Centro de Informação em Saúde Silvestre (CISS) - Fiocruz/RJ, Avenida Brasil, 4365. Manguinhos - Rio de Janeiro - RJ Cep: 21.040-360
| | - Luís Filipe Mucci
- Secretaria da Saúde (São Paulo - Estado), Av Dr. Enéas Carvalho de Aguiar, 188 - Cerqueira César, São Paulo - SP, 05403-000, Brazil
- Coordenadoria de Controle de Doenças (CCD), Av. Dr. Enéas Carvalho de Aguiar, 188 - Cerqueira César, São Paulo - SP, 05403-000, Brazil
- Instituto Pasteur (IP), Av. Paulista, 363 Cerqueira Cesar – São Paulo- SP – CEP:01311-000
| | - Renata Rispoli Gatti
- Secretaria de Estado da Saude de Santa Catarina, R. Esteves Júnior, 160 - Centro, Florianópolis - SC, 88015-130, Brazil
| | - Sabrina Fernandes Cardoso
- Secretaria de Estado da Saude de Santa Catarina, R. Esteves Júnior, 160 - Centro, Florianópolis - SC, 88015-130, Brazil
- Department of Cell Biology, Embryology and Genetics, Federal University of Santa Catarina (UFSC), Florianópolis, Brazil
| | - João Augusto Brancher Fuck
- Diretoria de Vigilância Epidemiológica da Secretaria de Estado da Saúde de Santa Catarina, R. Esteves Júnior, 160 - Centro, Florianópolis - SC, 88015-130, Brazil
| | - Maria Goretti David Lopes
- Secretaria de Estado da Saúde do Paraná, Brazil, R. Piquiri, 170 - Rebouças, Curitiba - PR, 80230-140
| | - Ivana Lucia Belmonte
- Secretaria de Estado da Saúde do Paraná, Brazil, R. Piquiri, 170 - Rebouças, Curitiba - PR, 80230-140
| | | | | | | | | | - Alceu Bisetto Junior
- Secretaria de Estado da Saúde do Paraná, Brazil, R. Piquiri, 170 - Rebouças, Curitiba - PR, 80230-140
| | - Emanuelle Gemin Pouzato
- Secretaria de Estado da Saúde do Paraná, Brazil, R. Piquiri, 170 - Rebouças, Curitiba - PR, 80230-140
| | - Laurina Setsuko Tanabe
- Secretaria de Estado da Saúde do Paraná, Brazil, R. Piquiri, 170 - Rebouças, Curitiba - PR, 80230-140
| | - Daniele Akemi Arita
- Secretaria de Estado da Saúde do Paraná, Brazil, R. Piquiri, 170 - Rebouças, Curitiba - PR, 80230-140
| | - Ricardo Matsuo
- Secretaria de Estado da Saúde do Paraná, Brazil, R. Piquiri, 170 - Rebouças, Curitiba - PR, 80230-140
| | | | | | | | - Sandra Samila
- Secretaria de Estado da Saúde do Paraná, Brazil, R. Piquiri, 170 - Rebouças, Curitiba - PR, 80230-140
| | - Glauco Carvalho
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Rodrigo Stabeli
- Organização Pan-Americana da Saúde/Organização Mundial da Saúde, Brasília, Distrito Federal, Brazil
| | - Wildo Navegantes
- Organização Pan-Americana da Saúde/Organização Mundial da Saúde, Brasília, Distrito Federal, Brazil
| | - Luciano Andrade Moreira
- Mosquitos Vetores: Endossimbiontes e Interação Patógeno-Vetor, Instituto René Rachou–Fiocruz, Belo Horizonte 30190-002, MG, Brazil
| | - Alvaro Gil A. Ferreira
- Mosquitos Vetores: Endossimbiontes e Interação Patógeno-Vetor, Instituto René Rachou–Fiocruz, Belo Horizonte 30190-002, MG, Brazil
| | | | | | | | | | | | - Wes Van Voorhis
- Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, WA, USA
| | | | - Maria Almiron
- Pan American Health Organization/World Health Organization, Washington, DC, USA
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | - Daniel Garkauskas Ramos
- Coordenação Geral das Arboviroses, Secretaria de Vigilância em Saúde/Ministério da Saúde (CGARB/SVS-MS), Brasília, Distrito Federal, Brazil
| | - Alessandro Romano
- Coordenação Geral das Arboviroses, Secretaria de Vigilância em Saúde/Ministério da Saúde (CGARB/SVS-MS), Brasília, Distrito Federal, Brazil
| | - José Lourenço
- BioISI (Biosystems and Integrative Sciences Institute), Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa Portugal
| | - Luiz Carlos Junior Alcantara
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
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21
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Giovanetti M, Vazquez C, Lima M, Castro E, Rojas A, Gomez de la Fuente A, Aquino C, Cantero C, Fleitas F, Torales J, Barrios J, Ortega MJ, Gamarra ML, Villalba S, Alfonzo T, Xavier J, Adelino T, Fritsch H, Iani FC, Pereira GC, de Oliveira C, Schuab G, Rodrigues ES, Kashima S, Leite J, Gresh L, Franco L, Tegally H, Van Voorhis WC, Lessels R, de Filippis AMB, Ojeda A, Sequera G, Montoya R, Holmes EC, de Oliveira T, Rico JM, Lourenço J, Fonseca V, Alcantara LC. Rapid Epidemic Expansion of Chikungunya Virus East/Central/South African Lineage, Paraguay. Emerg Infect Dis 2023; 29:1859-1863. [PMID: 37488810 PMCID: PMC10461647 DOI: 10.3201/eid2909.230523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023] Open
Abstract
The spread of Chikungunya virus is a major public health concern in the Americas. There were >120,000 cases and 51 deaths in 2023, of which 46 occurred in Paraguay. Using a suite of genomic, phylodynamic, and epidemiologic techniques, we characterized the ongoing large chikungunya epidemic in Paraguay.
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Affiliation(s)
| | | | | | | | - Analia Rojas
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Andrea Gomez de la Fuente
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Carolina Aquino
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Cesar Cantero
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Fatima Fleitas
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Juan Torales
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Julio Barrios
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Maria J. Ortega
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Maria L. Gamarra
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Shirley Villalba
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Tania Alfonzo
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Joilson Xavier
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Talita Adelino
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Hegger Fritsch
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Felipe C.M. Iani
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Glauco C. Pereira
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Carla de Oliveira
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Gabriel Schuab
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Evandra S. Rodrigues
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Simone Kashima
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Juliana Leite
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Lionel Gresh
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Leticia Franco
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Houriiyah Tegally
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Wesley C. Van Voorhis
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Richard Lessels
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Ana Maria Bispo de Filippis
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Andrea Ojeda
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Guillermo Sequera
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Romeo Montoya
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Edward C. Holmes
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Tulio de Oliveira
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Jairo M. Rico
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - José Lourenço
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Vagner Fonseca
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Luiz C.J. Alcantara
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
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22
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Le Lay C, Hamm JN, Williams TJ, Shi M, Cavicchioli R, Holmes EC. Viral community composition of hypersaline lakes. Virus Evol 2023; 9:vead057. [PMID: 37692898 PMCID: PMC10492444 DOI: 10.1093/ve/vead057] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/03/2023] [Accepted: 08/29/2023] [Indexed: 09/12/2023] Open
Abstract
Despite their widespread distribution and remarkable antiquity no RNA viruses definitively associated with the domain Archaea have been identified. In contrast, 17 families of DNA viruses are known to infect archaea. In an attempt to uncover more of the elusive archaeal virosphere, we investigated the metatranscriptomes of hypersaline lakes that are a rich source of archaea. We sequenced RNA extracted from water filter samples of Lake Tyrrell (Victoria, Australia) and cultures seeded from four lakes in Antarctica. To identify highly divergent viruses in these data, we employed a variety of search tools, including Hidden Markov models (HMMs) and position-specific scoring matrices (PSSMs). From this, we identified 12 highly divergent, RNA virus-like candidate sequences from the virus phyla Artverviricota, Duplornaviricota, Kitrinoviricota, Negarnaviricota, and Pisuviricota, including those with similarity to the RNA-dependent RNA polymerase (RdRp). An additional analysis with an artificial intelligence (AI)-based approach that utilises both sequence and structural information identified seven putative and highly divergent RdRp sequences of uncertain phylogenetic position. A sequence matching the Pisuviricota from Deep Lake in Antarctica had the strongest RNA virus signal. Analyses of the dinucleotide representation of the virus-like candidates in comparison to that of potential host species were in some cases compatible with an association to archaeal or bacterial hosts. Notably, however, the use of archaeal CRISPR spacers as a BLAST database failed to detect any RNA viruses. We also described DNA viruses from the families Pleolipoviridae, Sphaerolipoviridae, Halspiviridae, and the class Caudoviricetes. Although we were unable to provide definitive evidence the existence of an RNA virus of archaea in these hypersaline lakes, this study lays the foundations for further investigations of highly divergent RNA viruses in natural environments.
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Affiliation(s)
- Callum Le Lay
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | | | - Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Mang Shi
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, P.O. Box 59, Den Burg NL-1790 AB, The Netherlands
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23
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Wasik BR, Rothschild E, Voorhees IEH, Reedy SE, Murcia PR, Pusterla N, Chambers TM, Goodman LB, Holmes EC, Kile JC, Parrish CR. Understanding the divergent evolution and epidemiology of H3N8 influenza viruses in dogs and horses. Virus Evol 2023; 9:vead052. [PMID: 37692894 PMCID: PMC10484056 DOI: 10.1093/ve/vead052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/12/2023] [Accepted: 08/16/2023] [Indexed: 09/12/2023] Open
Abstract
Cross-species virus transmission events can lead to dire public health emergencies in the form of epidemics and pandemics. One example in animals is the emergence of the H3N8 equine influenza virus (EIV), first isolated in 1963 in Miami, FL, USA, after emerging among horses in South America. In the early 21st century, the American lineage of EIV diverged into two 'Florida' clades that persist today, while an EIV transferred to dogs around 1999 and gave rise to the H3N8 canine influenza virus (CIV), first reported in 2004. Here, we compare CIV in dogs and EIV in horses to reveal their host-specific evolution, to determine the sources and connections between significant outbreaks, and to gain insight into the factors controlling their different evolutionary fates. H3N8 CIV only circulated in North America, was geographically restricted after the first few years, and went extinct in 2016. Of the two EIV Florida clades, clade 1 circulates widely and shows frequent transfers between the USA and South America, Europe and elsewhere, while clade 2 was globally distributed early after it emerged, but since about 2018 has only been detected in Central Asia. Any potential zoonotic threat of these viruses to humans can only be determined with an understanding of its natural history and evolution. Our comparative analysis of these three viral lineages reveals distinct patterns and rates of sequence variation yet with similar overall evolution between clades, suggesting epidemiological intervention strategies for possible eradication of H3N8 EIV.
