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Munyeku-Bazitama Y, Saito T, Hattori T, Miyamoto H, Lombe BP, Mori-Kajihara A, Kajihara M, Muyembe-Tamfum JJ, Igarashi M, Park ES, Morikawa S, Makiala-Mandanda S, Takada A. Characterization of human tibrovirus envelope glycoproteins. J Virol 2024; 98:e0049924. [PMID: 38953631 PMCID: PMC11265436 DOI: 10.1128/jvi.00499-24] [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: 03/18/2024] [Accepted: 06/11/2024] [Indexed: 07/04/2024] Open
Abstract
Tibroviruses are novel rhabdoviruses detected in humans, cattle, and arthropods. Four tibroviruses are known to infect humans: Bas-Congo virus (BASV), Ekpoma virus 1 (EKV-1), Ekpoma virus 2, and Mundri virus. However, since none of them has been isolated, their biological properties are largely unknown. We aimed to characterize the human tibrovirus glycoprotein (G), which likely plays a pivotal role in viral tropism and pathogenicity. Human tibrovirus Gs were found to share some primary structures and display 14 conserved cysteine residues, although their overall amino acid homology was low (29%-48%). Multiple potential glycosylation sites were found on the G molecules, and endoglycosidase H- and peptide-N-glycosidase F-sensitive glycosylation was confirmed. AlphaFold-predicted three-dimensional (3D) structures of human tibrovirus Gs were overall similar. Membrane fusion mediated by these tibrovirus Gs was induced by acidic pH. The low pH-induced conformational change that triggers fusion was reversible. Virus-like particles (VLPs) were produced by transient expression of Gs in cultured cells and used to produce mouse antisera. Using vesicular stomatitis Indiana virus pseudotyped with Gs, we found that the antisera to the respective tibrovirus VLPs showed limited cross-neutralizing activity. It was also found that human C-type lectins and T-cell immunoglobulin mucin 1 acted as attachment factors for G-mediated entry into cells. Interestingly, BASV-G showed the highest ability to utilize these molecules. The viruses infected a wide range of cell lines with preferential tropism for human-derived cells whereas the preference of EKV-1 was unique compared with the other human tibroviruses. These findings provide fundamental information to understand the biological properties of the human tibroviruses. IMPORTANCE Human tibroviruses are poorly characterized emerging rhabdoviruses associated with either asymptomatic infection or severe disease with a case fatality rate as high as 60% in humans. However, the extent and burden of human infection as well as factors behind differences in infection outcomes are largely unknown. In this study, we characterized human tibrovirus glycoproteins, which play a key role in virus-host interactions, mainly focusing on their structural and antigenic differences and cellular tropism. Our results provide critical information for understanding the biological properties of these novel viruses and for developing appropriate preparedness interventions such as diagnostic tools, vaccines, and effective therapies.
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Affiliation(s)
- Yannick Munyeku-Bazitama
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of Congo
- Département de Biologie Médicale, Faculté de Médecine, Université de Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Takeshi Saito
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Takanari Hattori
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Hiroko Miyamoto
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Boniface Pongombo Lombe
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Faculté de Médecine Vétérinaire, Université Pédagogique National, Kinshasa, Democratic Republic of Congo
- Central Veterinary Laboratory of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Akina Mori-Kajihara
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Masahiro Kajihara
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Jean-Jacques Muyembe-Tamfum
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of Congo
- Département de Biologie Médicale, Faculté de Médecine, Université de Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Manabu Igarashi
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Eun-sil Park
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shigeru Morikawa
- Department of Microbiology, Faculty of Veterinary Medicine, Okayama University of Science, Ehime, Japan
| | - Sheila Makiala-Mandanda
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of Congo
- Département de Biologie Médicale, Faculté de Médecine, Université de Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Ayato Takada
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
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Shepherd JG, Ashraf S, Salazar-Gonzalez JF, Salazar MG, Downing RG, Bukenya H, Jerome H, Mpanga JT, Davis C, Tong L, Sreenu VB, Atiku LA, Logan N, Kajik E, Mukobi Y, Mungujakisa C, Olowo MV, Tibo E, Wunna F, Jackson Ireland H, Blunsum AE, Owolabi I, da Silva Filipe A, Bwogi J, Willett BJ, Lutwama JJ, Streicker DG, Kaleebu P, Thomson EC. Widespread human exposure to ledanteviruses in Uganda: A population study. PLoS Negl Trop Dis 2024; 18:e0012297. [PMID: 38976760 PMCID: PMC11257405 DOI: 10.1371/journal.pntd.0012297] [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: 11/30/2023] [Revised: 07/18/2024] [Accepted: 06/17/2024] [Indexed: 07/10/2024] Open
Abstract
Le Dantec virus (LDV), assigned to the species Ledantevirus ledantec, genus Ledantevirus, family Rhabdoviridae has been associated with human disease but has gone undetected since the 1970s. We describe the detection of LDV in a human case of undifferentiated fever in Uganda by metagenomic sequencing and demonstrate a serological response using ELISA and pseudotype neutralisation. By screening 997 individuals sampled in 2016, we show frequent exposure to ledanteviruses with 76% of individuals seropositive in Western Uganda, but lower seroprevalence in other areas. Serological cross-reactivity as measured by pseudotype-based neutralisation was confined to ledanteviruses, indicating population seropositivity may represent either exposure to LDV or related ledanteviruses. We also describe the discovery of a closely related ledantevirus in blood from the synanthropic rodent Mastomys erythroleucus. Ledantevirus infection is common in Uganda but is geographically heterogenous. Further surveys of patients presenting with acute fever are required to determine the contribution of these emerging viruses to febrile illness in Uganda.
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Affiliation(s)
- James G. Shepherd
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Shirin Ashraf
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Jesus F. Salazar-Gonzalez
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Maria G. Salazar
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | | | | | - Hanna Jerome
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | | | - Chris Davis
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Lily Tong
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Vattipally B. Sreenu
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | | | - Nicola Logan
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | | | | | | | | | | | - Fred Wunna
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Hollie Jackson Ireland
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Andrew E. Blunsum
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Iyanuoluwani Owolabi
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Ana da Silva Filipe
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | | | - Brian J. Willett
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | | | - Daniel G. Streicker
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Emma C. Thomson
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- London School of Hygiene and Tropical Medicine, London, United Kingdom
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3
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Munyeku-Bazitama Y, Okitale-Talunda P, Hattori T, Saito T, Lombe BP, Miyamoto H, Mori-Kajihara A, Kajihara M, Nkoy AB, Twabela AT, Masumu J, Ahuka-Mundeke S, Muyembe-Tamfum JJ, Igarashi M, Park ES, Morikawa S, Makiala-Mandanda S, Takada A. Seroprevalence of Bas-Congo virus in Mangala, Democratic Republic of the Congo: a population-based cross-sectional study. THE LANCET. MICROBE 2024; 5:e529-e537. [PMID: 38555924 DOI: 10.1016/s2666-5247(24)00021-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 04/02/2024]
Abstract
BACKGROUND Bas-Congo virus (BASV), an emerging tibrovirus, was associated with an outbreak of acute haemorrhagic fever in Mangala, Democratic Republic of the Congo, in 2009. In 2012, neutralising antibodies to BASV were detected in the lone survivor and one of his close contacts. However, subsequent serological and molecular surveys were unsuccessful as neither BASV antibodies nor its RNA were detected. In this study, we determined the seroprevalence of BASV infection in Mangala 13 years after the initial outbreak. METHODS We conducted a population-based serological survey from Jan 17 to Jan 23, 2022. Consenting individuals at least 5 years of age, living in Mangala for at least 4 weeks, and who had no contraindication to venepuncture were enrolled. Participants were interviewed using a pre-tested questionnaire for sociodemographic and clinical characteristics. We supplemented the collected serum samples with 284 archived samples from Matadi and Kinshasa. All samples were tested for antibodies to BASV and other tibroviruses using a pseudovirus-based neutralisation test. FINDINGS Among the 267 individuals from Mangala, the prevalence of BASV antibodies was 55% (95% CI 49-61; n=147). BASV seropositivity odds significantly increased with age (5·2 [95% CI 2·1-12·9] to 83·9 [20·8-337·7] times higher in participants aged 20 years or older than participants aged 5-19 years). Some occupational categories (eg, farmer or public servant) were associated with seropositivity. Only nine (6%) of 160 samples from Matadi and one (<1%) of 124 samples from Kinshasa had neutralising antibodies to BASV. Moreover, we also detected neutralising antibodies to other tibroviruses-Ekpoma virus 1, Ekpoma virus 2, and Mundri virus-in 84 (31%), 251 (94%), and 219 (82%) of 267 Mangala samples; 14 (9%), 62 (39%), and 120 (75%) of 160 Matadi samples; and six (5%), five (4%), and 33 (27%) of 124 Kinshasa samples, respectively. INTERPRETATION Human infection with BASV and other tibroviruses seems common in Mangala, although no deadly outbreak has been reported since 2009. Exposure to BASV might be highly restricted to Mangala and the increasing prevalence of neutralising antibodies with age suggests regular contact with the virus in this city. Altogether, our findings suggest that human infection with tibroviruses could be common in the study areas and not associated with deadly haemorrhagic or debilitating syndromes. FUNDING Japan Agency for Medical Research and Development (AMED) and Japan International Cooperation Agency (JICA) under the Science and Technology Research Partnership for Sustainable Development (SATREPS) and Japan Program for Infectious Diseases Research and Infrastructure from AMED.
