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Lee S, Baker CM, Sellens E, Stevenson MA, Roche S, Hall RN, Breed AC, Firestone SM. A systematic review of epidemiological modelling in response to lumpy skin disease outbreaks. Front Vet Sci 2024; 11:1459293. [PMID: 39376926 PMCID: PMC11456570 DOI: 10.3389/fvets.2024.1459293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Accepted: 08/28/2024] [Indexed: 10/09/2024] Open
Abstract
Lumpy skin disease (LSD) is an infectious disease currently spreading worldwide and poses a serious global threat. However, there is limited evidence and understanding to support the use of models to inform decision-making in LSD outbreak responses. This review aimed to identify modelling approaches that can be used before and during an outbreak of LSD, examining their characteristics and priorities, and proposing a structured workflow. We conducted a systematic review and identified 60 relevant publications on LSD outbreak modelling. The review identified six categories of question to be addressed following outbreak detection (origin, entry pathway, outbreak severity, risk factors, spread, and effectiveness of control measures), and five analytical techniques used to address them (descriptive epidemiology, risk factor analysis, spatiotemporal analysis, dynamic transmission modelling, and simulation modelling). We evaluated the questions each analytical technique can address, along with their data requirements and limitations, and accordingly assigned priorities to the modelling. Based on this, we propose a structured workflow for modelling during an LSD outbreak. Additionally, we emphasise the importance of pre-outbreak preparation and continuous updating of modelling post-outbreak for effective decision-making. This study also discusses the inherent limitations and uncertainties in the identified modelling approaches. To support this workflow, high-quality data must be collected in standardised formats, and efforts should be made to reduce inherent uncertainties of the models. The suggested modelling workflow can be used as a process to support rapid response for countries facing their first LSD occurrence and can be adapted to other transboundary diseases.
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Affiliation(s)
- Simin Lee
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Christopher M. Baker
- School of Mathematics and Statistics, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
- Melbourne Centre for Data Science, The University of Melbourne, Parkville, VIC, Australia
- The Centre of Excellence for Biosecurity Risk Analysis, School of Biosciences, The University of Melbourne, Parkville, VIC, Australia
| | - Emily Sellens
- Epidemiology, Surveillance and Laboratory Section, Australian Government Department of Agriculture, Fisheries and Forestry, Canberra, ACT, Australia
| | - Mark A. Stevenson
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Sharon Roche
- Epidemiology, Surveillance and Laboratory Section, Australian Government Department of Agriculture, Fisheries and Forestry, Canberra, ACT, Australia
| | | | - Andrew C. Breed
- Epidemiology, Surveillance and Laboratory Section, Australian Government Department of Agriculture, Fisheries and Forestry, Canberra, ACT, Australia
| | - Simon M. Firestone
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
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Naveca FG, Almeida TAPD, Souza V, Nascimento V, Silva D, Nascimento F, Mejía M, Oliveira YSD, Rocha L, Xavier N, Lopes J, Maito R, Meneses C, Amorim T, Fé L, Camelo FS, Silva SCDA, Melo AXD, Fernandes LG, Oliveira MAAD, Arcanjo AR, Araújo G, André Júnior W, Carvalho RLCD, Rodrigues R, Albuquerque S, Mattos C, Silva C, Linhares A, Rodrigues T, Mariscal F, Morais MA, Presibella MM, Marques NFQ, Paiva A, Ribeiro K, Vieira D, Queiroz JADS, Passos-Silva AM, Abdalla L, Santos JH, Figueiredo RMPD, Cruz ACR, Casseb LN, Chiang JO, Frutuoso LV, Rossi A, Freitas L, Campos TDL, Wallau GL, Moreira E, Lins Neto RD, Alexander LW, Sun Y, Filippis AMBD, Gräf T, Arantes I, Bento AI, Delatorre E, Bello G. Human outbreaks of a novel reassortant Oropouche virus in the Brazilian Amazon region. Nat Med 2024:10.1038/s41591-024-03300-3. [PMID: 39293488 DOI: 10.1038/s41591-024-03300-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Accepted: 09/15/2024] [Indexed: 09/20/2024]
Abstract
The Brazilian western Amazon is experiencing its largest laboratory-confirmed Oropouche virus (OROV) outbreak, with more than 6,300 reported cases between 2022 and 2024. In this study, we sequenced and analyzed 382 OROV genomes from human samples collected in Amazonas, Acre, Rondônia and Roraima states, between August 2022 and February 2024, to uncover the origin and genetic evolution of OROV in the current outbreak. Genomic analyses revealed that the upsurge of OROV cases in the Brazilian Amazon coincides with spread of a novel reassortant lineage containing the M segment of viruses detected in the eastern Amazon region (2009-2018) and the L and S segments of viruses detected in Peru, Colombia and Ecuador (2008-2021). The novel reassortant likely emerged in the Amazonas state between 2010 and 2014 and spread through long-range dispersion events during the second half of the 2010s. Phylodynamics reconstructions showed that the current OROV spread was driven mainly by short-range (< 2 km) movements consistent with the flight range of vectors. Nevertheless, a substantial proportion (22%) of long-range (>10 km) OROV migrations were also detected, consistent with viral dispersion by humans. Our data provide a view of the unprecedented spread and evolution of OROV in the Brazilian western Amazon region.