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Affiliation(s)
- Brian R Wasik
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Evin Rothschild
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Ian E H Voorhees
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Stephanie E Reedy
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA
| | - Pablo R Murcia
- MRC-University of Glasgow Centre for Virus Research, School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, Scotland
| | - Nicola Pusterla
- Department of Medicine & Epidemiology, School Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Thomas M Chambers
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA
| | - Laura B Goodman
- Baker Institute for Animal Health, Department of Public and Ecosystems Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - James C Kile
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Colin R Parrish
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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24
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He WT, Li D, Baele G, Zhao J, Jiang Z, Ji X, Veit M, Suchard MA, Holmes EC, Lemey P, Boni MF, Su S. Newly identified lineages of porcine hemagglutinating encephalomyelitis virus exhibit respiratory phenotype. Virus Evol 2023; 9:vead051. [PMID: 37711483 PMCID: PMC10499004 DOI: 10.1093/ve/vead051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/18/2023] [Accepted: 08/13/2023] [Indexed: 09/16/2023] Open
Abstract
Swine pathogens have a long history of zoonotic transmission to humans, occasionally leading to sustained outbreaks or pandemics. Through a retrospective epidemiological study of swine populations in China, we describe novel lineages of porcine hemagglutinating encephalomyelitis virus (PHEV) complex coronaviruses (CoVs) that cause exclusively respiratory symptoms with no signs of the neurological symptoms typically associated with classical PHEV infection. Through large-scale epidemiological surveillance, we show that these novel lineages have circulated in at least eight provinces in southeastern China. Phylogenetic and recombination analyses of twenty-four genomes identified two major viral lineages causing respiratory symptoms with extensive recombination within them, between them, and between classical PHEV and the novel respiratory variant PHEV (rvPHEV) lineages. Divergence times among the sampled lineages in the PHEV virus complex date back to 1886-1958 (mean estimate 1928), with the two major rvPHEV lineages separating approximately 20 years later. Many rvPHEV viruses show amino acid substitutions at the carbohydrate-binding site of hemagglutinin esterase (HE) and/or have lost the cysteine required for HE dimerization. This resembles the early adaptation of human CoVs, where HE lost its hemagglutination ability to adapt to growth in the human respiratory tract. Our study represents the first report of the evolutionary history of rvPHEV circulating in swine and highlights the importance of characterizing CoV diversity and recombination in swine to identify pathogens with outbreak potential that could threaten swine farming.
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Affiliation(s)
- Wan-Ting He
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven 3000, Belgium
| | - Dongyan Li
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven 3000, Belgium
| | - Jin Zhao
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhiwen Jiang
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiang Ji
- Department of Mathematics, School of Science & Engineering, Tulane University, New Orleans, LA 70118, USA
| | - Michael Veit
- Institute for Virology, Center for Infection Medicine, Veterinary Faculty, Free University Berlin, Berlin 14163, Germany
| | - Marc A Suchard
- Department of Biostatistics, Fielding School of Public Health, and Departments of Biomathematics and Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven 3000, Belgium
| | | | - Shuo Su
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
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25
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Brito BP, Frost MJ, Anantanawat K, Jaya F, Batterham T, Djordjevic SP, Chang WS, Holmes EC, Darling AE, Kirkland PD. Expanding the range of the respiratory infectome in Australian feedlot cattle with and without respiratory disease using metatranscriptomics. Microbiome 2023; 11:158. [PMID: 37491320 PMCID: PMC10367309 DOI: 10.1186/s40168-023-01591-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 06/03/2023] [Indexed: 07/27/2023]
Abstract
BACKGROUND Bovine respiratory disease (BRD) is one of the most common diseases in intensively managed cattle, often resulting in high morbidity and mortality. Although several pathogens have been isolated and extensively studied, the complete infectome of the respiratory complex consists of a more extensive range unrecognised species. Here, we used total RNA sequencing (i.e., metatranscriptomics) of nasal and nasopharyngeal swabs collected from animals with and without BRD from two cattle feedlots in Australia. RESULTS A high abundance of bovine nidovirus, influenza D, bovine rhinitis A and bovine coronavirus was found in the samples. Additionally, we obtained the complete or near-complete genome of bovine rhinitis B, enterovirus E1, bovine viral diarrhea virus (sub-genotypes 1a and 1c) and bovine respiratory syncytial virus, and partial sequences of other viruses. A new species of paramyxovirus was also identified. Overall, the most abundant RNA virus, was the bovine nidovirus. Characterisation of bacterial species from the transcriptome revealed a high abundance and diversity of Mollicutes in BRD cases and unaffected control animals. Of the non-Mollicutes species, Histophilus somni was detected, whereas there was a low abundance of Mannheimia haemolytica. CONCLUSION This study highlights the use of untargeted sequencing approaches to study the unrecognised range of microorganisms present in healthy or diseased animals and the need to study previously uncultured viral species that may have an important role in cattle respiratory disease. Video Abstract.
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Affiliation(s)
- Barbara P Brito
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, New South Wales, Australia.
- New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales, Australia.
- Present Address: Biosecurity and Food Safety, NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute (EMAI), Menangle, New South Wales, Australia.
| | - Melinda J Frost
- New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales, Australia
| | - Kay Anantanawat
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, New South Wales, Australia
- Illumina Australia, Ultimo, New South Wales, Australia
| | - Frederick Jaya
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, New South Wales, Australia
| | | | - Steven P Djordjevic
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Wei-Shan Chang
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Aaron E Darling
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, New South Wales, Australia
- Illumina Australia, Ultimo, New South Wales, Australia
| | - Peter D Kirkland
- New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales, Australia
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26
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Wang J, Pan YF, Yang LF, Yang WH, Lv K, Luo CM, Wang J, Kuang GP, Wu WC, Gou QY, Xin GY, Li B, Luo HL, Chen S, Shu YL, Guo D, Gao ZH, Liang G, Li J, Chen YQ, Holmes EC, Feng Y, Shi M. Individual bat virome analysis reveals co-infection and spillover among bats and virus zoonotic potential. Nat Commun 2023; 14:4079. [PMID: 37429936 DOI: 10.1038/s41467-023-39835-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 06/26/2023] [Indexed: 07/12/2023] Open
Abstract
Bats are reservoir hosts for many zoonotic viruses. Despite this, relatively little is known about the diversity and abundance of viruses within individual bats, and hence the frequency of virus co-infection and spillover among them. We characterize the mammal-associated viruses in 149 individual bats sampled from Yunnan province, China, using an unbiased meta-transcriptomics approach. This reveals a high frequency of virus co-infection (simultaneous infection of bat individuals by multiple viral species) and spillover among the animals studied, which may in turn facilitate virus recombination and reassortment. Of note, we identify five viral species that are likely to be pathogenic to humans or livestock, based on phylogenetic relatedness to known pathogens or in vitro receptor binding assays. This includes a novel recombinant SARS-like coronavirus that is closely related to both SARS-CoV and SARS-CoV-2. In vitro assays indicate that this recombinant virus can utilize the human ACE2 receptor such that it is likely to be of increased emergence risk. Our study highlights the common occurrence of co-infection and spillover of bat viruses and their implications for virus emergence.
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Affiliation(s)
- Jing Wang
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Yuan-Fei Pan
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Li-Fen Yang
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, China
| | - Wei-Hong Yang
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, China
| | - Kexin Lv
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Chu-Ming Luo
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Juan Wang
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, China
| | - Guo-Peng Kuang
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, China
| | - Wei-Chen Wu
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Qin-Yu Gou
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Gen-Yang Xin
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Bo Li
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Huan-le Luo
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Shoudeng Chen
- Molecular Imaging Center, Central Laboratory, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong, China
| | - Yue-Long Shu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Deyin Guo
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong Province, China
| | - Zi-Hou Gao
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, China
| | - Guodong Liang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Yao-Qing Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia.
| | - Yun Feng
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, China.
| | - Mang Shi
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
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27
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Long GS, Hider J, Duggan AT, Klunk J, Eaton K, Karpinski E, Giuffra V, Ventura L, Prowse TL, Fornaciari A, Fornaciari G, Holmes EC, Golding GB, Poinar HN. A 14th century CE Brucella melitensis genome and the recent expansion of the Western Mediterranean clade. PLoS Pathog 2023; 19:e1011538. [PMID: 37523413 PMCID: PMC10414615 DOI: 10.1371/journal.ppat.1011538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 08/10/2023] [Accepted: 07/05/2023] [Indexed: 08/02/2023] Open
Abstract
Brucellosis is a disease caused by the bacterium Brucella and typically transmitted through contact with infected ruminants. It is one of the most common chronic zoonotic diseases and of particular interest to public health agencies. Despite its well-known transmission history and characteristic symptoms, we lack a more complete understanding of the evolutionary history of its best-known species-Brucella melitensis. To address this knowledge gap we fortuitously found, sequenced and assembled a high-quality ancient B. melitensis draft genome from the kidney stone of a 14th-century Italian friar. The ancient strain contained fewer core genes than modern B. melitensis isolates, carried a complete complement of virulence genes, and did not contain any indication of significant antimicrobial resistances. The ancient B. melitensis genome fell as a basal sister lineage to a subgroup of B. melitensis strains within the Western Mediterranean phylogenetic group, with a short branch length indicative of its earlier sampling time, along with a similar gene content. By calibrating the molecular clock we suggest that the speciation event between B. melitensis and B. abortus is contemporaneous with the estimated time frame for the domestication of both sheep and goats. These results confirm the existence of the Western Mediterranean clade as a separate group in the 14th CE and suggest that its divergence was due to human and ruminant co-migration.