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Affiliation(s)
- Yannick Munyeku-Bazitama
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Département de Biologie Médicale, Faculté de Médecine, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Patient Okitale-Talunda
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Département de Biologie Médicale, Faculté de Médecine, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Takanari Hattori
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Takeshi Saito
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Boniface Pongombo Lombe
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; Central Veterinary Laboratory of Kinshasa, Kinshasa, Democratic Republic of the Congo; Faculté de Médecine Vétérinaire, Université Pédagogique Nationale, Kinshasa, Democratic Republic of the Congo
| | - Hiroko Miyamoto
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Akina Mori-Kajihara
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Masahiro Kajihara
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Agathe Bikupe Nkoy
- Division of Pediatric Nephrology, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Augustin Tshibwabwa Twabela
- Central Veterinary Laboratory of Kinshasa, Kinshasa, Democratic Republic of the Congo; Faculté de Médecine Vétérinaire, Université Pédagogique Nationale, Kinshasa, Democratic Republic of the Congo
| | - Justin Masumu
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Central Veterinary Laboratory of Kinshasa, Kinshasa, Democratic Republic of the Congo; Faculté de Médecine Vétérinaire, Université Pédagogique Nationale, Kinshasa, Democratic Republic of the Congo
| | - Steve Ahuka-Mundeke
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Département de Biologie Médicale, Faculté de Médecine, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Jean-Jacques Muyembe-Tamfum
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Département de Biologie Médicale, Faculté de Médecine, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Manabu Igarashi
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Eun-Sil Park
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shigeru Morikawa
- Department of Microbiology, Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Japan
| | - Sheila Makiala-Mandanda
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Département de Biologie Médicale, Faculté de Médecine, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Ayato Takada
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; One Health Research Center, Hokkaido University, Sapporo, Japan; Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia.
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4
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Kandathil AJ, Thomas DL. The Blood Virome: A new frontier in biomedical science. Biomed Pharmacother 2024; 175:116608. [PMID: 38703502 PMCID: PMC11184943 DOI: 10.1016/j.biopha.2024.116608] [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: 01/08/2024] [Revised: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 05/06/2024] Open
Abstract
Recent advances in metagenomic testing opened a new window into the mammalian blood virome. Comprised of well-known viruses like human immunodeficiency virus, hepatitis C virus, and hepatitis B virus, the virome also includes many other eukaryotic viruses and phages whose medical significance, lifecycle, epidemiology, and impact on human health are less well known and thus regarded as commensals. This review synthesizes available information for the so-called commensal virome members that circulate in the blood of humans considering their restriction to and interaction with the human host, their natural history, and their impact on human health and physiology.
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Affiliation(s)
- Abraham J Kandathil
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David L Thomas
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Chen H, Liu W, Coker OO, Qin N, Chen H, Wang Y, Liu X, Zhang L, Choi GY, Wong WT, Leung CC, Ling L, Hui M, Gin T, Wong SH, Chan MTV, Wu WKK. Blood microbial signatures associated with mortality in patients with sepsis: A pilot study. Heliyon 2024; 10:e29572. [PMID: 38699748 PMCID: PMC11063401 DOI: 10.1016/j.heliyon.2024.e29572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 05/05/2024] Open
Abstract
Sepsis is a life-threatening illness caused by the dysregulated host response to infection. Nevertheless, our current knowledge of the microbial landscape in the blood of septic patients is still limited. Next-generation sequencing (NGS) is a sensitive method to quantitatively characterize microbiomes at various sites of the human body. In this study, we analyzed the blood microbial DNA of 22 adult patients with sepsis and 3 healthy subjects. The presence of non-human DNA was identified in both healthy and septic subjects. Septic patients had a markedly altered microbial DNA profile compared to healthy subjects over α- and β-diversity. Unexpectedly, the patients could be further divided into two subgroups (C1 and C2) based on β-diversity analysis. C1 patients showed much higher bacteria, viruses, fungi, and archaea abundance, and a higher level of α-diversity (Chao1, Observed and Shannon index) than both C2 patients and healthy subjects. The most striking difference was seen in the case of Streptomyces violaceusniger, Phenylobacterium sp. HYN0004, Caulobacter flavus, Streptomyces sp. 11-1-2, and Phenylobacterium zucineum, the abundance of which was the highest in the C1 group. Notably, C1 patients had a significantly poorer outcome than C2 patients. Moreover, by analyzing the patterns of microbe-microbe interactions in healthy and septic subjects, we revealed that C1 and C2 patients exhibited distinct co-occurrence and co-exclusion relationships. Together, our study uncovered two distinct microbial signatures in the blood of septic patients. Compositional and ecological analysis of blood microbial DNA may thus be useful in predicting mortality of septic patients.
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Affiliation(s)
- Huarong Chen
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, China
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Weixin Liu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Olabisi Oluwabukola Coker
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Na Qin
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Hongyan Chen
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Yifei Wang
- Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong, China
| | - Xiaodong Liu
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Lin Zhang
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, China
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Gordon Y.S. Choi
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Wai Tat Wong
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Czarina C.H. Leung
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Mamie Hui
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Tony Gin
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Sunny Hei Wong
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Department of Gastroenterology and Hepatology, Tan Tock Seng Hospital, National Healthcare Group, Singapore
| | - Matthew Tak Vai Chan
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - William Ka Kei Wu
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, China
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
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Cebriá-Mendoza M, Díaz W, Sanjuán R, Cuevas JM. Optimized Recovery of Viral DNA and RNA from Blood Plasma for Viral Metagenomics. Methods Mol Biol 2024; 2732:155-164. [PMID: 38060124 DOI: 10.1007/978-1-0716-3515-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Metagenomics is vastly improving our ability to discover new viruses, as well as their possible associations with disease. However, metagenomics has also changed our understanding of viruses in general. This is because we can find viruses in healthy hosts in the absence of disease, which changes the perspective of viruses as mere pathogens and offers a new perspective in which viruses function as important components of ecosystems. In concrete, human blood metagenomics has revealed the presence of different types of viruses in apparently healthy subjects. These viruses are human anelloviruses and, to a lower extent, human pegiviruses. Viral metagenomics' major challenge is the correct isolation of the viral nucleic acids from a specific sample. For the protocol to be successful, all steps must be carefully chosen, in particular those that optimize the recovery of viral nucleic acids. Here, we present a procedure that allows the recovery of both DNA and RNA viruses from plasma samples.
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Affiliation(s)
- María Cebriá-Mendoza
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, València, Spain
| | - Wladimiro Díaz
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, València, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, València, Spain
| | - José M Cuevas
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, València, Spain.
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7
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Rajput M, Thakur N. Editorial: Advances in host-pathogen interactions for diseases in animals and birds. Front Vet Sci 2023; 10:1282110. [PMID: 37766859 PMCID: PMC10520279 DOI: 10.3389/fvets.2023.1282110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Affiliation(s)
- Mrigendra Rajput
- Department of Biology, University of Dayton, Dayton, OH, United States
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8
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Oguzie JU, Petros BA, Oluniyi PE, Mehta SB, Eromon PE, Nair P, Adewale-Fasoro O, Ifoga PD, Odia I, Pastusiak A, Gbemisola OS, Aiyepada JO, Uyigue EA, Edamhande AP, Blessing O, Airende M, Tomkins-Tinch C, Qu J, Stenson L, Schaffner SF, Oyejide N, Ajayi NA, Ojide K, Ogah O, Abejegah C, Adedosu N, Ayodeji O, Liasu AA, Okogbenin S, Okokhere PO, Park DJ, Folarin OA, Komolafe I, Ihekweazu C, Frost SDW, Jackson EK, Siddle KJ, Sabeti PC, Happi CT. Metagenomic surveillance uncovers diverse and novel viral taxa in febrile patients from Nigeria. Nat Commun 2023; 14:4693. [PMID: 37542071 PMCID: PMC10403498 DOI: 10.1038/s41467-023-40247-4] [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: 01/18/2023] [Accepted: 07/10/2023] [Indexed: 08/06/2023] Open
Abstract
Effective infectious disease surveillance in high-risk regions is critical for clinical care and pandemic preemption; however, few clinical diagnostics are available for the wide range of potential human pathogens. Here, we conduct unbiased metagenomic sequencing of 593 samples from febrile Nigerian patients collected in three settings: i) population-level surveillance of individuals presenting with symptoms consistent with Lassa Fever (LF); ii) real-time investigations of outbreaks with suspected infectious etiologies; and iii) undiagnosed clinically challenging cases. We identify 13 distinct viruses, including the second and third documented cases of human blood-associated dicistrovirus, and a highly divergent, unclassified dicistrovirus that we name human blood-associated dicistrovirus 2. We show that pegivirus C is a common co-infection in individuals with LF and is associated with lower Lassa viral loads and favorable outcomes. We help uncover the causes of three outbreaks as yellow fever virus, monkeypox virus, and a noninfectious cause, the latter ultimately determined to be pesticide poisoning. We demonstrate that a local, Nigerian-driven metagenomics response to complex public health scenarios generates accurate, real-time differential diagnoses, yielding insights that inform policy.