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Affiliation(s)
- Felipe Gomes Naveca
- Núcleo de Vigilância de Vírus Emergentes, Reemergentes ou Negligenciados - ViVER/EDTA, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil.
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil.
| | - Tatiana Amaral Pires de Almeida
- Núcleo de Vigilância de Vírus Emergentes, Reemergentes ou Negligenciados - ViVER/EDTA, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
- Diretoria de Ensino e Pesquisa, Fundação Centro de Controle de Oncologia do Estado do Amazonas, FCecon, Manaus, Brazil
| | - Victor Souza
- Núcleo de Vigilância de Vírus Emergentes, Reemergentes ou Negligenciados - ViVER/EDTA, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Valdinete Nascimento
- Núcleo de Vigilância de Vírus Emergentes, Reemergentes ou Negligenciados - ViVER/EDTA, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Dejanane Silva
- Núcleo de Vigilância de Vírus Emergentes, Reemergentes ou Negligenciados - ViVER/EDTA, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Fernanda Nascimento
- Núcleo de Vigilância de Vírus Emergentes, Reemergentes ou Negligenciados - ViVER/EDTA, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Matilde Mejía
- Núcleo de Vigilância de Vírus Emergentes, Reemergentes ou Negligenciados - ViVER/EDTA, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Yasmin Silva de Oliveira
- Núcleo de Vigilância de Vírus Emergentes, Reemergentes ou Negligenciados - ViVER/EDTA, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Luisa Rocha
- Laboratório Central de Saúde Pública de Roraima, Boa Vista, Brazil
| | - Natana Xavier
- Laboratório Central de Saúde Pública de Roraima, Boa Vista, Brazil
| | - Janis Lopes
- Laboratório Central de Saúde Pública de Roraima, Boa Vista, Brazil
| | - Rodrigo Maito
- Laboratório Central de Saúde Pública de Roraima, Boa Vista, Brazil
| | - Cátia Meneses
- Laboratório Central de Saúde Pública de Roraima, Boa Vista, Brazil
| | - Tatyana Amorim
- Fundação de Vigilância em Saúde - Dra. Rosemary Costa Pinto, Manaus, Brazil
| | - Luciana Fé
- Fundação de Vigilância em Saúde - Dra. Rosemary Costa Pinto, Manaus, Brazil
| | | | | | | | | | | | - Ana Ruth Arcanjo
- Laboratório Central de Saúde Pública do Amazonas, Manaus, Brazil
| | - Guilherme Araújo
- Laboratório Central de Saúde Pública do Amazonas, Manaus, Brazil
| | | | | | - Rosiane Rodrigues
- Laboratório Central de Saúde Pública de Rondônia, Porto Velho, Brazil
| | | | - Cristiane Mattos
- Laboratório Central de Saúde Pública de Rondônia, Porto Velho, Brazil
| | - Ciciléia Silva
- Laboratório Central de Saúde Pública de Rondônia, Porto Velho, Brazil
| | - Aline Linhares
- Laboratório Central de Saúde Pública de Rondônia, Porto Velho, Brazil
| | - Taynã Rodrigues
- Laboratório Central de Saúde Pública do Acre, Rio Branco, Brazil
| | - Francy Mariscal
- Laboratório Central de Saúde Pública do Acre, Rio Branco, Brazil
| | - Márcia Andréa Morais
- Núcleo de Doenças de Transmissão Vetorial, Secretaria Estadual de Saúde do Acre, Rio Branco, Brazil
| | | | | | - Anne Paiva
- Coordenação Geral de Laboratórios de Saúde Pública - CGLAB, Ministério da Saúde, Brasília, Brazil
| | - Karina Ribeiro
- Coordenação Geral de Laboratórios de Saúde Pública - CGLAB, Ministério da Saúde, Brasília, Brazil
| | - Deusilene Vieira
- Laboratório de Virologia Molecular, Fiocruz Rondônia, Porto Velho, Brazil
| | | | | | | | | | | | - Ana Cecília Ribeiro Cruz
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua, Brazil
| | - Livia Neves Casseb
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua, Brazil
| | - Jannifer Oliveira Chiang
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua, Brazil
| | - Livia Vinhal Frutuoso
- Coordenação-Geral de Vigilância de Arboviroses - CGARB, Departamento de Doenças Transmissíveis, Secretaria de Vigilância em Saúde e Ambiente, Ministério da Saúde, Brasília, Brazil
| | - Agata Rossi
- Laboratório de Genômica e Ecologia Viral, Departamento de Patologia, Centro de Ciências da Saúde, Universidade Federal do Espírito Santo, Vitória, Brazil
| | - Lucas Freitas
- GISAID Global Data Science Initiative, Munich, Germany
| | | | - Gabriel Luz Wallau