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Affiliation(s)
- George S. Long
- Department of Biology, McMaster University, Hamilton, Canada
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
| | - Jessica Hider
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
- Department of Anthropology, McMaster University, Hamilton, Canada
| | - Ana T. Duggan
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
- Department of Anthropology, McMaster University, Hamilton, Canada
| | - Jennifer Klunk
- Department of Biology, McMaster University, Hamilton, Canada
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
- Daicel Arbor Biosciences, Ann Arbor, Michigan, United States of America
| | - Katherine Eaton
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
- Department of Anthropology, McMaster University, Hamilton, Canada
| | - Emil Karpinski
- Department of Biology, McMaster University, Hamilton, Canada
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
| | - Valentina Giuffra
- Division of Paleopathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Luca Ventura
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
- Division of Pathology, San Salvatore Hospital, Coppito, Italy
| | - Tracy L. Prowse
- Department of Anthropology, McMaster University, Hamilton, Canada
| | - Antonio Fornaciari
- Division of Paleopathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | | | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney, Australia
| | | | - Hendrik N. Poinar
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
- Department of Anthropology, McMaster University, Hamilton, Canada
- Department of Biochemistry, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- CIFAR Humans and the Microbiome Program, Toronto, Canada
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28
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López-Astacio RA, Adu OF, Goetschius DJ, Lee H, Weichert WS, Wasik BR, Frueh SP, Alford BK, Voorhees IEH, Flint JF, Saddoris S, Goodman LB, Holmes EC, Hafenstein SL, Parrish CR. Viral Capsid, Antibody, and Receptor Interactions: Experimental Analysis of the Antibody Escape Evolution of Canine Parvovirus. J Virol 2023; 97:e0009023. [PMID: 37199627 PMCID: PMC10308881 DOI: 10.1128/jvi.00090-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/23/2023] [Indexed: 05/19/2023] Open
Abstract
Canine parvovirus (CPV) is a small nonenveloped single-stranded DNA virus that causes serious diseases in dogs worldwide. The original strain of the virus (CPV-2) emerged in dogs during the late 1970s due to a host range switch of a virus similar to the feline panleukopenia virus that infected another host. The virus that emerged in dogs had altered capsid receptor and antibody binding sites, with some changes affecting both functions. Further receptor and antibody binding changes arose when the virus became better adapted to dogs or to other hosts. Here, we used in vitro selection and deep sequencing to reveal how two antibodies with known interactions select for escape mutations in CPV. The antibodies bound two distinct epitopes, and one largely overlapped the host receptor binding site. We also generated mutated antibody variants with altered binding structures. Viruses were passaged with wild-type (WT) or mutated antibodies, and their genomes were deep sequenced during the selective process. A small number of mutations were detected only within the capsid protein gene during the first few passages of selection, and most sites remained polymorphic or were slow to go to fixation. Mutations arose both within and outside the antibody binding footprints on the capsids, and all avoided the transferrin receptor type 1 binding footprint. Many selected mutations matched those that have arisen in the natural evolution of the virus. The patterns observed reveal the mechanisms by which these variants have been selected in nature and provide a better understanding of the interactions between antibody and receptor selections. IMPORTANCE Antibodies protect animals against infection by many different viruses and other pathogens, and we are gaining new information about the epitopes that induce antibody responses against viruses and the structures of the bound antibodies. However, less is known about the processes of antibody selection and antigenic escape and the constraints that apply in this system. Here, we used an in vitro model system and deep genome sequencing to reveal the mutations that arose in the virus genome during selection by each of two monoclonal antibodies or their mutated variants. High-resolution structures of each of the Fab:capsid complexes revealed their binding interactions. The wild-type antibodies or their mutated variants allowed us to examine how changes in antibody structure influence the mutational selection patterns seen in the virus. The results shed light on the processes of antibody binding, neutralization escape, and receptor binding, and they likely have parallels for many other viruses.
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Affiliation(s)
- Robert A. López-Astacio
- James A. Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Oluwafemi F. Adu
- James A. Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Daniel J. Goetschius
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA
| | - Hyunwook Lee
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA
| | - Wendy S. Weichert
- James A. Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Brian R. Wasik
- James A. Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Simon P. Frueh
- James A. Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
- Department for Veterinary Sciences, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Brynn K. Alford
- James A. Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Ian E. H. Voorhees
- James A. Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Joseph F. Flint
- James A. Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Sarah Saddoris
- James A. Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Laura B. Goodman
- James A. Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Susan L. Hafenstein
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA
| | - Colin R. Parrish
- James A. Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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Chen P, Jin Z, Peng L, Zheng Z, Cheung YM, Guan J, Chen L, Huang Y, Fan X, Zhang Z, Shi D, Xie J, Chen R, Xiao B, Yip CH, Smith DK, Hong W, Liu Y, Li L, Wang J, Holmes EC, Lam TTY, Zhu H, Guan Y. Characterization of an Emergent Chicken H3N8 Influenza Virus in Southern China: a Potential Threat to Public Health. J Virol 2023; 97:e0043423. [PMID: 37289052 PMCID: PMC10308888 DOI: 10.1128/jvi.00434-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 05/08/2023] [Indexed: 06/09/2023] Open
Abstract
Although influenza A viruses of several subtypes have occasionally infected humans, to date only those of the H1, H2, and H3 subtypes have led to pandemics and become established in humans. The detection of two human infections by avian H3N8 viruses in April and May of 2022 raised pandemic concerns. Recent studies have shown the H3N8 viruses were introduced into humans from poultry, although their genesis, prevalence, and transmissibility in mammals have not been fully elucidated. Findings generated from our systematic influenza surveillance showed that this H3N8 influenza virus was first detected in chickens in July 2021 and then disseminated and became established in chickens over wider regions of China. Phylogenetic analyses revealed that the H3 HA and N8 NA were derived from avian viruses prevalent in domestic ducks in the Guangxi-Guangdong region, while all internal genes were from enzootic poultry H9N2 viruses. The novel H3N8 viruses form independent lineages in the glycoprotein gene trees, but their internal genes are mixed with those of H9N2 viruses, indicating continuous gene exchange among these viruses. Experimental infection of ferrets with three chicken H3N8 viruses showed transmission through direct contact and inefficient transmission by airborne exposure. Examination of contemporary human sera detected only very limited antibody cross-reaction to these viruses. The continuing evolution of these viruses in poultry could pose an ongoing pandemic threat. IMPORTANCE A novel H3N8 virus with demonstrated zoonotic potential has emerged and disseminated in chickens in China. It was generated by reassortment between avian H3 and N8 virus(es) and long-term enzootic H9N2 viruses present in southern China. This H3N8 virus has maintained independent H3 and N8 gene lineages but continues to exchange internal genes with other H9N2 viruses to form novel variants. Our experimental studies showed that these H3N8 viruses were transmissible in ferrets, and serological data suggest that the human population lacks effective immunological protection against it. With its wide geographical distribution and continuing evolution in chickens, other spillovers to humans can be expected and might lead to more efficient transmission in humans.
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Affiliation(s)
- Peiwen Chen
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
| | - Ziying Jin
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
| | - Liuxia Peng
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
| | - Zuoyi Zheng
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
| | - Yiu-Man Cheung
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
| | - Jing Guan
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
| | - Liming Chen
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- The First Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, China
| | - Yiteng Huang
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- The First Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, China
| | - Xiaohui Fan
- Department of Microbiology, Guangxi Medical University, Nanning, Guangxi, China
| | - Zengfeng Zhang
- Department of Microbiology, Guangxi Medical University, Nanning, Guangxi, China
| | - Dongmei Shi
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
| | - Jin Xie
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
| | - Rirong Chen
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
| | - Boheng Xiao
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
| | - Chun Hung Yip
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
| | - David K. Smith
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
| | - Wenshan Hong
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
| | - Yongmei Liu
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Lifeng Li
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
| | - Jia Wang
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
| | - Edward C. Holmes
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Tommy Tsan-Yuk Lam
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
| | - Huachen Zhu
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
| | - Yi Guan
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (STU/HKU), Shantou University, Shantou, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases (SKLEID), School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Shenzhen, Guangdong, China
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
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30
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Liang X, Chen X, Zhai J, Li X, Zhang X, Zhang Z, Zhang P, Wang X, Cui X, Wang H, Zhou N, Chen ZJ, Su R, Zhou F, Holmes EC, Irwin DM, Chen RA, He Q, Wu YJ, Wang C, Du XQ, Peng SM, Xie WJ, Shan F, Li WP, Dai JW, Shen X, Feng Y, Xiao L, Chen W, Shen Y. Pathogenicity, tissue tropism and potential vertical transmission of SARSr-CoV-2 in Malayan pangolins. PLoS Pathog 2023; 19:e1011384. [PMID: 37196026 DOI: 10.1371/journal.ppat.1011384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/30/2023] [Accepted: 04/24/2023] [Indexed: 05/19/2023] Open
Abstract
Malayan pangolin SARS-CoV-2-related coronavirus (SARSr-CoV-2) is closely related to SARS-CoV-2. However, little is known about its pathogenicity in pangolins. Using CT scans we show that SARSr-CoV-2 positive Malayan pangolins are characterized by bilateral ground-glass opacities in lungs in a similar manner to COVID-19 patients. Histological examination and blood gas tests are indicative of dyspnea. SARSr-CoV-2 infected multiple organs in pangolins, with the lungs the major target, and histological expression data revealed that ACE2 and TMPRSS2 were co-expressed with viral RNA. Transcriptome analysis indicated that virus-positive pangolins were likely to have inadequate interferon responses, with relative greater cytokine and chemokine activity in the lung and spleen. Notably, both viral RNA and viral proteins were detected in three pangolin fetuses, providing initial evidence for vertical virus transmission. In sum, our study outlines the biological framework of SARSr-CoV-2 in pangolins, revealing striking similarities to COVID-19 in humans.