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Affiliation(s)
- Judith U Oguzie
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Brittany A Petros
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA, 02139, USA
- Harvard/MIT MD-PhD Program, Boston, MA, 02115, USA
- Systems, Synthetic, and Quantitative Biology PhD Program, Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Paul E Oluniyi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Samar B Mehta
- Department of Medicine, University of Maryland Medical Center, Baltimore, MA, USA
| | - Philomena E Eromon
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Parvathy Nair
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Opeoluwa Adewale-Fasoro
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Peace Damilola Ifoga
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Ikponmwosa Odia
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | - Otitoola Shobi Gbemisola
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | | | | | | | - Osiemi Blessing
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Michael Airende
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Christopher Tomkins-Tinch
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - James Qu
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Liam Stenson
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Nicholas Oyejide
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Nnenna A Ajayi
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Kingsley Ojide
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Onwe Ogah
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | | | | | | | | | | | | | - Daniel J Park
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Onikepe A Folarin
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Isaac Komolafe
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | | | - Simon D W Frost
- Microsoft Premonition, Redmond, WA, USA
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Katherine J Siddle
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA.
| | - Pardis C Sabeti
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
| | - Christian T Happi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria.
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
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9
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Shepherd JG, Davis C, Streicker DG, Thomson EC. Emerging Rhabdoviruses and Human Infection. BIOLOGY 2023; 12:878. [PMID: 37372162 PMCID: PMC10294888 DOI: 10.3390/biology12060878] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/09/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023]
Abstract
Rhabdoviridae is a large viral family, with members infecting a diverse range of hosts including, vertebrate species, arthropods, and plants. The predominant human pathogen within the family is Rabies lyssavirus, the main cause of human rabies. While rabies is itself a neglected disease, there are other, less well studied, rhabdoviruses known to cause human infection. The increasing application of next-generation sequencing technology to clinical samples has led to the detection of several novel or rarely detected rhabdoviruses associated with febrile illness. Many of these viruses have been detected in low- and middle-income countries where the extent of human infection and the burden of disease remain largely unquantified. This review describes the rhabdoviruses other than Rabies lyssavirus that have been associated with human infection. The discovery of the Bas Congo virus and Ekpoma virus is discussed, as is the re-emergence of species such as Le Dantec virus, which has recently been detected in Africa 40 years after its initial isolation. Chandipura virus and the lyssaviruses that are known to cause human rabies are also described. Given their association with human disease, the viruses described in this review should be prioritised for further study.
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Affiliation(s)
- James G. Shepherd
- Centre for Virus Research, MRC-University of Glasgow, Glasgow G61 1QH, UK; (C.D.); (D.G.S.)
| | - Chris Davis
- Centre for Virus Research, MRC-University of Glasgow, Glasgow G61 1QH, UK; (C.D.); (D.G.S.)
| | - Daniel G. Streicker
- Centre for Virus Research, MRC-University of Glasgow, Glasgow G61 1QH, UK; (C.D.); (D.G.S.)
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Emma C. Thomson
- Centre for Virus Research, MRC-University of Glasgow, Glasgow G61 1QH, UK; (C.D.); (D.G.S.)
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10
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Feng B, Liu B, Cheng M, Dong J, Hu Y, Jin Q, Yang F. An atlas of the blood virome in healthy individuals. Virus Res 2023; 323:199004. [PMID: 36402209 PMCID: PMC10194198 DOI: 10.1016/j.virusres.2022.199004] [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: 07/22/2022] [Revised: 10/14/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022]
Abstract
Emerging evidence indicates that gut virome plays a role in human health and disease, however, much less is known about the viral communities in blood. Here we conducted a direct metatranscriptomic sequencing of virus-like-particles in blood from 1200 healthy individuals, without prior amplification to avoid potential amplification bias and with a strictly bioinformatic and manual check for candidate viral reads to reduce false-positive matches. We identified 55 different viruses from 36 viral families, including 24 human DNA, RNA and retroviruses in 70% of the studied pools. The study showed that anelloviruses are widely distributed and dominate the blood virome in healthy individuals. Human herpesviruses and pegivirus-1 are commonly prevalent in asymptomatic humans. We identified the prevalence of RNA viruses often causing acute infection, like HEV, HPIV, RSV and HCoV-HKU1, revealing of a transmissible risk of asymptomatic infection. Several viruses possible related to transfusion safety were identified, including human Merkel cell polyomavirus, papillomavirus, parvovirus B19 and herpesvirus 8 in addition to HBV. In addition, phages in Caudovirales and Microviridae, were commonly found in pools of samples with a very low abundance; a few sequences for invertebrate, plant and giant viruses were found in some of individuals; however, the remaining 31 viruses mostly reflect extensive contamination from commercial reagents and the work environments. In conclusion, this study is the first comprehensive investigation of blood virome in healthy individuals by metatranscriptomic sequencing of VLP in China. Further investigation of potential false positives representing a major challenge for the identification of novel viruses in mNGS, will offer a systemic idea and means to reveal true viral infections of human.
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Affiliation(s)
- Bo Feng
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, CAMS&PUMC, Beijing 100730, PR China
| | - Bo Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, CAMS&PUMC, Beijing 100730, PR China
| | - Min Cheng
- China Institute of Veterinary Drug Control, Beijing 100081, PR China
| | - Jie Dong
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, CAMS&PUMC, Beijing 100730, PR China
| | - Yongfeng Hu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, CAMS&PUMC, Beijing 100730, PR China.
| | - Qi Jin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, CAMS&PUMC, Beijing 100730, PR China.
| | - Fan Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, CAMS&PUMC, Beijing 100730, PR China.
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11
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Dunay E, Owens LA, Dunn CD, Rukundo J, Atencia R, Cole MF, Cantwell A, Emery Thompson M, Rosati AG, Goldberg TL. Viruses in sanctuary chimpanzees across Africa. Am J Primatol 2023; 85:e23452. [PMID: 36329642 PMCID: PMC9812903 DOI: 10.1002/ajp.23452] [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: 07/07/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022]
Abstract
Infectious disease is a major concern for both wild and captive primate populations. Primate sanctuaries in Africa provide critical protection to thousands of wild-born, orphan primates confiscated from the bushmeat and pet trades. However, uncertainty about the infectious agents these individuals potentially harbor has important implications for their individual care and long-term conservation strategies. We used metagenomic next-generation sequencing to identify viruses in blood samples from chimpanzees (Pan troglodytes) in three sanctuaries in West, Central, and East Africa. Our goal was to evaluate whether viruses of human origin or other "atypical" or unknown viruses might infect these chimpanzees. We identified viruses from eight families: Anelloviridae, Flaviviridae, Genomoviridae, Hepadnaviridae, Parvoviridae, Picobirnaviridae, Picornaviridae, and Rhabdoviridae. The majority (15/26) of viruses identified were members of the family Anelloviridae and represent the genera Alphatorquevirus (torque teno viruses) and Betatorquevirus (torque teno mini viruses), which are common in chimpanzees and apathogenic. Of the remaining 11 viruses, 9 were typical constituents of the chimpanzee virome that have been identified in previous studies and are also thought to be apathogenic. One virus, a novel tibrovirus (Rhabdoviridae: Tibrovirus) is related to Bas-Congo virus, which was originally thought to be a human pathogen but is currently thought to be apathogenic, incidental, and vector-borne. The only virus associated with disease was rhinovirus C (Picornaviridae: Enterovirus) infecting one chimpanzee subsequent to an outbreak of respiratory illness at that sanctuary. Our results suggest that the blood-borne virome of African sanctuary chimpanzees does not differ appreciably from that of their wild counterparts, and that persistent infection with exogenous viruses may be less common than often assumed.
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Affiliation(s)
- Emily Dunay
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Leah A Owens
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Christopher D Dunn
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Joshua Rukundo
- Ngamba Island Chimpanzee Sanctuary/Chimpanzee Trust, Entebbe, Uganda
| | - Rebeca Atencia
- Jane Goodall Institute Congo, Pointe-Noire, Republic of Congo
| | - Megan F Cole
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Averill Cantwell
- Department of Psychology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Alexandra G Rosati
- Department of Psychology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Anthropology, University of Michigan, Ann Arbor, Michigan, USA
| | - Tony L Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
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12
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van der Kuyl AC. Historic and Prehistoric Epidemics: An Overview of Sources Available for the Study of Ancient Pathogens. EPIDEMIOLOGIA (BASEL, SWITZERLAND) 2022; 3:443-464. [PMID: 36547255 PMCID: PMC9778136 DOI: 10.3390/epidemiologia3040034] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 12/24/2022]
Abstract
Since life on earth developed, parasitic microbes have thrived. Increases in host numbers, or the conquest of a new species, provide an opportunity for such a pathogen to enjoy, before host defense systems kick in, a similar upsurge in reproduction. Outbreaks, caused by "endemic" pathogens, and epidemics, caused by "novel" pathogens, have thus been creating chaos and destruction since prehistorical times. To study such (pre)historic epidemics, recent advances in the ancient DNA field, applied to both archeological and historical remains, have helped tremendously to elucidate the evolutionary trajectory of pathogens. These studies have offered new and unexpected insights into the evolution of, for instance, smallpox virus, hepatitis B virus, and the plague-causing bacterium Yersinia pestis. Furthermore, burial patterns and historical publications can help in tracking down ancient pathogens. Another source of information is our genome, where selective sweeps in immune-related genes relate to past pathogen attacks, while multiple viruses have left their genomes behind for us to study. This review will discuss the sources available to investigate (pre)historic diseases, as molecular knowledge of historic and prehistoric pathogens may help us understand the past and the present, and prepare us for future epidemics.