- Instituto Aggeu Magalhães, Fiocruz, Recife, Brazil
- Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference and Research, National Reference Center for Tropical Infectious Diseases, Hamburg, Germany
| | | | | | - Laura W Alexander
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Yining Sun
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | | | - Tiago Gräf
- Laboratório de Virologia Molecular, Instituto Carlos Chagas, Fiocruz, Curitiba, Brazil
| | - Ighor Arantes
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Ana I Bento
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Edson Delatorre
- Laboratório de Genômica e Ecologia Viral, Departamento de Patologia, Centro de Ciências da Saúde, Universidade Federal do Espírito Santo, Vitória, Brazil
| | - Gonzalo Bello
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil.
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Lähteenaro M, Benda D, Straka J, Nylander JAA, Bergsten J. Phylogenomic analysis of Stylops reveals the evolutionary history of a Holarctic Strepsiptera radiation parasitizing wild bees. Mol Phylogenet Evol 2024; 195:108068. [PMID: 38554985 DOI: 10.1016/j.ympev.2024.108068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/07/2024] [Accepted: 03/24/2024] [Indexed: 04/02/2024]
Abstract
Holarctic Stylops is the largest genus of the enigmatic insect order Strepsiptera, twisted winged parasites. Members of Stylops are obligate endoparasites of Andrena mining bees and exhibit extreme sexual dimorphism typical of Strepsiptera. So far, molecular studies on Stylops have focused on questions on species delimitation. Here, we utilize the power of whole genome sequencing to infer the phylogeny of this morphologically challenging genus from thousands of loci. We use a species tree method, concatenated maximum likelihood analysis and Bayesian analysis with a relaxed clock model to reconstruct the phylogeny of 46 Stylops species, estimate divergence times, evaluate topological consistency across methods and infer the root position. Furthermore, the biogeographical history and coevolutionary patterns with host species are assessed. All methods recovered a well resolved topology with close to all nodes maximally supported and only a handful of minor topological variations. Based on the result, we find that included species can be divided into 12 species groups, seven of them including only Palaearctic species, three Nearctic and two were geographically mixed. We find a strongly supported root position between a clade formed by the spreta, thwaitesi and gwynanae species groups and the remaining species and that the sister group of Stylops is Eurystylops or Eurystylops + Kinzelbachus. Our results indicate that Stylops originated in the Western Palaearctic or Western Palaearctic and Nearctic in the early Neogene or late Paleogene, with four independent dispersal events to the Nearctic. Cophylogenetic analyses indicate that the diversification of Stylops has been shaped by both significant coevolution with the mining bee hosts and host-shifting. The well resolved and strongly supported phylogeny will provide a valuable phylogenetic basis for further studies into the fascinating world of Strepsipterans.
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Affiliation(s)
- Meri Lähteenaro
- Department of Zoology, Swedish Museum of Natural History, P. O. Box 50007, SE-104 05 Stockholm, Sweden; Department of Zoology, Faculty of Science, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Daniel Benda
- Department of Zoology, Faculty of Science, Charles University, Vinicna 7, CZ-128 44, Prague 2, Czech Republic; Department of Entomology, National Museum of the Czech Republic, Cirkusová 1740, CZ-19300 Prague 9, Czech Republic.
| | - Jakub Straka
- Department of Zoology, Faculty of Science, Charles University, Vinicna 7, CZ-128 44, Prague 2, Czech Republic.
| | - Johan A A Nylander
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-106 91 Stockholm, Sweden.
| | - Johannes Bergsten
- Department of Zoology, Swedish Museum of Natural History, P. O. Box 50007, SE-104 05 Stockholm, Sweden; Department of Zoology, Faculty of Science, Stockholm University, SE-106 91 Stockholm, Sweden.