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Affiliation(s)
- Xianghui Liang
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiaoyuan Chen
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Junqiong Zhai
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, China
| | - Xiaobing Li
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- College of Life Sciences, Longyan University, Longyan, China
| | - Xu Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Zhipeng Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Ping Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiao Wang
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xinyuan Cui
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Hai Wang
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Niu Zhou
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, China
| | - Zu-Jin Chen
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, China
| | - Renwei Su
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Fuqing Zhou
- Department of Radiology, the First Affiliated Hospital, Nanchang University, Nanchang, China
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Banting and Best Diabetes Centre, University of Toronto, Toronto, Canada
| | - Rui-Ai Chen
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing, China
| | - Qian He
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Ya-Jiang Wu
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, China
| | - Chen Wang
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, China
| | - Xue-Qing Du
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, China
| | - Shi-Ming Peng
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, China
| | - Wei-Jun Xie
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, China
| | - Fen Shan
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, China
| | - Wan-Ping Li
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, China
| | - Jun-Wei Dai
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, China
| | - Xuejuan Shen
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yaoyu Feng
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Lihua Xiao
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Wu Chen
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, China
| | - Yongyi Shen
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, Guangzhou, China
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31
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Lu M, He WT, Pettersson JHO, Baele G, Shi M, Holmes EC, He N, Su S. Zoonotic risk assessment among farmed mammals. Cell 2023; 186:2040-2040.e1. [PMID: 37116474 DOI: 10.1016/j.cell.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Farmed mammals may act as hosts for zoonotic viruses that can cause disease outbreaks in humans. This SnapShot shows which farmed mammals, and to what extent, are of particular risk of harboring and spreading viruses from viral families that are commonly associated with zoonotic disease. It also discusses genome surveillance methods and biosafety measures. To view this SnapShot, open or download the PDF.
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Affiliation(s)
- Meng Lu
- Fudan University, Shanghai, China
| | - Wan-Ting He
- China Pharmaceutical University, Nanjing, China
| | - John H-O Pettersson
- Uppsala University, Uppsala, Sweden; University of Sydney, Sydney, Australia
| | | | - Mang Shi
- Sun Yat-sen University, Shenzhen, China
| | | | - Na He
- Fudan University, Shanghai, China
| | - Shuo Su
- Fudan University, Shanghai, China.
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32
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Tulloch RL, Kim K, Sikazwe C, Michie A, Burrell R, Holmes EC, Dwyer DE, Britton PN, Kok J, Eden JS. RAPID prep: A Simple, Fast Protocol for RNA Metagenomic Sequencing of Clinical Samples. Viruses 2023; 15:v15041006. [PMID: 37112986 PMCID: PMC10146689 DOI: 10.3390/v15041006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Emerging infectious disease threats require rapid response tools to inform diagnostics, treatment, and outbreak control. RNA-based metagenomics offers this; however, most approaches are time-consuming and laborious. Here, we present a simple and fast protocol, the RAPIDprep assay, with the aim of providing a cause-agnostic laboratory diagnosis of infection within 24 h of sample collection by sequencing ribosomal RNA-depleted total RNA. The method is based on the synthesis and amplification of double-stranded cDNA followed by short-read sequencing, with minimal handling and clean-up steps to improve processing time. The approach was optimized and applied to a range of clinical respiratory samples to demonstrate diagnostic and quantitative performance. Our results showed robust depletion of both human and microbial rRNA, and library amplification across different sample types, qualities, and extraction kits using a single workflow without input nucleic-acid quantification or quality assessment. Furthermore, we demonstrated the genomic yield of both known and undiagnosed pathogens with complete genomes recovered in most cases to inform molecular epidemiological investigations and vaccine design. The RAPIDprep assay is a simple and effective tool, and representative of an important shift toward the integration of modern genomic techniques with infectious disease investigations.
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Affiliation(s)
- Rachel L Tulloch
- Centre for Virus Research, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Karan Kim
- Centre for Virus Research, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Chisha Sikazwe
- PathWest Laboratory Medicine WA, Department of Microbiology, Nedlands, WA 6009, Australia
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Alice Michie
- PathWest Laboratory Medicine WA, Department of Microbiology, Nedlands, WA 6009, Australia
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Rebecca Burrell
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Departments of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Dominic E Dwyer
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- NSW Health Pathology Institute for Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Philip N Britton
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Departments of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Jen Kok
- NSW Health Pathology Institute for Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - John-Sebastian Eden
- Centre for Virus Research, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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33
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Giovanetti M, Vazquez C, Lima M, Castro E, Rojas A, de la Fuente AG, Aquino C, Cantero C, Fleitas F, Torales J, Barrios J, Ortega MJ, Gamarra ML, Villalba S, Alfonzo T, Xavier J, Adelino T, Fritsch H, Iani FCM, Pereira GC, de Oliveira C, Schuab G, Rodrigues ES, Kashima S, Leite J, Gresh L, Franco L, Tegally H, Van Voorhis WC, Lessels R, de Filippis AMB, Ojeda A, Sequera G, Montoya R, Holmes EC, de Oliveira T, Rico JM, Lourenço J, Fonseca V, Alcantara LCJ. Rapid epidemic expansion of chikungunya virus-ECSA lineage in Paraguay. medRxiv 2023:2023.04.16.23288635. [PMID: 37131602 PMCID: PMC10153315 DOI: 10.1101/2023.04.16.23288635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The spread of vector-borne viruses, such as CHIKV, is a significant public health concern in the Americas, with over 120,000 cases and 51 deaths in 2023, of which 46 occurred in Paraguay. Using a suite of genomic, phylodynamic, and epidemiological techniques, we characterized the ongoing large CHIKV epidemic in Paraguay. Article Summary Line Genomic and epidemiological characterization of the ongoing Chikungunya virus epidemic in Paraguay.
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Affiliation(s)
- Marta Giovanetti
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Minas Gerais, Brazil
- Sciences and Technologies for Sustainable Development and One Health, University of Campus Bio-Medico,Rome, Italy
| | | | - Mauricio Lima
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Minas Gerais, Brazil
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Brazil
| | - Emerson Castro
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Minas Gerais, Brazil
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Brazil
| | - Analia Rojas
- Laboratorio Central de Salud Pública, Asunción, Paraguay
| | | | | | - Cesar Cantero
- Laboratorio Central de Salud Pública, Asunción, Paraguay
| | - Fatima Fleitas
- Laboratorio Central de Salud Pública, Asunción, Paraguay
| | - Juan Torales
- Laboratorio Central de Salud Pública, Asunción, Paraguay
| | - Julio Barrios
- Laboratorio Central de Salud Pública, Asunción, Paraguay
| | | | | | | | - Tania Alfonzo
- Laboratorio Central de Salud Pública, Asunción, Paraguay
| | - Joilson Xavier
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Minas Gerais, Brazil
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Talita Adelino
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Brazil
| | - Hegger Fritsch
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Minas Gerais, Brazil
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Felipe C. M. Iani
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Brazil
| | - Glauco Carvalho Pereira
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Brazil
| | - Carla de Oliveira
- Laboratório de Arbovírus e Vírus Hemorrágicos (LARBOH), Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Gabriel Schuab
- Laboratório de Arbovírus e Vírus Hemorrágicos (LARBOH), Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Evandra Strazza Rodrigues
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Simone Kashima
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Juliana Leite
- Infectious Hazards Management, Health Emergencies Department (PHE), Pan American Health Organization / World Health Organization (PAHO/WHO), Washington DC, USA
| | - Lionel Gresh
- Infectious Hazards Management, Health Emergencies Department (PHE), Pan American Health Organization / World Health Organization (PAHO/WHO), Washington DC, USA
| | - Leticia Franco
- Infectious Hazards Management, Health Emergencies Department (PHE), Pan American Health Organization / World Health Organization (PAHO/WHO), Washington DC, USA
| | - Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Wesley C. Van Voorhis
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, USA
| | - Richard Lessels
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Ana Maria Bispo de Filippis
- Laboratório de Arbovírus e Vírus Hemorrágicos (LARBOH), Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Andrea Ojeda
- Dirección General de Vigilancia de la Salud, Asunción, Paraguay
| | | | - Romeo Montoya
- Enfermedades Trasmisibles y Determinantes Ambientales de la Salud CDE/HA/PHE, Organización Panamericana de la Salud / Organización Mundial de la Salud (OPS/OMS), Asuncion, Paraguay
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Jairo Mendez Rico
- Infectious Hazards Management, Health Emergencies Department (PHE), Pan American Health Organization / World Health Organization (PAHO/WHO), Washington DC, USA
| | - José Lourenço
- Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, 1749-016, Portugal
| | - Vagner Fonseca
- Coordenação de Vigilância, Preparação e Resposta à Emergências e Desastres (PHE), Organização Pan-Americana da Saúde / Organização Mundial da Saúde (OPAS/OMS), Brasilia DF, Brazil
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Petrone ME, Lucas C, Menasche B, Breban MI, Yildirim I, Campbell M, Omer SB, Holmes EC, Ko AI, Grubaugh ND, Iwasaki A, Wilen CB, Vogels CBF, Fauver JR. Nonsystematic Reporting Biases of the SARS-CoV-2 Variant Mu Could Impact Our Understanding of the Epidemiological Dynamics of Emerging Variants. Genome Biol Evol 2023; 15:evad052. [PMID: 36974986 PMCID: PMC10113931 DOI: 10.1093/gbe/evad052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/16/2023] [Accepted: 03/09/2023] [Indexed: 03/29/2023] Open
Abstract
Developing a timely and effective response to emerging SARS-CoV-2 variants of concern (VOCs) is of paramount public health importance. Global health surveillance does not rely on genomic data alone to identify concerning variants when they emerge. Instead, methods that utilize genomic data to estimate the epidemiological dynamics of emerging lineages have the potential to serve as an early warning system. However, these methods assume that genomic data are uniformly reported across circulating lineages. In this study, we analyze differences in reporting delays among SARS-CoV-2 VOCs as a plausible explanation for the timing of the global response to the former VOC Mu. Mu likely emerged in South America in mid-2020, where its circulation was largely confined. In this study, we demonstrate that Mu was designated as a VOC ∼1 year after it emerged and find that the reporting of genomic data for Mu differed significantly than that of other VOCs within countries, states, and individual laboratories. Our findings suggest that nonsystematic biases in the reporting of genomic data may have delayed the global response to Mu. Until they are resolved, the surveillance gaps that affected the global response to Mu could impede the rapid and accurate assessment of future emerging variants.