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Affiliation(s)
- Antoinette C. van der Kuyl
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; ; Tel.: +31-205-666-778
- Amsterdam Institute for Infection and Immunity, 1100 DD Amsterdam, The Netherlands
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13
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Zhang F, Chase-Topping M, Guo CG, Woolhouse MEJ. Predictors of human-infective RNA virus discovery in the United States, China, and Africa, an ecological study. eLife 2022; 11:e72123. [PMID: 35666108 PMCID: PMC9278958 DOI: 10.7554/elife.72123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
Background The variation in the pathogen type as well as the spatial heterogeneity of predictors make the generality of any associations with pathogen discovery debatable. Our previous work confirmed that the association of a group of predictors differed across different types of RNA viruses, yet there have been no previous comparisons of the specific predictors for RNA virus discovery in different regions. The aim of the current study was to close the gap by investigating whether predictors of discovery rates within three regions-the United States, China, and Africa-differ from one another and from those at the global level. Methods Based on a comprehensive list of human-infective RNA viruses, we collated published data on first discovery of each species in each region. We used a Poisson boosted regression tree (BRT) model to examine the relationship between virus discovery and 33 predictors representing climate, socio-economics, land use, and biodiversity across each region separately. The discovery probability in three regions in 2010-2019 was mapped using the fitted models and historical predictors. Results The numbers of human-infective virus species discovered in the United States, China, and Africa up to 2019 were 95, 80, and 107 respectively, with China lagging behind the other two regions. In each region, discoveries were clustered in hotspots. BRT modelling suggested that in all three regions RNA virus discovery was better predicted by land use and socio-economic variables than climatic variables and biodiversity, although the relative importance of these predictors varied by region. Map of virus discovery probability in 2010-2019 indicated several new hotspots outside historical high-risk areas. Most new virus species since 2010 in each region (6/6 in the United States, 19/19 in China, 12/19 in Africa) were discovered in high-risk areas as predicted by our model. Conclusions The drivers of spatiotemporal variation in virus discovery rates vary in different regions of the world. Within regions virus discovery is driven mainly by land-use and socio-economic variables; climate and biodiversity variables are consistently less important predictors than at a global scale. Potential new discovery hotspots in 2010-2019 are identified. Results from the study could guide active surveillance for new human-infective viruses in local high-risk areas. Funding FFZ is funded by the Darwin Trust of Edinburgh (https://darwintrust.bio.ed.ac.uk/). MEJW has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No. 874735 (VEO) (https://www.veo-europe.eu/).
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Affiliation(s)
- Feifei Zhang
- Usher Institute, University of EdinburghEdinburghUnited Kingdom
| | - Margo Chase-Topping
- Usher Institute, University of EdinburghEdinburghUnited Kingdom
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of EdinburghEdinburghUnited Kingdom
| | - Chuan-Guo Guo
- Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong KongHong KongChina
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14
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Edridge AWD, Abd-Elfarag G, Deijs M, Jebbink MF, Boele van Hensbroek M, van der Hoek L. Divergent Rhabdovirus Discovered in a Patient with New-Onset Nodding Syndrome. Viruses 2022; 14:v14020210. [PMID: 35215803 PMCID: PMC8880091 DOI: 10.3390/v14020210] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 12/15/2022] Open
Abstract
A divergent rhabdovirus was discovered in the bloodstream of a 15-year-old girl with Nodding syndrome from Mundri West County in South Sudan. Nodding syndrome is a progressive degenerative neuropathy of unknown cause affecting thousands of individuals in Sub-Saharan Africa. The index case was previously healthy until she developed head-nodding seizures four months prior to presentation. Virus discovery by VIDISCA-NGS on the patient’s plasma detected multiple sequence reads belonging to a divergent rhabdovirus. The viral load was 3.85 × 103 copies/mL in the patient’s plasma and undetectable in her cerebrospinal fluid. Further genome walking allowed for the characterization of full coding sequences of all the viral proteins (N, P, M, U1, U2, G, U3, and L). We tentatively named the virus “Mundri virus” (MUNV) and classified it as a novel virus species based on the high divergence from other known viruses (all proteins had less than 43% amino acid identity). Phylogenetic analysis revealed that MUNV forms a monophyletic clade with several human-infecting tibroviruses prevalent in Central Africa. A bioinformatic machine-learning algorithm predicted MUNV to be an arbovirus (bagged prediction strength (BPS) of 0.9) transmitted by midges (BPS 0.4) with an artiodactyl host reservoir (BPS 0.9). An association between MUNV infection and Nodding syndrome was evaluated in a case–control study of 72 patients with Nodding syndrome (including the index case) matched to 65 healthy households and 48 community controls. No subject, besides the index case, was positive for MUNV RNA in their plasma. A serological assay detecting MUNV anti-nucleocapsid found, respectively, in 28%, 22%, and 16% of cases, household controls and community controls to be seropositive with no significant differences between cases and either control group. This suggests that MUNV commonly infects children in South Sudan yet may not be causally associated with Nodding syndrome.
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Affiliation(s)
- Arthur W. D. Edridge
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (M.D.); (M.F.J.)
- Center for Global Child Health, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (G.A.-E.); (M.B.v.H.)
- Correspondence: (A.W.D.E.); (L.v.d.H.)
| | - Gasim Abd-Elfarag
- Center for Global Child Health, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (G.A.-E.); (M.B.v.H.)
| | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (M.D.); (M.F.J.)
| | - Maarten F. Jebbink
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (M.D.); (M.F.J.)
| | - Michael Boele van Hensbroek
- Center for Global Child Health, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (G.A.-E.); (M.B.v.H.)
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (M.D.); (M.F.J.)
- Correspondence: (A.W.D.E.); (L.v.d.H.)
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15
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Allali I, Abotsi RE, Tow LA, Thabane L, Zar HJ, Mulder NM, Nicol MP. Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research. MICROBIOME 2021; 9:241. [PMID: 34911583 PMCID: PMC8672519 DOI: 10.1186/s40168-021-01195-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/14/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND The role of the human microbiome in health and disease is an emerging and important area of research; however, there is a concern that African populations are under-represented in human microbiome studies. We, therefore, conducted a systematic survey of African human microbiome studies to provide an overview and identify research gaps. Our secondary objectives were: (i) to determine the number of peer-reviewed publications; (ii) to identify the extent to which the researches focused on diseases identified by the World Health Organization [WHO] State of Health in the African Region Report as being the leading causes of morbidity and mortality in 2018; (iii) to describe the extent and pattern of collaborations between researchers in Africa and the rest of the world; and (iv) to identify leadership and funders of the studies. METHODOLOGY We systematically searched Medline via PubMed, Scopus, CINAHL, Academic Search Premier, Africa-Wide Information through EBSCOhost, and Web of Science from inception through to 1st April 2020. We included studies that characterized samples from African populations using next-generation sequencing approaches. Two reviewers independently conducted the literature search, title and abstract, and full-text screening, as well as data extraction. RESULTS We included 168 studies out of 5515 records retrieved. Most studies were published in PLoS One (13%; 22/168), and samples were collected from 33 of the 54 African countries. The country where most studies were conducted was South Africa (27/168), followed by Kenya (23/168) and Uganda (18/168). 26.8% (45/168) focused on diseases of significant public health concern in Africa. Collaboration between scientists from the United States of America and Africa was most common (96/168). The first and/or last authors of 79.8% of studies were not affiliated with institutions in Africa. Major funders were the United States of America National Institutes of Health (45.2%; 76/168), Bill and Melinda Gates Foundation (17.8%; 30/168), and the European Union (11.9%; 20/168). CONCLUSIONS There are significant gaps in microbiome research in Africa, especially those focusing on diseases of public health importance. There is a need for local leadership, capacity building, intra-continental collaboration, and national government investment in microbiome research within Africa. Video Abstract.
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Affiliation(s)
- Imane Allali
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Centre of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Regina E Abotsi
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
- Department of Pharmaceutical Microbiology, School of Pharmacy, University of Health and Allied Sciences, Ho, Ghana
| | - Lemese Ah Tow
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Lehana Thabane
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
- Biostatistics Unit, Father Sean O'Sullivan Research Centre, St Joseph's Healthcare, Hamilton, Ontario, Canada
- Departments of Paediatrics and Anaesthesia, McMaster University, Hamilton, Ontario, Canada
- Centre for Evaluation of Medicine, St Joseph's Healthcare, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton Health Sciences, Hamilton, Ontario, Canada
- Centre for Evidence-based Health Care, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
- MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Nicola M Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mark P Nicol
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- School of Biomedical Sciences, University of Western Australia, M504, Perth, WA, 6009, Australia.
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16
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Cebriá-Mendoza M, Bracho MA, Arbona C, Larrea L, Díaz W, Sanjuán R, Cuevas JM. Exploring the Diversity of the Human Blood Virome. Viruses 2021; 13:v13112322. [PMID: 34835128 PMCID: PMC8621239 DOI: 10.3390/v13112322] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/15/2021] [Accepted: 11/18/2021] [Indexed: 01/01/2023] Open
Abstract
Metagenomics is greatly improving our ability to discover new viruses, as well as their possible associations with disease. However, metagenomics has also changed our understanding of viruses in general. The vast expansion of currently known viral diversity has revealed a large fraction of non-pathogenic viruses, and offers a new perspective in which viruses function as important components of many ecosystems. In this vein, studies of the human blood virome are often motivated by the search for new viral diseases, especially those associated with blood transfusions. However, these studies have revealed the common presence of apparently non-pathogenic viruses in blood, particularly human anelloviruses and, to a lower extent, human pegiviruses (HPgV). To shed light on the diversity of the human blood virome, we subjected pooled plasma samples from 587 healthy donors in Spain to a viral enrichment protocol, followed by massive parallel sequencing. This showed that anelloviruses were clearly the major component of the blood virome and showed remarkable diversity. In total, we assembled 332 complete or near-complete anellovirus genomes, 50 of which could be considered new species. HPgV was much less frequent, but we, nevertheless, recovered 17 different isolates that we subsequently used for characterizing the diversity of this virus. In-depth investigation of the human blood virome should help to elucidate the ecology of these viruses, and to unveil potentially associated diseases.