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4
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Tan CCS, van Dorp L, Balloux F. The evolutionary drivers and correlates of viral host jumps. Nat Ecol Evol 2024; 8:960-971. [PMID: 38528191 DOI: 10.1038/s41559-024-02353-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 01/29/2024] [Indexed: 03/27/2024]
Abstract
Most emerging and re-emerging infectious diseases stem from viruses that naturally circulate in non-human vertebrates. When these viruses cross over into humans, they can cause disease outbreaks, epidemics and pandemics. While zoonotic host jumps have been extensively studied from an ecological perspective, little attention has gone into characterizing the evolutionary drivers and correlates underlying these events. To address this gap, we harnessed the entirety of publicly available viral genomic data, employing a comprehensive suite of network and phylogenetic analyses to investigate the evolutionary mechanisms underpinning recent viral host jumps. Surprisingly, we find that humans are as much a source as a sink for viral spillover events, insofar as we infer more viral host jumps from humans to other animals than from animals to humans. Moreover, we demonstrate heightened evolution in viral lineages that involve putative host jumps. We further observe that the extent of adaptation associated with a host jump is lower for viruses with broader host ranges. Finally, we show that the genomic targets of natural selection associated with host jumps vary across different viral families, with either structural or auxiliary genes being the prime targets of selection. Collectively, our results illuminate some of the evolutionary drivers underlying viral host jumps that may contribute to mitigating viral threats across species boundaries.
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Affiliation(s)
- Cedric C S Tan
- UCL Genetics Institute, University College London, London, UK.
- The Francis Crick Institute, London, UK.
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London, UK
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5
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Liu F, Deng P, He J, Chen X, Jiang X, Yan Q, Xu J, Hu S, Yan J. A regional genomic surveillance program is implemented to monitor the occurrence and emergence of SARS-CoV-2 variants in Yubei District, China. Virol J 2024; 21:13. [PMID: 38191416 PMCID: PMC10775548 DOI: 10.1186/s12985-023-02279-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 12/27/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND In December 2022, Chongqing experienced a significant surge in coronavirus disease 2019 (COVID-19) epidemic after adjusting control measures in China. Given the widespread immunization of the population with the BA.5 variant, it is crucial to actively monitor severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant evolution in Chongqing's Yubei district. METHODS In this retrospective study based on whole genome sequencing, we collected oropharyngeal and nasal swab of native COVID-19 cases from Yubei district between January to May 2023, along with imported cases from January 2022 to January 2023. Through second-generation sequencing, we generated a total of 578 genomes. RESULTS Phylogenetic analyses revealed these genomes belong to 47 SARS-CoV-2 Pango lineages. BA.5.2.48 was dominant from January to April 2023, rapidly replaced by XBB* variants from April to May 2023. Bayesian Skyline Plot reconstructions indicated a higher evolutionary rate (6.973 × 10-4 subs/site/year) for the XBB.1.5* lineage compared to others. The mean time to the most recent common ancestor (tMRCA) of BA.5.2.48* closely matched BA.2.75* (May 27, 2022). Using multinomial logistic regression, we estimated growth advantages, with XBB.1.9.1 showing the highest growth advantage (1.2, 95% HPI:1.1-1.2), followed by lineage FR.1 (1.1, 95% HPI:1.1-1.2). CONCLUSIONS Our monitoring reveals the rapid replacement of the previously prevalent BA.5.2.48 variant by XBB and its sub-variants, underscoring the ineffectiveness of herd immunity and breakthrough BA.5 infections against XBB variants. Given the ongoing evolutionary pressure, sustaining a SARS-CoV-2 genomic surveillance program is imperative.