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Affiliation(s)
- Mary E Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, NSW, Australia
| | - Carolina Lucas
- Department of Immunobiology, Yale University School of Medicine
| | - Bridget Menasche
- Department of Laboratory Medicine, Yale University School of Medicine
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health
| | - Inci Yildirim
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health
- Department of Pediatric, Section of Infectious Diseases and Global Health, Yale University School of Medicine
- Yale Institute for Global Health, Yale University
| | - Melissa Campbell
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine
| | - Saad B Omer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health
- Yale Institute for Global Health, Yale University
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, NSW, Australia
| | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health
- Department of Ecology and Evolutionary Biology, Yale University
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine
- Howard Hughes Medical Institute
| | - Craig B Wilen
- Department of Immunobiology, Yale University School of Medicine
- Department of Laboratory Medicine, Yale University School of Medicine
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health
| | - Joseph R Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health
- College of Public Health, University of Nebraska Medical Center
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Abstract
Ticks harbour a high diversity of viruses, bacteria and protozoa. The soft tick Carios vespertilionis (Argasidae) is a common ectoparasite of bats in the Palearctic region and is suspected to be vector and reservoir of viruses and other microbial species in bat populations, some of which may act as zoonotic agents for human disease. The Soprano pipistrelle (Pipistrellus pygmaeus, Vespertilionidae) is widely distributed in Europe, where it can be found inside or close to human habitation. We used meta-transcriptomic sequencing to determine the RNA virome and common microbiota in blood-fed C. vespertilionis ticks collected from a Soprano pipistrelle bat roosting site in south-central Sweden. Our analyses identified 16 viruses from 11 virus families, of which 15 viruses were novel. For the first time in Sweden we identified Issuk-Kul virus, a zoonotic arthropod-borne virus previously associated with outbreaks of acute febrile illness in humans. Probable bat-associated and tick-borne viruses were classified within the families Nairoviridae, Caliciviridae and Hepeviridae, while other invertebrate-associated viruses included members of the Dicistroviridae, Iflaviridae, Nodaviridae, Partitiviridae, Permutotetraviridae, Polycipiviridae and Solemoviridae. Similarly, we found abundant bacteria in C. vespertilionis, including genera with known tick-borne bacteria, such as Coxiella spp. and Rickettsia spp. These findings demonstrate the remarkable diversity of RNA viruses and bacteria present in C. vespertilionis and highlight the importance of bat-associated ectoparasite surveillance as an effective and non-invasive means to track viruses and bacteria circulating in bats and ticks.
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Affiliation(s)
- Ayda Susana Ortiz-Baez
- Sydney Institute for Infectious Diseases, School of Medical Sciences, the University of Sydney, Sydney, New South Wales 2006, Australia
| | - Thomas G T Jaenson
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, the University of Sydney, Sydney, New South Wales 2006, Australia
| | - John H-O Pettersson
- Sydney Institute for Infectious Diseases, School of Medical Sciences, the University of Sydney, Sydney, New South Wales 2006, Australia.,Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, University of Uppsala, SE-751 23 Uppsala, Sweden.,Clinical Microbiology and Hospital Hygiene, Uppsala University Hospital, 75237 Uppsala, Sweden
| | - Peter Wilhelmsson
- Department of Biomedical and Clinical Sciences, Division of Inflammation and Infection, Linköping University, SE-581 83 Linköping, Sweden.,Department of Clinical Microbiology, Region Jönköping County, SE-553 05 Jönköping, Sweden
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Xu L, Liu W, Bie M, Hu T, Yan D, Xiao Z, Holmes EC, Shi W. Identification of bovine coronavirus in a Daurian ground squirrel expands the host range of Betacoronavirus 1. Virol Sin 2023; 38:321-323. [PMID: 36863412 PMCID: PMC10176439 DOI: 10.1016/j.virs.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 02/23/2023] [Indexed: 03/04/2023] Open
Affiliation(s)
- Lin Xu
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China; Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai'an, 271000, China
| | - Wei Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mengyu Bie
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China; Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai'an, 271000, China
| | - Tao Hu
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai'an, 271000, China
| | - Dong Yan
- Anti-plague Institute of Hebei Province, Zhangjiakou, 075000, China
| | - Zhishu Xiao
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Weifeng Shi
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China; Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai'an, 271000, China.
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37
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Eaton K, Sidhu RK, Klunk J, Gamble JA, Boldsen JL, Carmichael AG, Varlık N, Duchene S, Featherstone L, Grimes V, Golding GB, DeWitte SN, Holmes EC, Poinar HN. Emergence, continuity, and evolution of Yersinia pestis throughout medieval and early modern Denmark. Curr Biol 2023; 33:1147-1152.e5. [PMID: 36841239 DOI: 10.1016/j.cub.2023.01.064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/08/2022] [Accepted: 01/30/2023] [Indexed: 02/27/2023]
Abstract
The historical epidemiology of plague is controversial due to the scarcity and ambiguity of available data.1,2 A common source of debate is the extent and pattern of plague re-emergence and local continuity in Europe during the 14th-18th century CE.3 Despite having a uniquely long history of plague (∼5,000 years), Scandinavia is relatively underrepresented in the historical archives.4,5 To better understand the historical epidemiology and evolutionary history of plague in this region, we performed in-depth (n = 298) longitudinal screening (800 years) for the plague bacterium Yersinia pestis (Y. pestis) across 13 archaeological sites in Denmark from 1000 to 1800 CE. Our genomic and phylogenetic data captured the emergence, continuity, and evolution of Y. pestis in this region over a period of 300 years (14th-17th century CE), for which the plague-positivity rate was 8.3% (3.3%-14.3% by site). Our phylogenetic analysis revealed that the Danish Y. pestis sequences were interspersed with those from other European countries, rather than forming a single cluster, indicative of the generation, spread, and replacement of bacterial variants through communities rather than their long-term local persistence. These results provide an epidemiological link between Y. pestis and the unknown pestilence that afflicted medieval and early modern Europe. They also demonstrate how population-scale genomic evidence can be used to test hypotheses on disease mortality and epidemiology and help pave the way for the next generation of historical disease research.
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Affiliation(s)
- Katherine Eaton
- McMaster Ancient DNA Centre, McMaster University, Hamilton, ON L8S 4L9, Canada; Department of Anthropology, McMaster University, Hamilton, ON L8S 4L9, Canada
| | - Ravneet K Sidhu
- McMaster Ancient DNA Centre, McMaster University, Hamilton, ON L8S 4L9, Canada; Department of Biology, McMaster University, Hamilton, ON L8S 4E8, Canada
| | - Jennifer Klunk
- McMaster Ancient DNA Centre, McMaster University, Hamilton, ON L8S 4L9, Canada; Daicel Arbor Biosciences, Ann Arbor, MI 48103, USA
| | - Julia A Gamble
- Department of Anthropology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Jesper L Boldsen
- Department of Forensic Medicine, Unit of Anthropology (ADBOU), University of Southern Denmark, 5260 Odense, Denmark
| | - Ann G Carmichael
- Department of History, Indiana University Bloomington, Bloomington, IN 47405, USA
| | - Nükhet Varlık
- Department of History, Rutgers University - Newark, Newark, NJ 07102, USA
| | - Sebastian Duchene
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne 3004, Australia
| | - Leo Featherstone
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne 3004, Australia
| | - Vaughan Grimes
- Department of Archaeology, Memorial University of Newfoundland, St. Johns, SC A1C 5S7, Canada
| | - G Brian Golding
- Department of Biology, McMaster University, Hamilton, ON L8S 4E8, Canada
| | - Sharon N DeWitte
- Department of Anthropology, University of South Carolina, Columbia, SC 29208, USA
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney 2006, Australia
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, McMaster University, Hamilton, ON L8S 4L9, Canada; Department of Anthropology, McMaster University, Hamilton, ON L8S 4L9, Canada; Department of Biochemistry, McMaster University, Hamilton, ON L82 4K1, Canada; Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada.
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38
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Li C, Liu S, Zhou H, Zhu W, Cui M, Li J, Wang J, Liu J, Zhu J, Li W, Bi Y, Carr MJ, Holmes EC, Shi W. Metatranscriptomic Sequencing Reveals Host Species as an Important Factor Shaping the Mosquito Virome. Microbiol Spectr 2023; 11:e0465522. [PMID: 36786616 PMCID: PMC10101097 DOI: 10.1128/spectrum.04655-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/18/2023] [Indexed: 02/15/2023] Open
Abstract
Mosquitoes are important vector hosts for numerous viral pathogens and harbor a large number of mosquito-specific viruses as well as human-infecting viruses. Previous studies have mainly focused on the discovery of mosquito viruses, and our understanding of major ecological factors associated with virome structure in mosquitoes remains limited. We utilized metatranscriptomic sequencing to characterize the viromes of five mosquito species sampled across eight locations in Yunnan Province, China. This revealed the presence of 52 viral species, of which 19 were novel, belonging to 15 viral families/clades. Of particular note was Culex hepacivirus 1, clustering within the avian clade of hepaciviruses. Notably, both the viromic diversity and abundance of Aedes genus mosquitoes were significantly higher than those of the Culex genus, while Aedes albopictus mosquitoes harbored a higher diversity than Aedes aegypti mosquitoes. Our findings thus point to discernible differences in viromic structure between mosquito genera and even between mosquito species within the same genus. Importantly, such differences were not attributable to differences in sampling between geographical location. Our study also revealed the ubiquitous presence of the endosymbiont bacterium Wolbachia, with the genetic diversity and abundance also varying between mosquito species. In conclusion, our results suggested that the mosquito host species play an important role in shaping the virome's structure. IMPORTANCE This study revealed the huge capability of mosquitoes in harboring a rich diversity of RNA viruses, although relevant studies have characterized the intensively unparalleled diversity of RNA viruses previously. Furthermore, our findings showed discernible differences not only in viromic structure between mosquito genera and even between mosquito species within the same genus but also in the genetic diversity and abundance of Wolbachia between different mosquito populations. These findings emphasize the importance of host genetic background in shaping the virome composition of mosquitoes.