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Affiliation(s)
- María Cebriá-Mendoza
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, 46980 València, Spain; (M.C.-M.); (W.D.); (R.S.)
| | - María A. Bracho
- Joint Research Unit “Infection and Public Health”, FISABIO-Universitat de València I2SysBio, 46020 València, Spain;
- CIBER in Epidemiology and Public Health (CIBERESP), 46020 València, Spain
| | - Cristina Arbona
- Centro de Transfusión de la Comunidad Valenciana, 46020 València, Spain; (C.A.); (L.L.)
| | - Luís Larrea
- Centro de Transfusión de la Comunidad Valenciana, 46020 València, Spain; (C.A.); (L.L.)
| | - Wladimiro Díaz
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, 46980 València, Spain; (M.C.-M.); (W.D.); (R.S.)
- Department of Informatics, Universitat de València, 46020 València, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, 46980 València, Spain; (M.C.-M.); (W.D.); (R.S.)
- Department of Genetics, Universitat de València, 46020 València, Spain
| | - José M. Cuevas
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, 46980 València, Spain; (M.C.-M.); (W.D.); (R.S.)
- Department of Genetics, Universitat de València, 46020 València, Spain
- Correspondence:
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17
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Deep viral blood metagenomics reveals extensive anellovirus diversity in healthy humans. Sci Rep 2021; 11:6921. [PMID: 33767340 PMCID: PMC7994813 DOI: 10.1038/s41598-021-86427-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/15/2021] [Indexed: 02/08/2023] Open
Abstract
Human blood metagenomics has revealed the presence of different types of viruses in apparently healthy subjects. By far, anelloviruses constitute the viral family that is more frequently found in human blood, although amplification biases and contaminations pose a major challenge in this field. To investigate this further, we subjected pooled plasma samples from 120 healthy donors in Spain to high-speed centrifugation, RNA and DNA extraction, random amplification, and massive parallel sequencing. Our results confirm the extensive presence of anelloviruses in such samples, which represented nearly 97% of the total viral sequence reads obtained. We assembled 114 different viral genomes belonging to this family, revealing remarkable diversity. Phylogenetic analysis of ORF1 suggested 28 potentially novel anellovirus species, 24 of which were validated by Sanger sequencing to discard artifacts. These findings underscore the importance of implementing more efficient purification procedures that enrich the viral fraction as an essential step in virome studies and question the suggested pathological role of anelloviruses.
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18
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Fahsbender E, Charlys da-Costa A, Elise Gill D, Augusto de Padua Milagres F, Brustulin R, Julio Costa Monteiro F, Octavio da Silva Rego M, Soares D’Athaide Ribeiro E, Cerdeira Sabino E, Delwart E. Plasma virome of 781 Brazilians with unexplained symptoms of arbovirus infection include a novel parvovirus and densovirus. PLoS One 2020; 15:e0229993. [PMID: 32134963 PMCID: PMC7058308 DOI: 10.1371/journal.pone.0229993] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 02/19/2020] [Indexed: 12/16/2022] Open
Abstract
Plasma from patients with dengue-like symptoms was collected in 2013 to 2016 from the Brazilian states of Tocantins and Amapa. 781 samples testing negative for IgM against Dengue, Zika, and Chikungunya viruses and for flaviviruses, alphaviruses and enteroviruses RNA using RT-PCRs were analyzed using viral metagenomics. Viral particles-associated nucleic acids were enriched, randomly amplified, and deep sequenced in 102 mini-pools generating over 2 billion reads. Sequence data was analyzed for the presence of known and novel eukaryotic viral reads. Anelloviruses were detected in 80%, human pegivirus 1 in 19%, and parvovirus B19 in 17% of plasma pools. HIV and enteroviruses were detected in two pools each. Previously uncharacterized viral genomes were also identified, and their presence in single plasma samples confirmed by PCR. Chapparvovirus and ambidensovirus genomes, both in the Parvoviridae family, were partially characterized showing 33% and 34% identity in their NS1 sequences to their closest relative. Molecular surveillance using pre-existing plasma from febrile patients provides a readily scalable approach for the detection of novel, potentially emerging, viruses.
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Affiliation(s)
- Elizabeth Fahsbender
- Vitalant Research Institute, San Francisco, CA, United States of America
- UCSF Dept. of Laboratory Medicine, University of California–San Francisco, San Francisco, CA, United States of America
| | - Antonio Charlys da-Costa
- School of Medicine & Institute of Tropical Medicine, University of Sao Paulo, Infectious Disease, Sao Paulo, Brazil
| | - Danielle Elise Gill
- School of Medicine & Institute of Tropical Medicine, University of Sao Paulo, Infectious Disease, Sao Paulo, Brazil
| | - Flavio Augusto de Padua Milagres
- Public Health Laboratory State (LACEN/TO), Secretary of Health of Tocantins, Palmas, TO, Brazil
- Federal University of Tocantins, Palmas, Tocantins, Brazil
| | - Rafael Brustulin
- Public Health Laboratory State (LACEN/TO), Secretary of Health of Tocantins, Palmas, TO, Brazil
- Federal University of Tocantins, Palmas, Tocantins, Brazil
| | | | | | | | - Ester Cerdeira Sabino
- School of Medicine & Institute of Tropical Medicine, University of Sao Paulo, Infectious Disease, Sao Paulo, Brazil
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA, United States of America
- UCSF Dept. of Laboratory Medicine, University of California–San Francisco, San Francisco, CA, United States of America
- * E-mail:
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19
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Human Tibroviruses: Commensals or Lethal Pathogens? Viruses 2020; 12:v12030252. [PMID: 32106547 PMCID: PMC7150972 DOI: 10.3390/v12030252] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/21/2020] [Accepted: 02/21/2020] [Indexed: 12/16/2022] Open
Abstract
Rhabdoviruses are a large and ecologically diverse family of negative-sense RNA viruses (Mononegavirales: Rhabdoviridae). These viruses are capable of infecting an unexpectedly wide variety of plants, vertebrates, and invertebrates distributed over all human-inhabited continents. However, only a few rhabdoviruses are known to infect humans: a ledantevirus (Le Dantec virus), several lyssaviruses (in particular, rabies virus), and several vesiculoviruses (e.g., Chandipura virus, vesicular stomatitis Indiana virus). Recently, several novel rhabdoviruses have been discovered in the blood of both healthy and severely ill individuals living in Central and Western Africa. These viruses—Bas-Congo virus, Ekpoma virus 1, and Ekpoma virus 2—are members of the little-understood rhabdoviral genus Tibrovirus. Other than the basic genomic architecture, tibroviruses bear little resemblance to well-studied rhabdoviruses such as rabies virus and vesicular stomatitis Indiana virus. These three human tibroviruses are quite divergent from each other, and each of them clusters closely with tibroviruses currently known only from biting midges or healthy cattle. Seroprevalence studies suggest that human tibrovirus infections may be common but are almost entirely unrecognized. The pathogenic potential of this diverse group of viruses remains unknown. Although certain tibroviruses may be benign and well-adapted to humans, others could be newly emerging and produce serious disease. Here, we review the current knowledge of tibroviruses and argue that assessing their impact on human health should be an urgent priority.
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20
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Teng TZ, Beavogui AH, Diarra B, Delamou A, Holl J, Maiga AI, Sadio Sarro YD, Kone A, Kone B, Fofana DB, Dembele E, Sow MS, Seydi M, Oumar AA, Diakité M, Diallo S, Doumbia S, Dao S, Murphy RL, Maiga M. Diagnostic Laboratories' Capacities and Preparedness for Emerging Viral Diseases in Guinea and Mali. INFECTIOUS DISEASES DIAGNOSIS & TREATMENT 2020; 4:135. [PMID: 34532653 PMCID: PMC8442766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The 2014-2016 Ebola epidemic in Guinea highlighted the need for more extensive evaluation of laboratories diagnostic capacities and preparedness in anticipation of future emerging viral disease outbreaks. We developed a questionnaire to assess the diagnostic capacities and preparedness of the four major medical laboratories in Guinea and Mali that are responsible for the provision of Ebola, Lassa, and Dengue diagnostics. The questionnaire inquired about the current state and need for equipment and reagents and adequacy of equipment and training received. In Guinea, all three diagnostic laboratories have the capacity and are well-prepared to perform Ebola diagnostics, however, only two have the capacity and trained staff to diagnose Lassa and none are currently prepared to diagnose Dengue infection. In Mali, the University Clinical Research Center (UCRC) laboratory, which was in charge of Ebola diagnostics during the last epidemic, currently has the capacity and is prepared to diagnose Ebola, Lassa, and Dengue infections. Combined, Guinea and Mali appear to have complementary capacity and preparedness to diagnose these Category A Priority Pathogens. While, the equipment, reagents and training efforts should be maintained, the gap in Dengue diagnostic capability in Guinea should be addressed with further equipping and training of additional district laboratories to strengthen the public health response for all viral diseases in these high-risk, yet, low-resource settings.