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Affiliation(s)
- Fangyuan Liu
- Chongqing Yubei Center for Disease Control and Prevention, Chongqing, China
| | - Peng Deng
- Chongqing Yubei Center for Disease Control and Prevention, Chongqing, China
| | - Jiuhong He
- Chongqing Yubei Center for Disease Control and Prevention, Chongqing, China
| | - Xiaofeng Chen
- Chongqing Yubei Center for Disease Control and Prevention, Chongqing, China
| | - Xinyu Jiang
- Chongqing Yubei Center for Disease Control and Prevention, Chongqing, China
| | - Qi Yan
- Chongqing Yubei Center for Disease Control and Prevention, Chongqing, China
| | - Jing Xu
- Chongqing Yubei Center for Disease Control and Prevention, Chongqing, China
| | - Sihan Hu
- Chongqing Yubei Center for Disease Control and Prevention, Chongqing, China
| | - Jin Yan
- Chongqing Yubei Center for Disease Control and Prevention, Chongqing, China.
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6
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Justo Arevalo S, Uribe Calampa CS, Jimenez Silva C, Quiñones Aguilar M, Bouckaert R, Rebello Pinho JR. Phylodynamic of SARS-CoV-2 during the second wave of COVID-19 in Peru. Nat Commun 2023; 14:3557. [PMID: 37322028 PMCID: PMC10272135 DOI: 10.1038/s41467-023-39216-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/02/2023] [Indexed: 06/17/2023] Open
Abstract
At over 0.6% of the population, Peru has one of the highest SARS-CoV-2 mortality rate in the world. Much effort to sequence genomes has been done in this country since mid-2020. However, an adequate analysis of the dynamics of the variants of concern and interest (VOCIs) is missing. We investigated the dynamics of the COVID-19 pandemic in Peru with a focus on the second wave, which had the greatest case fatality rate. The second wave in Peru was dominated by Lambda and Gamma. Analysis of the origin of Lambda shows that it most likely emerged in Peru before the second wave (June-November, 2020). After its emergence it reached Argentina and Chile from Peru where it was locally transmitted. During the second wave in Peru, we identify the coexistence of two Lambda and three Gamma sublineages. Lambda sublineages emerged in the center of Peru whereas the Gamma sublineages more likely originated in the north-east and mid-east. Importantly, it is observed that the center of Peru played a prominent role in transmitting SARS-CoV-2 to other regions within Peru.
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Affiliation(s)
- Santiago Justo Arevalo
- Facultad de Ciencias Biológicas, Universidad Ricardo Palma, Lima, Peru.
- Laboratório Clínico do Hospital Israelita Albert Einstein, São Paulo, Brasil.
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brasil.
| | | | | | | | - Remco Bouckaert
- School of Computer Science, University of Auckland, Auckland, New Zealand
| | - Joao Renato Rebello Pinho
- Laboratório Clínico do Hospital Israelita Albert Einstein, São Paulo, Brasil
- LIM03/07, Department of Gastroenterology and Pathology, University of São Paulo School of Medicine, São Paulo, Brazil
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Joshi MS, Walimbe AM, Arya SA, Gopalkrishna V. Evolutionary analysis of all eleven genes of species C rotaviruses circulating in humans and domestic animals. Mol Phylogenet Evol 2023:107854. [PMID: 37302675 DOI: 10.1016/j.ympev.2023.107854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/24/2023] [Accepted: 06/06/2023] [Indexed: 06/13/2023]
Abstract
Species C rotaviruses (RVC) are the second most common rotavirus species known to cause gastroenteritis in humans and pigs and with occurrence documented in cattle, dogs, ferrets, and sloth bears. Despite the host-specific nature of RVC genotypes, cross-species transmission, reassortment, and recombination events are also documented. In the present study, we inferred the evolutionary history of globally circulating RVC strains, including time scale stasis, the most probable ancestral country, and the most probable source host using Bayesian methods implemented in BEAST v.1.8.4. The human-derived RVC strains were majorly monophyletic and further grouped into two lineages. The RVC strains derived from pigs were monophyletic for the VP1 and the remaining genes were classified into 2 to 4 groups based on the high posterior support. The root mean age for all the genes indicated the circulation of RVC for over 800 years. Overall, the time to Most Recent Common Ancestor of human RVC strains dated back to the beginning of the 20th century. The VP7 and NSP2 genes had the lowest rates of evolution compared to other genes. The majority of the genes of RVC showed their origin in Japan except for VP7 and VP4 genes in South Korea. The phylogeographic analysis with the country as a trait showed the role of Japan, China, and India in the dispersion of the virus. In the current study, significant transmission links between different hosts were analyzed for the first time using the host as a trait. Significant transmission links between pigs and other animal species as well as humans indicate possible transmission from the pig as a source host and suggest monitoring of proximity with animals.