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Affiliation(s)
- Cixiu Li
- Department of Pathogen Biology, School of Clinical and Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
| | - Shuqi Liu
- Department of Pathogen Biology, School of Clinical and Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
| | - Hong Zhou
- Department of Pathogen Biology, School of Clinical and Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
| | - Wei Zhu
- Department of Pathogen Biology, School of Clinical and Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
| | - Mingxue Cui
- Department of Pathogen Biology, School of Clinical and Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
| | - Juan Li
- Department of Pathogen Biology, School of Clinical and Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
| | - Jiao Wang
- Mengla County Center for Disease Control and Prevention, Mengla, China
| | - Jiangyun Liu
- Mengla County Center for Disease Control and Prevention, Mengla, China
| | - Jin Zhu
- Xishuangbanna Prefecture Center for Disease Control and Prevention, Jinghong, China
| | - Weiping Li
- Xishuangbanna Prefecture Center for Disease Control and Prevention, Jinghong, China
| | - Yuhai Bi
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Michael J. Carr
- National Virus Reference Laboratory, School of Medicine, University College Dublin, Dublin, Ireland
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Weifeng Shi
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
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Petrone ME, Holmes EC, Harvey E. Through an ecological lens: An ecosystem-based approach to zoonotic risk assessment: An ecosystem-based approach to zoonotic risk assessment. EMBO Rep 2023; 24:e56578. [PMID: 36651521 PMCID: PMC9900328 DOI: 10.15252/embr.202256578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/05/2022] [Indexed: 01/19/2023] Open
Abstract
Public health strategies to mitigate the emergence of novel pathogenic viruses should implement longitudinal metagenomic surveillance of ecosystems experiencing biodiversity changes to identify generalist viruses.
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Affiliation(s)
- Mary E Petrone
- Sydney Institute for Infectious Diseases, School of Medical SciencesThe University of SydneySydneyNSWAustralia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical SciencesThe University of SydneySydneyNSWAustralia
| | - Erin Harvey
- Sydney Institute for Infectious Diseases, School of Medical SciencesThe University of SydneySydneyNSWAustralia
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40
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Wille M, Lisovski S, Roshier D, Ferenczi M, Hoye BJ, Leen T, Warner S, Fouchier RAM, Hurt AC, Holmes EC, Klaassen M. Strong host phylogenetic and ecological effects on host competency for avian influenza in Australian wild birds. Proc Biol Sci 2023; 290:20222237. [PMID: 36651046 PMCID: PMC9845974 DOI: 10.1098/rspb.2022.2237] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Host susceptibility to parasites is mediated by intrinsic and external factors such as genetics, ecology, age and season. While waterfowl are considered central to the reservoir community for low pathogenic avian influenza A viruses (LPAIV), the role of host phylogeny has received limited formal attention. Herein, we analysed 12 339 oropharyngeal and cloacal swabs and 10 826 serum samples collected over 11 years from wild birds in Australia. As well as describing age and species-level differences in prevalence and seroprevalence, we reveal that host phylogeny is a key driver in host range. Seasonality effects appear less pronounced than in the Northern Hemisphere, while annual variations are potentially linked to El Niño-Southern Oscillation. Our study provides a uniquely detailed insight into the evolutionary ecology of LPAIV in its avian reservoir community, defining distinctive processes on the continent of Australia and expanding our understanding of LPAIV globally.
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Affiliation(s)
- Michelle Wille
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia,WHO Collaborating Centre for Reference and Research on Influenza, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia,Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Simeon Lisovski
- Centre for Integrative Ecology, Deakin University, Geelong, VIC 3217, Australia
| | - David Roshier
- Centre for Integrative Ecology, Deakin University, Geelong, VIC 3217, Australia
| | - Marta Ferenczi
- Centre for Integrative Ecology, Deakin University, Geelong, VIC 3217, Australia
| | - Bethany J. Hoye
- Centre for Integrative Ecology, Deakin University, Geelong, VIC 3217, Australia
| | - Trent Leen
- Geelong Field and Game, Geelong, VIC 3340, Australia,Wetlands Environmental Taskforce, Field and Game Australia, Seymour, VIC 3660, Australia
| | - Simone Warner
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, VIC 3083, Australia
| | - Ron A. M. Fouchier
- Department of Viroscience, Erasmus Medical Centre, Rotterdam 3015GE, The Netherlands
| | - Aeron C. Hurt
- WHO Collaborating Centre for Reference and Research on Influenza, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Marcel Klaassen
- Centre for Integrative Ecology, Deakin University, Geelong, VIC 3217, Australia,Victorian Wader Study Group, Thornbury, Victoria 3071, Australia,Australasian Wader Studies Group, Curtin, ACT 2605, Australia
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López-Astacio RA, Adu OF, Goetschius DJ, Lee H, Weichert WS, Wasik BR, Frueh SP, Alford BK, Voorhees IE, Flint JF, Saddoris S, Goodman LB, Holmes EC, Hafenstein SL, Parrish CR. Viral capsid, antibody, and receptor interactions: experimental analysis of the antibody escape evolution of canine parvovirus. bioRxiv 2023:2023.01.18.524668. [PMID: 36711712 PMCID: PMC9882321 DOI: 10.1101/2023.01.18.524668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Canine parvovirus (CPV) is a small non-enveloped single-stranded DNA virus that causes serious diseases in dogs worldwide. The original strain of the virus (CPV-2) emerged in dogs during the late-1970s due to a host range switch of a virus similar to the feline panleukopenia virus (FPV) that infected another host. The virus that emerged in dogs had altered capsid receptor- and antibody-binding sites, with some changes affecting both functions. Further receptor and antibody binding changes arose when the virus became better adapted to dogs or to other hosts. Here, we use in vitro selection and deep sequencing to reveal how two antibodies with known interactions select for escape mutations in CPV. The antibodies bind two distinct epitopes, and one largely overlaps the host receptor binding site. We also engineered antibody variants with altered binding structures. Viruses were passaged with the wild type or mutated antibodies, and their genomes deep sequenced during the selective process. A small number of mutations were detected only within the capsid protein gene during the first few passages of selection, and most sites remained polymorphic or were slow to go to fixation. Mutations arose both within and outside the antibody binding footprints on the capsids, and all avoided the TfR-binding footprint. Many selected mutations matched those that have arisen in the natural evolution of the virus. The patterns observed reveal the mechanisms by which these variants have been selected in nature and provide a better understanding of the interactions between antibody and receptor selections. IMPORTANCE Antibodies protect animals against infection by many different viruses and other pathogens, and we are gaining new information about the epitopes that induce antibody responses against viruses and the structures of the bound antibodies. However, less is known about the processes of antibody selection and antigenic escape and the constraints that apply in this system. Here, we use an in vitro model system and deep genome sequencing to reveal the mutations that arise in the virus genome during selection by each of two monoclonal antibodies or their engineered variants. High-resolution structures of each of the Fab: capsid complexes revealed their binding interactions. The engineered forms of the wild-type antibodies or mutant forms allowed us to examine how changes in antibody structure influence the mutational selection patterns seen in the virus. The results shed light on the processes of antibody binding, neutralization escape, and receptor binding, and likely have parallels for many other viruses.
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Li N, Li C, Hu T, Li J, Zhou H, Ji J, Wu J, Kang W, Holmes EC, Shi W, Xu S. Nationwide genomic surveillance reveals the prevalence and evolution of honeybee viruses in China. Microbiome 2023; 11:6. [PMID: 36631833 PMCID: PMC9832778 DOI: 10.1186/s40168-022-01446-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 12/08/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND The economic and environmental value of honeybees has been severely challenged in recent years by the collapse of their colonies worldwide, often caused by outbreaks of infectious diseases. However, our understanding of the diversity, prevalence, and transmission of honeybee viruses is largely obscure due to a lack of large-scale and longitudinal genomic surveillance on a global scale. RESULTS We report the meta-transcriptomic sequencing of nearly 2000 samples of the two most important economic and widely maintained honeybee species, as well as an associated ectoparasite mite, collected across China during 2016-2019. We document the natural diversity and evolution of honeybee viruses in China, providing evidence that multiple viruses commonly co-circulate within individual bee colonies. We also expanded the genomic data for 12 important honeybee viruses and revealed novel genetic variants and lineages associated with China. We identified more than 23 novel viruses from the honeybee and mite viromes, with some exhibiting ongoing replication in their respective hosts. Together, these data provide additional support to the idea that mites are an important reservoir and spill-over host for honeybee viruses. CONCLUSIONS Our data show that honeybee viruses are more widespread, prevalent, and genetically diverse than previously realized. The information provided is important in mitigating viral infectious diseases in honeybees, in turn helping to maintain sustainable productive agriculture on a global scale. Video Abstract.
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Affiliation(s)
- Nannan Li
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Cixiu Li
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China
| | - Tao Hu
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China
| | - Juan Li
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China
| | - Hong Zhou
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China
| | - Jingkai Ji
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China
| | - Jiangli Wu
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Weipeng Kang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Edward C Holmes
- Sydeny Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Weifeng Shi
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China.
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China.
| | - Shufa Xu
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Costa VA, Bellwood DR, Mifsud JCO, Van Brussel K, Geoghegan JL, Holmes EC, Harvey E. Limited cross-species virus transmission in a spatially restricted coral reef fish community. Virus Evol 2023; 9:vead011. [PMID: 36910859 PMCID: PMC9994595 DOI: 10.1093/ve/vead011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/18/2023] [Accepted: 02/01/2023] [Indexed: 02/04/2023] Open
Abstract
The Great Barrier Reef (GBR)-the largest coral reef ecosystem in the world-supports over 1,200 fish species with some of the highest population densities and diversities observed in vertebrates, offering a high potential for virus transmission among species. As such, the GBR represents an exceptional natural ecosystem to determine the impact of host community diversity on virus evolution and emergence. In recent decades, the GBR has also experienced significant threats of extinction, making it one of the most vulnerable ecosystems on the planet. Despite the global importance of the GBR, our understanding of virus diversity and connectivity in tropical reef fishes remains poor. Here, we employed metatranscriptomic sequencing to reveal the viromes of sixty-one reef fish species. This identified transcripts representing 132 putative viral sequences, 38 of which exhibited strong phylogenetic relationships with known vertebrate-associated viral genera, including a novel Santee-Cooper ranavirus (Iridoviridae). We found little evidence for virus transmission between fish species living within a very restricted geographical space-a 100-m2 coral reef ecosystem-suggesting that there might be important host barriers to successful cross-species transmission despite regular exposure. We also identified differences in virome composition among reef fish families, such that cryptobenthic reef fishes-characterized by small body sizes and short life spans-exhibited greater virome richness compared to large reef fishes. This study suggests that there are important barriers to cross-species virus transmission and that successful emergence in a reef fish community likely requires active host adaptation, even among closely related host species.