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Affiliation(s)
- Tiffany Zhang Teng
- Institute for Global Health, Northwestern University, Chicago, Illinois, USA
| | - Abdoul Habib Beavogui
- Centre National de Formation et de Recherche en Santé Rurale de Maferinyah, Forécariah, Guinea
- African Center of Excellence for Prevention and Control of Transmissible Diseases (CEA-PCMT), Gamal Abdel Nasser University of Conakry, Conakry, Guinea
| | - Bassirou Diarra
- University Clinical Research Center (UCRC)-SEREFO, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Alexandre Delamou
- Centre National de Formation et de Recherche en Santé Rurale de Maferinyah, Forécariah, Guinea
- African Center of Excellence for Prevention and Control of Transmissible Diseases (CEA-PCMT), Gamal Abdel Nasser University of Conakry, Conakry, Guinea
| | - Jane Holl
- Center for Healthcare Delivery Science and Innovation, The University of Chicago, Chicago, Illinois, USA
| | - Almoustapha Issiaka Maiga
- University Clinical Research Center (UCRC)-SEREFO, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Yeya Dit Sadio Sarro
- University Clinical Research Center (UCRC)-SEREFO, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Amadou Kone
- University Clinical Research Center (UCRC)-SEREFO, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Bourahima Kone
- University Clinical Research Center (UCRC)-SEREFO, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Djeneba Bocar Fofana
- University Clinical Research Center (UCRC)-SEREFO, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Etienne Dembele
- Institute for Global Health, Northwestern University, Chicago, Illinois, USA
| | - Mamadou Saliou Sow
- Centre de Recherche et de Formation en Infectiologie de Guinée, University of Conakry, Conakry, Guinea
| | | | - Aboubacar Alassane Oumar
- University Clinical Research Center (UCRC)-SEREFO, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Mahamadou Diakité
- University Clinical Research Center (UCRC)-SEREFO, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Souleymane Diallo
- University Clinical Research Center (UCRC)-SEREFO, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Seydou Doumbia
- University Clinical Research Center (UCRC)-SEREFO, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Sounkalo Dao
- University Clinical Research Center (UCRC)-SEREFO, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Robert L Murphy
- Institute for Global Health, Northwestern University, Chicago, Illinois, USA
| | - Mamoudou Maiga
- Institute for Global Health, Northwestern University, Chicago, Illinois, USA
- University Clinical Research Center (UCRC)-SEREFO, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
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21
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Noad RJ, Simpson K, Fooks AR, Hewson R, Gilbert SC, Stevens MP, Hosie MJ, Prior J, Kinsey AM, Entrican G, Simpson A, Whitty CJM, Carroll MW. UK vaccines network: Mapping priority pathogens of epidemic potential and vaccine pipeline developments. Vaccine 2019; 37:6241-6247. [PMID: 31522809 PMCID: PMC7127063 DOI: 10.1016/j.vaccine.2019.09.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 09/01/2019] [Accepted: 09/03/2019] [Indexed: 12/27/2022]
Abstract
During the 2013-2016 Ebola outbreak in West Africa an expert panel was established on the instructions of the UK Prime Minister to identify priority pathogens for outbreak diseases that had the potential to cause future epidemics. A total of 13 priority pathogens were identified, which led to the prioritisation of spending in emerging diseases vaccine research and development from the UK. This meeting report summarises the process used to develop the UK pathogen priority list, compares it to lists generated by other organisations (World Health Organisation, National Institutes of Allergy and Infectious Diseases) and summarises clinical progress towards the development of vaccines against priority diseases. There is clear technical progress towards the development of vaccines. However, the availability of these vaccines will be dependent on sustained funding for clinical trials and the preparation of clinically acceptable manufactured material during inter-epidemic periods.
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Affiliation(s)
- Rob J Noad
- Pathobiology and Population Science, The Royal Veterinary College, Hawkshead Lane, Hatfield AL9 7TA, UK.
| | - Karl Simpson
- JKS Bioscience Ltd, 2 Midanbury Court, 44 Midanbury Lane, Southampton SO18 4HF, UK.
| | | | - Roger Hewson
- National Infection Service, Public Health England, Porton Down, Salisbury, Wiltshire SP4 0JG, UK
| | - Sarah C Gilbert
- Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK.
| | - Mark P Stevens
- The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.
| | - Margaret J Hosie
- MRC-University of Glasgow Centre for Virus Research, College of Veterinary, Medical and Life Sciences, Garscube Estate, Bearsden, Glasgow G61 1QH, UK.
| | - Joann Prior
- CBR Division, Dstl Porton Down, Wiltshire SP3 4DZ, UK.
| | - Anna M Kinsey
- Medical Research Council, One Kemble Street, London WC2B 4AN, UK.
| | - Gary Entrican
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Near Edinburgh, Scotland EH26 0PZ, UK.
| | - Andrew Simpson
- National Infection Service, Public Health England, Porton Down, Salisbury, Wiltshire SP4 0JG, UK.
| | | | - Miles W Carroll
- National Infection Service, Public Health England, Porton Down, Salisbury, Wiltshire SP4 0JG, UK.
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22
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Maabar M, Davison AJ, Vučak M, Thorburn F, Murcia PR, Gunson R, Palmarini M, Hughes J. DisCVR: Rapid viral diagnosis from high-throughput sequencing data. Virus Evol 2019; 5:vez033. [PMID: 31528358 PMCID: PMC6735924 DOI: 10.1093/ve/vez033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
High-throughput sequencing (HTS) enables most pathogens in a clinical sample to be detected from a single analysis, thereby providing novel opportunities for diagnosis, surveillance, and epidemiology. However, this powerful technology is difficult to apply in diagnostic laboratories because of its computational and bioinformatic demands. We have developed DisCVR, which detects known human viruses in clinical samples by matching sample k-mers (twenty-two nucleotide sequences) to k-mers from taxonomically labeled viral genomes. DisCVR was validated using published HTS data for eighty-nine clinical samples from adults with upper respiratory tract infections. These samples had been tested for viruses metagenomically and also by real-time polymerase chain reaction assay, which is the standard diagnostic method. DisCVR detected human viruses with high sensitivity (79%) and specificity (100%), and was able to detect mixed infections. Moreover, it produced results comparable to those in a published metagenomic analysis of 177 blood samples from patients in Nigeria. DisCVR has been designed as a user-friendly tool for detecting human viruses from HTS data using computers with limited RAM and processing power, and includes a graphical user interface to help users interpret and validate the output. It is written in Java and is publicly available from http://bioinformatics.cvr.ac.uk/discvr.php.
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Affiliation(s)
- Maha Maabar
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Andrew J Davison
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Matej Vučak
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Fiona Thorburn
- Microbiology Department, Glasgow Royal Infirmary, Glasgow G4 0SF, UK
| | - Pablo R Murcia
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Rory Gunson
- West of Scotland Specialist Virology Centre, Glasgow Royal Infirmary, Glasgow G4 0SF, UK
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
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23
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Vasilakis N, Tesh RB, Popov VL, Widen SG, Wood TG, Forrester NL, Gonzalez JP, Saluzzo JF, Alkhovsky S, Lam SK, Mackenzie JS, Walker PJ. Exploiting the Legacy of the Arbovirus Hunters. Viruses 2019; 11:E471. [PMID: 31126128 PMCID: PMC6563318 DOI: 10.3390/v11050471] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/15/2019] [Accepted: 05/21/2019] [Indexed: 12/13/2022] Open
Abstract
In recent years, it has become evident that a generational gap has developed in the community of arbovirus research. This apparent gap is due to the dis-investment of training for the next generation of arbovirologists, which threatens to derail the rich history of virus discovery, field epidemiology, and understanding of the richness of diversity that surrounds us. On the other hand, new technologies have resulted in an explosion of virus discovery that is constantly redefining the virosphere and the evolutionary relationships between viruses. This paradox presents new challenges that may have immediate and disastrous consequences for public health when yet to be discovered arboviruses emerge. In this review we endeavor to bridge this gap by providing a historical context for the work being conducted today and provide continuity between the generations. To this end, we will provide a narrative of the thrill of scientific discovery and excitement and the challenges lying ahead.
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Affiliation(s)
- Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
| | - Robert B Tesh
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
| | - Vsevolod L Popov
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
| | - Steve G Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Blvd, Galveston TX 77555, USA.
| | - Thomas G Wood
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Blvd, Galveston TX 77555, USA.
| | - Naomi L Forrester
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
| | - Jean Paul Gonzalez
- Center of Excellence for Emerging & Zoonotic Animal Disease, Kansas State University, Manhattan, KS 66502, USA.
| | | | - Sergey Alkhovsky
- Ivanovsky Institute of Virology, N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, 123098, 18 Gamaleya str., Moscow, Russia.
| | - Sai Kit Lam
- Department of Medical Microbiology, University of Malaya, Kuala Lumpur 50603, Malaysia.
| | - John S Mackenzie
- Faculty of Medical Sciences, Curtin University, Perth, Western Australia 6102, Australia.
| | - Peter J Walker
- School of Biological Sciences, The University of Queensland, St Lucia, QLD 4072, Australia.
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24
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Castillo DJ, Rifkin RF, Cowan DA, Potgieter M. The Healthy Human Blood Microbiome: Fact or Fiction? Front Cell Infect Microbiol 2019; 9:148. [PMID: 31139578 PMCID: PMC6519389 DOI: 10.3389/fcimb.2019.00148] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/23/2019] [Indexed: 12/21/2022] Open
Abstract
The blood that flows perpetually through our veins and arteries performs numerous functions essential to our survival. Besides distributing oxygen, this vast circulatory system facilitates nutrient transport, deters infection and dispenses heat throughout our bodies. Since human blood has traditionally been considered to be an entirely sterile environment, comprising only blood-cells, platelets and plasma, the detection of microbes in blood was consistently interpreted as an indication of infection. However, although a contentious concept, evidence for the existence of a healthy human blood-microbiome is steadily accumulating. While the origins, identities and functions of these unanticipated micro-organisms remain to be elucidated, information on blood-borne microbial phylogeny is gradually increasing. Given recent advances in microbial-hematology, we review current literature concerning the composition and origin of the human blood-microbiome, focusing on bacteria and their role in the configuration of both the diseased and healthy human blood-microbiomes. Specifically, we explore the ways in which dysbiosis in the supposedly innocuous blood-borne bacterial microbiome may stimulate pathogenesis. In addition to exploring the relationship between blood-borne bacteria and the development of complex disorders, we also address the matter of contamination, citing the influence of contaminants on the interpretation of blood-derived microbial datasets and urging the routine analysis of laboratory controls to ascertain the taxonomic and metabolic characteristics of environmentally-derived contaminant-taxa.