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Affiliation(s)
- Madhuri S Joshi
- Enteric Viruses Group, ICMR- National Institute of Virology, Pune, India.
| | - Atul M Walimbe
- Bioinformatics Group, ICMR- National Institute of Virology, Pune, India.
| | - Shalu A Arya
- Enteric Viruses Group, ICMR- National Institute of Virology, Pune, India
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8
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Pillai TK, Johnson KE, Song T, Gregianini TS, Tatiana G. B, Wang G, Medina RA, Van Bakel H, García-Sastre A, Nelson MI, Ghedin E, Veiga ABG. Tracking the emergence of antigenic variants in influenza A virus epidemics in Brazil. Virus Evol 2023; 9:vead027. [PMID: 37207002 PMCID: PMC10191192 DOI: 10.1093/ve/vead027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/04/2023] [Accepted: 04/20/2023] [Indexed: 05/21/2023] Open
Abstract
Influenza A virus (IAV) circulation patterns differ in North America and South America, with influenza seasons often characterized by different subtypes and strains. However, South America is relatively undersampled considering the size of its population. To address this gap, we sequenced the complete genomes of 220 IAVs collected between 2009 and 2016 from hospitalized patients in southern Brazil. New genetic drift variants were introduced into southern Brazil each season from a global gene pool, including four H3N2 clades (3c, 3c2, 3c3, and 3c2a) and five H1N1pdm clades (clades 6, 7, 6b, 6c, and 6b1). In 2016, H1N1pdm viruses belonging to a new 6b1 clade caused a severe influenza epidemic in southern Brazil that arrived early and spread rapidly, peaking mid-autumn. Inhibition assays showed that the A/California/07/2009(H1N1) vaccine strain did not protect well against 6b1 viruses. Phylogenetically, most 6b1 sequences that circulated in southern Brazil belong to a single transmission cluster that rapidly diffused across susceptible populations, leading to the highest levels of influenza hospitalization and mortality seen since the 2009 pandemic. Continuous genomic surveillance is needed to monitor rapidly evolving IAVs for vaccine strain selection and understand their epidemiological impact in understudied regions.
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Affiliation(s)
- Tara K Pillai
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIH, 50 South Drive, Bethesda, MD 20894, USA
| | - Katherine E Johnson
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIH, 50 South Drive, Bethesda, MD 20894, USA
- Department of Biology, Center for Genomics & Systems Biology, New York University, 12 Waverly Place, New York, NY 10003, USA
| | - Timothy Song
- Department of Biology, Center for Genomics & Systems Biology, New York University, 12 Waverly Place, New York, NY 10003, USA
| | - Tatiana S Gregianini
- Laboratório Central de Saúde Pública, Centro Estadual de Vigilância em Saúde da Secretaria de Saúde do Estado do Rio Grande do Sul—LACEN/CEVS/SES‐RS, Av. Ipiranga, 5400, Porto Alegre, RS 90450-190, Brazil
| | - Baccin Tatiana G.
- Graduate Program in Pathology, Universidade Federal de Ciências da Saúde de Porto Alegre, Rua Sarmento Leite, 245, Rio Grande do Sul, RS 90050-170, Brazil
- Department of Pediatric Infectious Diseases and Immunology, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, RM 8330024, Chile
| | - Guojun Wang
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai Hospital, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Rafael A Medina
- Department of Pediatric Infectious Diseases and Immunology, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, RM 8330024, Chile
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
- Department of Pathology and Experimental Medicine, School of Medicine, Emory University, 1462 Clifton Road, Office 429, Atlanta, GA 30322, USA
| | - Harm Van Bakel
- Laboratory of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai Hospital, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai Hospital, 1 Gustave L. Levy Place, New York, NY 10029, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai Hospital, 1 Gustave L. Levy Place, New York, NY 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai Hospital, 1 Gustave L. Levy Place, New York, NY 10029, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai Hospital, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Martha I Nelson
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIH, 50 South Drive, Bethesda, MD 20894, USA
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, NIH, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Elodie Ghedin
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIH, 50 South Drive, Bethesda, MD 20894, USA
- Department of Biology, Center for Genomics & Systems Biology, New York University, 12 Waverly Place, New York, NY 10003, USA
| | - Ana B G Veiga
- Graduate Program in Pathology, Universidade Federal de Ciências da Saúde de Porto Alegre, Rua Sarmento Leite, 245, Rio Grande do Sul, RS 90050-170, Brazil
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai Hospital, 1 Gustave L. Levy Place, New York, NY 10029, USA
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