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Affiliation(s)
- Vincenzo A Costa
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - David R Bellwood
- Research Hub for Coral Reef Ecosystem Functions, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
| | - Jonathon C O Mifsud
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Kate Van Brussel
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand.,Institute of Environmental Science and Research, Wellington 5022, New Zealand
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Erin Harvey
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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Mifsud JCO, Costa VA, Petrone ME, Marzinelli EM, Holmes EC, Harvey E. Transcriptome mining extends the host range of the Flaviviridae to non-bilaterians. Virus Evol 2022; 9:veac124. [PMID: 36694816 PMCID: PMC9854234 DOI: 10.1093/ve/veac124] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/20/2022] [Accepted: 12/26/2022] [Indexed: 12/27/2022] Open
Abstract
The flavivirids (family Flaviviridae) are a group of positive-sense RNA viruses that include well-documented agents of human disease. Despite their importance and ubiquity, the timescale of flavivirid evolution is uncertain. An ancient origin, spanning millions of years, is supported by their presence in both vertebrates and invertebrates and by the identification of a flavivirus-derived endogenous viral element in the peach blossom jellyfish genome (Craspedacusta sowerbii, phylum Cnidaria), implying that the flaviviruses arose early in the evolution of the Metazoa. To date, however, no exogenous flavivirid sequences have been identified in these hosts. To help resolve the antiquity of the Flaviviridae, we mined publicly available transcriptome data across the Metazoa. From this, we expanded the diversity within the family through the identification of 32 novel viral sequences and extended the host range of the pestiviruses to include amphibians, reptiles, and ray-finned fish. Through co-phylogenetic analysis we found cross-species transmission to be the predominate macroevolutionary event across the non-vectored flavivirid genera (median, 68 per cent), including a cross-species transmission event between bats and rodents, although long-term virus-host co-divergence was still a regular occurrence (median, 23 per cent). Notably, we discovered flavivirus-like sequences in basal metazoan species, including the first associated with Cnidaria. This sequence formed a basal lineage to the genus Flavivirus and was closer to arthropod and crustacean flaviviruses than those in the tamanavirus group, which includes a variety of invertebrate and vertebrate viruses. Combined, these data attest to an ancient origin of the flaviviruses, likely close to the emergence of the metazoans 750-800 million years ago.
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Affiliation(s)
| | - Vincenzo A Costa
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney NSW 2006, Australia
| | - Mary E Petrone
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney NSW 2006, Australia
| | - Ezequiel M Marzinelli
- School of Life and Environmental Sciences, The University of Sydney, Sydney NSW 2006, Australia,Sydney Institute of Marine Science, 19 Chowder Bay Rd, Mosman, NSW 2088, Australia,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551 Singapore
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Sghaier S, Sailleau C, Marcacci M, Thabet S, Curini V, Ben Hassine T, Teodori L, Portanti O, Hammami S, Jurisic L, Spedicato M, Postic L, Gazani I, Ben Osman R, Zientara S, Bréard E, Calistri P, Richt JA, Holmes EC, Savini G, Di Giallonardo F, Lorusso A. Epizootic Haemorrhagic Disease Virus Serotype 8 in Tunisia, 2021. Viruses 2022; 15:16. [PMID: 36680057 PMCID: PMC9866946 DOI: 10.3390/v15010016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/10/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Epizootic haemorrhagic disease (EHD) is a Culicoides-borne viral disease caused by the epizootic haemorrhagic disease virus (EHDV) associated with clinical manifestations in domestic and wild ruminants, primarily white-tailed deer (Odocoileus virginianus) and cattle (Bos taurus). In late September 2021, EHDV was reported in cattle farms in central/western Tunisia. It rapidly spread throughout the country with more than 200 confirmed outbreaks. We applied a combination of classical and molecular techniques to characterize the causative virus as a member of the serotype EHDV-8. This is the first evidence of EHDV- 8 circulation since 1982 when the prototype EHDV-8 strain was isolated in Australia. This work highlights the urgent need for vaccines for a range of EHDV serotypes.
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Affiliation(s)
- Soufien Sghaier
- Institut de la Recherche Vétérinaire de Tunisie, Tunis 1006, Tunisia
| | - Corinne Sailleau
- UMR VIROLOGIE, INRAE, École Nationale Vétérinaire d’Alfort, ANSES Laboratoire de Santé Animale, Université Paris-Est, 94700 Maisons-Alfort, France
| | - Maurilia Marcacci
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy
| | - Sarah Thabet
- Institut de la Recherche Vétérinaire de Tunisie, Tunis 1006, Tunisia
| | - Valentina Curini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy
| | - Thameur Ben Hassine
- Direction Générale des Services Vétérinaires, Commissariat Régional au Développement Agricole de Nabeul, Nabeul 1082, Tunisia
| | - Liana Teodori
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy
| | - Ottavio Portanti
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy
| | - Salah Hammami
- Service de Microbiologie, Immunologie et Pathologie Générale, École Nationale de Médecine Vétérinaire de Sidi Thabet, IRESA, Universitè de la Manouba, Winnipeg 2010, Tunisia
| | - Lucija Jurisic
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy
- Facoltà di Medicina Veterinaria, Università degli Studi di Teramo, 64100 Piano D’Accio-Teramo, Italy
| | - Massimo Spedicato
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy
| | - Lydie Postic
- UMR VIROLOGIE, INRAE, École Nationale Vétérinaire d’Alfort, ANSES Laboratoire de Santé Animale, Université Paris-Est, 94700 Maisons-Alfort, France
| | - Ines Gazani
- CRDA Ministère d’Agriculture, Avenue Habib Bourguiba, Kasserine 1200, Tunisia
| | - Raja Ben Osman
- National Drug Control Laboratory, Vaccine Control Unit, Tunis 1002, Tunisia
| | - Stephan Zientara
- UMR VIROLOGIE, INRAE, École Nationale Vétérinaire d’Alfort, ANSES Laboratoire de Santé Animale, Université Paris-Est, 94700 Maisons-Alfort, France
| | - Emmanuel Bréard
- UMR VIROLOGIE, INRAE, École Nationale Vétérinaire d’Alfort, ANSES Laboratoire de Santé Animale, Université Paris-Est, 94700 Maisons-Alfort, France
| | - Paolo Calistri
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy
| | - Jürgen A. Richt
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney 2006, Australia
| | - Giovanni Savini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy
| | | | - Alessio Lorusso
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy
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Wang J, Pan YF, Yang LF, Yang WH, Luo CM, Wang J, Kuang GP, Wu WC, Gou QY, Xin GY, Li B, Luo HL, Chen YQ, Shu YL, Guo D, Gao ZH, Liang G, Li J, Holmes EC, Feng Y, Shi M. Individual bat viromes reveal the co-infection, spillover and emergence risk of potential zoonotic viruses. bioRxiv 2022:2022.11.23.517609. [PMID: 36451889 PMCID: PMC9709790 DOI: 10.1101/2022.11.23.517609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Bats are reservoir hosts for many zoonotic viruses. Despite this, relatively little is known about the diversity and abundance of viruses within bats at the level of individual animals, and hence the frequency of virus co-infection and inter-species transmission. Using an unbiased meta-transcriptomics approach we characterised the mammalian associated viruses present in 149 individual bats sampled from Yunnan province, China. This revealed a high frequency of virus co-infection and species spillover among the animals studied, with 12 viruses shared among different bat species, which in turn facilitates virus recombination and reassortment. Of note, we identified five viral species that are likely to be pathogenic to humans or livestock, including a novel recombinant SARS-like coronavirus that is closely related to both SARS-CoV-2 and SARS-CoV, with only five amino acid differences between its receptor-binding domain sequence and that of the earliest sequences of SARS-CoV-2. Functional analysis predicts that this recombinant coronavirus can utilize the human ACE2 receptor such that it is likely to be of high zoonotic risk. Our study highlights the common occurrence of inter-species transmission and co-infection of bat viruses, as well as their implications for virus emergence.
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Brian I, Manuzzi A, Dalla Rovere G, Giussani E, Palumbo E, Fusaro A, Bonfante F, Bortolami A, Quaranta EG, Monne I, Patarnello T, Bargelloni L, Terregino C, Holmes EC, Todesco G, Sorrentino F, Berton A, Badetti C, Carrer C, Ferrari G, Zincone C, Milan M, Panzarin V. Molecular Monitoring of SARS-CoV-2 in Different Sewage Plants in Venice and the Implications for Genetic Surveillance. ACS ES T Water 2022; 2:1953-1963. [PMID: 37552713 PMCID: PMC9115883 DOI: 10.1021/acsestwater.2c00013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 05/20/2023]
Abstract
Wastewater-based epidemiology is now widely used as an indirect tool to monitor the spread of SARS-CoV-2. In this study, five different sample matrices representing diverse phases of the wastewater treatment process were collected during the second wave of SARS-CoV-2 from two wastewater treatment plants (WWTPs) serving the Civil Hospital and Sacca Fisola island in Venice, Italy. Positive SARS-CoV-2 detections occurred at both WWTPs, and data on viral genome detection rate and quantification suggest that the pellet (i.e., the particulate resulting from the influent) is a sensitive matrix that permits reliable assessment of infection prevalence while reducing time to results. On the contrary, analysis of post-treatment matrices provides evidence of the decontamination efficacy of both WWTPs. Finally, direct sequencing of wastewater samples enabled us to identify B.1.177 and B.1.160 as the prevalent SARS-CoV-2 lineages circulating in Venice at the time of sampling. This study confirmed the suitability of wastewater testing for studying SARS-CoV-2 circulation and established a simplified workflow for the prompt detection and characterization of the virus.