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Affiliation(s)
- Diego J Castillo
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Riaan F Rifkin
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa.,Human Origins and Palaeo Environmental Research Group, Department of Anthropology and Geography, Oxford Brookes University, Oxford, United Kingdom
| | - Don A Cowan
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Marnie Potgieter
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
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25
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Caì Y, Yú S, Jangra RK, Postnikova EN, Wada J, Tesh RB, Whelan SPJ, Lauck M, Wiley MR, Finch CL, Radoshitzky SR, O’Connor DH, Palacios G, Chandran K, Chiu CY, Kuhn JH. Human, Nonhuman Primate, and Bat Cells Are Broadly Susceptible to Tibrovirus Particle Cell Entry. Front Microbiol 2019; 10:856. [PMID: 31105663 PMCID: PMC6499107 DOI: 10.3389/fmicb.2019.00856] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 04/03/2019] [Indexed: 12/23/2022] Open
Abstract
In 2012, the genome of a novel rhabdovirus, Bas-Congo virus (BASV), was discovered in the acute-phase serum of a Congolese patient with presumed viral hemorrhagic fever. In the absence of a replicating virus isolate, fulfilling Koch's postulates to determine whether BASV is indeed a human virus and/or pathogen has been impossible. However, experiments with vesiculoviral particles pseudotyped with Bas-Congo glycoprotein suggested that BASV particles can enter cells from multiple animals, including humans. In 2015, genomes of two related viruses, Ekpoma virus 1 (EKV-1) and Ekpoma virus 2 (EKV-2), were detected in human sera in Nigeria. Isolates could not be obtained. Phylogenetic analyses led to the classification of BASV, EKV-1, and EKV-2 in the same genus, Tibrovirus, together with five biting midge-borne rhabdoviruses [i.e., Beatrice Hill virus (BHV), Bivens Arm virus (BAV), Coastal Plains virus (CPV), Sweetwater Branch virus (SWBV), and Tibrogargan virus (TIBV)] not known to infect humans. Using individual recombinant vesiculoviruses expressing the glycoproteins of all eight known tibroviruses and more than 75 cell lines representing different animal species, we demonstrate that the glycoproteins of all tibroviruses can mediate vesiculovirus particle entry into human, bat, nonhuman primate, cotton rat, boa constrictor, and Asian tiger mosquito cells. Using four of five isolated authentic tibroviruses (i.e., BAV, CPV, SWBV, and TIBV), our experiments indicate that many cell types may be partially resistant to tibrovirus replication after virion cell entry. Consequently, experimental data solely obtained from experiments using tibrovirus surrogate systems (e.g., vesiculoviral pseudotypes, recombinant vesiculoviruses) cannot be used to predict whether BASV, or any other tibrovirus, infects humans.
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Affiliation(s)
- Yíngyún Caì
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, United States
| | - Shuǐqìng Yú
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, United States
| | - Rohit K. Jangra
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Elena N. Postnikova
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, United States
| | - Jiro Wada
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, United States
| | - Robert B. Tesh
- Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, The University of Texas Medical Branch, Galveston, TX, United States
| | - Sean P. J. Whelan
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, United States
| | - Michael Lauck
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, WI, United States
| | - Michael R. Wiley
- United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Courtney L. Finch
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, United States
| | - Sheli R. Radoshitzky
- United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, WI, United States
| | - Gustavo Palacios
- United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Charles Y. Chiu
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, United States
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, United States
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26
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Huang B, Jennison A, Whiley D, McMahon J, Hewitson G, Graham R, De Jong A, Warrilow D. Illumina sequencing of clinical samples for virus detection in a public health laboratory. Sci Rep 2019; 9:5409. [PMID: 30931974 PMCID: PMC6443674 DOI: 10.1038/s41598-019-41830-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 01/31/2019] [Indexed: 11/29/2022] Open
Abstract
High-throughput sequencing (HTS) provides the opportunity, once a diagnostic result is obtained, to extract additional information from a virus-containing sample. Hence, it offers advantages over established quantitative amplification technology, such as quantitative PCR, particularly in a public health environment. At this early stage of its clinical application, there have been limited studies comparing HTS performance to that of the more established quantitative PCR technology for direct detection of viruses. In this pilot-scale study, we tested HTS with a range of viruses and sample types routinely encountered in a public health virology laboratory. In comparison with quantitative PCR, our HTS method was able to sensitively (92%) detect all viruses in any sample type with the exception of certain tissues. Moreover, sufficient nucleotide sequence information was obtained to enable genotyping of strains detected, thus providing additional useful epidemiological information. While HTS sensitivity may not yet match that of PCR, the added value through enhanced epidemiological data has considerable potential to enable real-time surveillance of circulating strains so as to facilitate rapid and appropriate response to outbreaks and virus zoonotic spillover events.
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Affiliation(s)
- Bixing Huang
- Public Health Virology Laboratory, Queensland Health Forensic and Scientific Services, PO Box 594, Archerfield, Queensland, 4108, Australia
| | - Amy Jennison
- Public Health Microbiology Laboratory, Queensland Health Forensic and Scientific Services, PO Box 594, Archerfield, Queensland, 4108, Australia
| | - David Whiley
- Microbiology Division, Pathology Queensland Central Laboratory, Brisbane, Queensland, 4029, Australia.,Faculty of Medicine, University of Queensland Centre for Clinical Research, The University of Queensland, Brisbane, Queensland, 4029, Australia
| | - Jamie McMahon
- Public Health Virology Laboratory, Queensland Health Forensic and Scientific Services, PO Box 594, Archerfield, Queensland, 4108, Australia
| | - Glen Hewitson
- Public Health Virology Laboratory, Queensland Health Forensic and Scientific Services, PO Box 594, Archerfield, Queensland, 4108, Australia
| | - Rikki Graham
- Public Health Microbiology Laboratory, Queensland Health Forensic and Scientific Services, PO Box 594, Archerfield, Queensland, 4108, Australia
| | - Amanda De Jong
- Public Health Virology Laboratory, Queensland Health Forensic and Scientific Services, PO Box 594, Archerfield, Queensland, 4108, Australia
| | - David Warrilow
- Public Health Virology Laboratory, Queensland Health Forensic and Scientific Services, PO Box 594, Archerfield, Queensland, 4108, Australia.
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27
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Metsky HC, Siddle KJ, Gladden-Young A, Qu J, Yang DK, Brehio P, Goldfarb A, Piantadosi A, Wohl S, Carter A, Lin AE, Barnes KG, Tully DC, Corleis B, Hennigan S, Barbosa-Lima G, Vieira YR, Paul LM, Tan AL, Garcia KF, Parham LA, Odia I, Eromon P, Folarin OA, Goba A, Simon-Lorière E, Hensley L, Balmaseda A, Harris E, Kwon DS, Allen TM, Runstadler JA, Smole S, Bozza FA, Souza TML, Isern S, Michael SF, Lorenzana I, Gehrke L, Bosch I, Ebel G, Grant DS, Happi CT, Park DJ, Gnirke A, Sabeti PC, Matranga CB. Capturing sequence diversity in metagenomes with comprehensive and scalable probe design. Nat Biotechnol 2019; 37:160-168. [PMID: 30718881 PMCID: PMC6587591 DOI: 10.1038/s41587-018-0006-x] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 12/18/2018] [Indexed: 01/24/2023]
Abstract
Metagenomic sequencing has the potential to transform microbial detection and characterization, but new tools are needed to improve its sensitivity. Here we present CATCH, a computational method to enhance nucleic acid capture for enrichment of diverse microbial taxa. CATCH designs optimal probe sets, with a specified number of oligonucleotides, that achieve full coverage of, and scale well with, known sequence diversity. We focus on applying CATCH to capture viral genomes in complex metagenomic samples. We design, synthesize, and validate multiple probe sets, including one that targets the whole genomes of the 356 viral species known to infect humans. Capture with these probe sets enriches unique viral content on average 18-fold, allowing us to assemble genomes that could not be recovered without enrichment, and accurately preserves within-sample diversity. We also use these probe sets to recover genomes from the 2018 Lassa fever outbreak in Nigeria and to improve detection of uncharacterized viral infections in human and mosquito samples. The results demonstrate that CATCH enables more sensitive and cost-effective metagenomic sequencing.