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Affiliation(s)
- Irene Brian
- Division of Comparative Biomedical Sciences,
Istituto Zooprofilattico Sperimentale delle Venezie, Viale
dell’Università 10, 35020 Legnaro, Padova, Italy
| | - Alice Manuzzi
- Department of Comparative Biomedicine and Food
Science, University of Padova, Viale
dell’Università 16, 35020 Legnaro, Padova, Italy
| | - Giulia Dalla Rovere
- Department of Comparative Biomedicine and Food
Science, University of Padova, Viale
dell’Università 16, 35020 Legnaro, Padova, Italy
| | - Edoardo Giussani
- Division of Comparative Biomedical Sciences,
Istituto Zooprofilattico Sperimentale delle Venezie, Viale
dell’Università 10, 35020 Legnaro, Padova, Italy
| | - Elisa Palumbo
- Division of Comparative Biomedical Sciences,
Istituto Zooprofilattico Sperimentale delle Venezie, Viale
dell’Università 10, 35020 Legnaro, Padova, Italy
| | - Alice Fusaro
- Division of Comparative Biomedical Sciences,
Istituto Zooprofilattico Sperimentale delle Venezie, Viale
dell’Università 10, 35020 Legnaro, Padova, Italy
| | - Francesco Bonfante
- Division of Comparative Biomedical Sciences,
Istituto Zooprofilattico Sperimentale delle Venezie, Viale
dell’Università 10, 35020 Legnaro, Padova, Italy
| | - Alessio Bortolami
- Division of Comparative Biomedical Sciences,
Istituto Zooprofilattico Sperimentale delle Venezie, Viale
dell’Università 10, 35020 Legnaro, Padova, Italy
| | - Erika Giorgia Quaranta
- Division of Comparative Biomedical Sciences,
Istituto Zooprofilattico Sperimentale delle Venezie, Viale
dell’Università 10, 35020 Legnaro, Padova, Italy
| | - Isabella Monne
- Division of Comparative Biomedical Sciences,
Istituto Zooprofilattico Sperimentale delle Venezie, Viale
dell’Università 10, 35020 Legnaro, Padova, Italy
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food
Science, University of Padova, Viale
dell’Università 16, 35020 Legnaro, Padova, Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food
Science, University of Padova, Viale
dell’Università 16, 35020 Legnaro, Padova, Italy
| | - Calogero Terregino
- Division of Comparative Biomedical Sciences,
Istituto Zooprofilattico Sperimentale delle Venezie, Viale
dell’Università 10, 35020 Legnaro, Padova, Italy
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Life
and Environmental Sciences and School of Medical Sciences, University of
Sydney, Sydney 2006, Australia
| | | | - Francesco Sorrentino
- Provveditorato interregionale per il
Veneto, Trentino AA, Friuli Venezia Giulia, Ponte di Rialto, 19, Venezia,
30125, Italy
| | | | | | | | | | - Cinzia Zincone
- Provveditorato interregionale per il
Veneto, Trentino AA, Friuli Venezia Giulia, Ponte di Rialto, 19, Venezia,
30125, Italy
| | - Massimo Milan
- Department of Comparative Biomedicine and Food
Science, University of Padova, Viale
dell’Università 16, 35020 Legnaro, Padova, Italy
| | - Valentina Panzarin
- Division of Comparative Biomedical Sciences,
Istituto Zooprofilattico Sperimentale delle Venezie, Viale
dell’Università 10, 35020 Legnaro, Padova, Italy
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French RK, Stone ZL, Parker KA, Holmes EC. Novel viral and microbial species in a translocated Toutouwai (Petroica longipes) population from Aotearoa/New Zealand. One Health Outlook 2022; 4:16. [PMID: 36224666 PMCID: PMC9558408 DOI: 10.1186/s42522-022-00072-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Translocation is a common tool in wildlife management and its implementation has resulted in many conservation successes. During translocations, any associated infectious agents are moved with their wildlife hosts. Accordingly, translocations can present a risk of infectious disease emergence, although they also provide an opportunity to restore natural infectious communities ('infectome') and mitigate the long-term risks of reduced natural resistance. METHODS We used metatranscriptomic sequencing to characterise the cloacal infectome of 41 toutouwai (North Island robin, Petroica longipes) that were translocated to establish a new population within the North Island of New Zealand. We also screened for pathogenic bacteria, fungi and parasites. RESULTS Although we did not detect any known avian diseases, which is a positive outcome for the translocated toutouwai population, we identified a number of novel viruses of interest, including a novel avian hepatovirus, as well as a divergent calici-like virus and four hepe-like viruses of which the host species is unknown. We also revealed a novel spirochete bacterium and a coccidian eukaryotic parasite. CONCLUSIONS The presumably non-pathogenic viruses and microbial species identified here support the idea that most microorganisms likely do not cause disease in their hosts, and that translocations could serve to help restore and maintain native infectious communities. We advise greater surveillance of infectious communities of both native and non-native wildlife before and after translocations to better understand the impact, positive or negative, that such movements may have on both host and infectome ecology.
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Affiliation(s)
- Rebecca K French
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia.
| | - Zoë L Stone
- Zoology and Ecology Group, School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Kevin A Parker
- Parker Conservation Ltd, 549 Rocks Road, Nelson, New Zealand
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia.
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Tian J, Hou X, Ge M, Xu H, Yu B, Liu J, Shao R, Holmes EC, Lei C, Shi M. The diversity and evolutionary relationships of ticks and tick-borne bacteria collected in China. Parasit Vectors 2022; 15:352. [PMID: 36182913 PMCID: PMC9526939 DOI: 10.1186/s13071-022-05485-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 09/13/2022] [Indexed: 01/12/2023] Open
Abstract
Background Ticks (order Ixodida) are ectoparasites, vectors and reservoirs of many infectious agents affecting humans and domestic animals. However, the lack of information on tick genomic diversity leaves significant gaps in the understanding of the evolution of ticks and associated bacteria. Results We collected > 20,000 contemporary and historical (up to 60 years of preservation) tick samples representing a wide range of tick biodiversity across diverse geographic regions in China. Metagenomic sequencing was performed on individual ticks to obtain the complete or near-complete mitochondrial (mt) genome sequences from 46 tick species, among which mitochondrial genomes of 23 species were recovered for the first time. These new mt genomes data greatly expanded the diversity of many tick groups and revealed five cryptic species. Utilizing the same metagenomic sequence data we identified divergent and abundant bacteria in Haemaphysalis, Ixodes, Dermacentor and Carios ticks, including nine species of pathogenetic bacteria and potentially new species within the genus Borrelia. We also used these data to explore the evolutionary relationship between ticks and their associated bacteria, revealing a pattern of long-term co-divergence relationship between ticks and Rickettsia and Coxiella bacteria. Conclusions In sum, our study provides important new information on the genetic diversity of ticks based on an analysis of mitochondrial DNA as well as on the prevalence of tick-borne pathogens in China. It also sheds new light on the long-term evolutionary and ecological relationships between ticks and their associated bacteria. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05485-3.
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Affiliation(s)
- JunHua Tian
- Hubei Key Laboratory of Resources Utilization and Sustainable Pest Management, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China.,Wuhan Centers for Disease Control and Prevention, Wuhan, Hubei Province, 430015, China
| | - Xin Hou
- School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, Guangdong Province, 518107, China
| | - MiHong Ge
- Wuhan Academy of Agricultural Sciences, Wuhan, Hubei Province, 430345, China
| | - HongBin Xu
- Jiangxi Province Center for Disease Control and Prevention, Nanchang, Jiangxi Province, 330029, China
| | - Bin Yu
- Wuhan Centers for Disease Control and Prevention, Wuhan, Hubei Province, 430015, China
| | - Jing Liu
- Wuhan Centers for Disease Control and Prevention, Wuhan, Hubei Province, 430015, China
| | - RenFu Shao
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, 4558, Australia.,GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, 4558, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - ChaoLiang Lei
- Hubei Key Laboratory of Resources Utilization and Sustainable Pest Management, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China.
| | - Mang Shi
- School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, Guangdong Province, 518107, China.
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Ortiz-Baez AS, Holmes EC, Charon J, Pettersson JHO, Hesson JC. Meta-transcriptomics reveals potential virus transfer between Aedes communis mosquitoes and their parasitic water mites. Virus Evol 2022; 8:veac090. [PMID: 36320615 PMCID: PMC9604308 DOI: 10.1093/ve/veac090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/29/2022] [Accepted: 09/23/2022] [Indexed: 11/14/2022] Open
Abstract
Arthropods harbor a largely undocumented diversity of RNA viruses. Some arthropods, like mosquitoes, can transmit viruses to vertebrates but are themselves parasitized by other arthropod species, such as mites. Very little is known about the viruses of these ectoparasites and how they move through the host–parasite relationship. To address this, we determined the virome of both mosquitoes and the mites that feed on them. The mosquito Aedes communis is an abundant and widely distributed species in Sweden, in northern Europe. These dipterans are commonly parasitized by water mite larvae (Trombidiformes: Mideopsidae) that are hypothesized to impose negative selection pressures on the mosquito by reducing fitness. In turn, viruses are dual-host agents in the mosquito–mite interaction. We determined the RNA virus diversity of mite-free and mite-detached mosquitoes, as well as their parasitic mites, using meta-transcriptomic sequencing. Our results revealed an extensive RNA virus diversity in both mites and mosquitoes, including thirty-seven putative novel RNA viruses that cover a wide taxonomic range. Notably, a high proportion of viruses (20/37) were shared between mites and mosquitoes, while a limited number of viruses were present in a single host. Comparisons of virus composition and abundance suggest potential virus transfer between mosquitoes and mites during their symbiotic interaction. These findings shed light on virome diversity and ecology in the context of arthropod host–parasite–virus relationships.
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Affiliation(s)
- Ayda Susana Ortiz-Baez
- Sydney Institute for Infectious Diseases, School of Medical Sciences, the University of Sydney , Sydney, New South Wales 2006, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, the University of Sydney , Sydney, New South Wales 2006, Australia
| | - Justine Charon
- Sydney Institute for Infectious Diseases, School of Medical Sciences, the University of Sydney , Sydney, New South Wales 2006, Australia
| | - John H.-O Pettersson
- Sydney Institute for Infectious Diseases, School of Medical Sciences, the University of Sydney , Sydney, New South Wales 2006, Australia
- Clinical Microbiology and Hospital Hygiene,Uppsala University Hospital , 75237 Uppsala, Sweden
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, University of Uppsala , SE-751 23 Uppsala, Sweden
| | - Jenny C Hesson
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, University of Uppsala , SE-751 23 Uppsala, Sweden
- Biologisk Myggkontroll, Nedre Dalälven Utvecklings AB , Vårdsätravägen 5, SE-75646 Uppsala, Sweden
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