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Affiliation(s)
- Hayden C. Metsky
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,0000 0001 2341 2786grid.116068.8Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Katherine J. Siddle
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | | | - James Qu
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - David K. Yang
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | - Patrick Brehio
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Andrew Goldfarb
- 000000041936754Xgrid.38142.3cFaculty of Arts and Sciences, Harvard University, Cambridge, MA USA
| | - Anne Piantadosi
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,0000 0004 0386 9924grid.32224.35Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA USA
| | - Shirlee Wohl
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | - Amber Carter
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Aaron E. Lin
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | - Kayla G. Barnes
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA USA
| | - Damien C. Tully
- 0000 0004 0489 3491grid.461656.6The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA USA
| | - Bjӧrn Corleis
- 0000 0004 0489 3491grid.461656.6The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA USA
| | - Scott Hennigan
- 0000 0004 0378 6934grid.416511.6Massachusetts Department of Public Health, Boston, MA USA
| | - Giselle Barbosa-Lima
- 0000 0001 0723 0931grid.418068.3Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Yasmine R. Vieira
- 0000 0001 0723 0931grid.418068.3Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lauren M. Paul
- 0000 0001 0647 2963grid.255962.fDepartment of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL USA
| | - Amanda L. Tan
- 0000 0001 0647 2963grid.255962.fDepartment of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL USA
| | - Kimberly F. Garcia
- 0000 0001 2297 2829grid.10601.36Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Leda A. Parham
- 0000 0001 2297 2829grid.10601.36Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Ikponmwosa Odia
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Philomena Eromon
- grid.442553.1African Center of Excellence for Genomics of Infectious Disease (ACEGID), Redeemer’s University, Ede, Nigeria
| | - Onikepe A. Folarin
- grid.442553.1African Center of Excellence for Genomics of Infectious Disease (ACEGID), Redeemer’s University, Ede, Nigeria ,grid.442553.1Department of Biological Sciences, College of Natural Sciences, Redeemer’s University, Ede, Nigeria
| | - Augustine Goba
- Lassa Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
| | | | - Etienne Simon-Lorière
- 0000 0001 2353 6535grid.428999.7Evolutionary Genomics of RNA Viruses, Virology Department, Institut Pasteur, Paris, France
| | - Lisa Hensley
- 0000 0001 2164 9667grid.419681.3Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Frederick, MD USA
| | - Angel Balmaseda
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Eva Harris
- 0000 0001 2181 7878grid.47840.3fDivision of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA USA
| | - Douglas S. Kwon
- 0000 0004 0386 9924grid.32224.35Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA USA ,0000 0004 0489 3491grid.461656.6The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA USA
| | - Todd M. Allen
- 0000 0004 0489 3491grid.461656.6The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA USA
| | - Jonathan A. Runstadler
- 0000 0004 1936 7531grid.429997.8Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA USA
| | - Sandra Smole
- 0000 0004 0378 6934grid.416511.6Massachusetts Department of Public Health, Boston, MA USA
| | - Fernando A. Bozza
- 0000 0001 0723 0931grid.418068.3Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thiago M. L. Souza
- 0000 0001 0723 0931grid.418068.3Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sharon Isern
- 0000 0001 0647 2963grid.255962.fDepartment of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL USA
| | - Scott F. Michael
- 0000 0001 0647 2963grid.255962.fDepartment of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL USA
| | - Ivette Lorenzana
- 0000 0001 2297 2829grid.10601.36Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Lee Gehrke
- 0000 0001 2341 2786grid.116068.8Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Microbiology and Immunobiology, Harvard Medical School, Boston, MA USA
| | - Irene Bosch
- 0000 0001 2341 2786grid.116068.8Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Gregory Ebel
- 0000 0004 1936 8083grid.47894.36Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO USA
| | - Donald S. Grant
- Lassa Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone ,0000 0001 2290 9707grid.442296.fCollege of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | - Christian T. Happi
- 000000041936754Xgrid.38142.3cDepartment of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA USA ,Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria ,grid.442553.1African Center of Excellence for Genomics of Infectious Disease (ACEGID), Redeemer’s University, Ede, Nigeria ,grid.442553.1Department of Biological Sciences, College of Natural Sciences, Redeemer’s University, Ede, Nigeria
| | - Daniel J. Park
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Andreas Gnirke
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Pardis C. Sabeti
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA USA ,0000 0001 2167 1581grid.413575.1Howard Hughes Medical Institute, Chevy Chase, MD USA
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28
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Greninger AL, Naccache SN. Metagenomics to Assist in the Diagnosis of Bloodstream Infection. J Appl Lab Med 2018; 3:643-653. [PMID: 31639732 DOI: 10.1373/jalm.2018.026120] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 11/08/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) has emerged as a promising technology that enables pan-pathogen detection from any source. However, clinical utility and practical integration into the clinical microbiology work flow and a bloodstream infection detection algorithm are currently uncharted. In the context of bloodstream infections, the challenges associated with blood culture, including sensitivity, postantibiotic treatment, attaining sufficient volumes sufficient volumes, and turnaround time, are well-known. Molecular assays have helped expedite turnaround time, especially when performed directly from positive culture media bottles. mNGS offers an unbiased but more complex version of molecular testing directly from sample, but it is unclear how and if it should be implemented in the clinical microbiology laboratory today. CONTENT Here we map out the potential utility and application of mNGS tests to infectious disease diagnostics from blood sources, including intrinsic limitations of the methodology in diagnosing bloodstream infections and sepsis vs DNAemia, current barriers to integration into routine workup, and milestones that may need to be met before implementation. SUMMARY Polymerases and pores move faster than bugs divide, so the thermodynamics of mNGS adoption for bloodstream infection is favorable. Nonetheless, considerable activation barriers exist that will slow this likely diagnostic transition. We eagerly await the manufacturer who designs an integrated sample-to-answer box to do for mNGS what has been done for other aspects of molecular detection.
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Affiliation(s)
| | - Samia N Naccache
- Department of Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA
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29
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Choi K, Ryu H, Siddle KJ, Piantadosi A, Freimark L, Park DJ, Sabeti P, Han J. Negative Selection by Spiral Inertial Microfluidics Improves Viral Recovery and Sequencing from Blood. Anal Chem 2018; 90:4657-4662. [PMID: 29536737 PMCID: PMC6195311 DOI: 10.1021/acs.analchem.7b05200] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In blood samples from patients with viral infection, it is often important to separate viral particles from human cells, for example, to minimize background in performing viral whole genome sequencing. Here, we present a microfluidic device that uses spiral inertial microfluidics with continuous circulation to separate host cells from viral particles and free nucleic acid. We demonstrate that this device effectively reduces white blood cells, red blood cells, and platelets from both whole blood and plasma samples with excellent recovery of viral nucleic acid. Furthermore, microfluidic separation leads to greater viral genome coverage and depth, highlighting an important application of this device in processing clinical samples for viral genome sequencing.
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Affiliation(s)
- Kyungyong Choi
- Research Laboratory of Electronics,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | | | - Katherine J Siddle
- Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, MA 02142, USA,Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Anne Piantadosi
- Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, MA 02142, USA,Division of Infectious Disease, Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114
| | - Lisa Freimark
- Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, MA 02142, USA
| | - Daniel J Park
- Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, MA 02142, USA
| | - Pardis Sabeti
- Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, MA 02142, USA,Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA,Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Jongyoon Han
- Research Laboratory of Electronics,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA,Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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30
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Phan TG, Del Valle Mendoza J, Sadeghi M, Altan E, Deng X, Delwart E. Sera of Peruvians with fever of unknown origins include viral nucleic acids from non-vertebrate hosts. Virus Genes 2018; 54:33-40. [PMID: 29043660 PMCID: PMC5826777 DOI: 10.1007/s11262-017-1514-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 10/06/2017] [Indexed: 12/11/2022]
Abstract
Serum samples collected from 88 Peruvians with unexplained fever were analyzed for viral sequences using metagenomics. Nucleic acids of anelloviruses, pegivirus A (GBV-C), HIV, Dengue virus, and Oropouche virus were detected. We also characterized from two sera the RNA genomes of new species of partitivirus and dicistrovirus belonging to viral families known to infect fungi or arthropod, respectively. Genomic DNA of a putative fungal cellular host could be PCR amplified from the partitivirus-containing serum sample. The detection in human serum of nucleic acids from viral families not known to infect vertebrates may indicate contamination during sample collection and aliquoting or human infection by their presumed cellular host, here a fungus. The role, if any, of the non-vertebrate infecting viruses detected in serum in inducing fever is unknown.
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Affiliation(s)
- Tung Gia Phan
- Blood Systems Research Institute, San Francisco, CA, 94118, USA
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94118, USA
| | - Juana Del Valle Mendoza
- School of Medicine, Research and Innovation Centre of the Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima, Peru
- Instituto de Investigación Nutricional, Lima, Peru
| | - Mohammadreza Sadeghi
- Blood Systems Research Institute, San Francisco, CA, 94118, USA
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94118, USA
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Eda Altan
- Blood Systems Research Institute, San Francisco, CA, 94118, USA
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94118, USA
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, CA, 94118, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, 94118, USA.
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94118, USA.
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31
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Zárate S, Taboada B, Yocupicio-Monroy M, Arias CF. Human Virome. Arch Med Res 2017; 48:701-716. [DOI: 10.1016/j.arcmed.2018.01.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/22/2018] [Indexed: 12/16/2022]
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32
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Robinson ML, Manabe YC. Reducing Uncertainty for Acute Febrile Illness in Resource-Limited Settings: The Current Diagnostic Landscape. Am J Trop Med Hyg 2017; 96:1285-1295. [PMID: 28719277 DOI: 10.4269/ajtmh.16-0667] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
AbstractDiagnosing the cause of acute febrile illness in resource-limited settings is important-to give the correct antimicrobials to patients who need them, to prevent unnecessary antimicrobial use, to detect emerging infectious diseases early, and to guide vaccine deployment. A variety of approaches are yielding more rapid and accurate tests that can detect more pathogens in a wider variety of settings. After decades of slow progress in diagnostics for acute febrile illness in resource-limited settings, a wave of converging advancements will enable clinicians in resource-limited settings to reduce uncertainty for the diagnosis of acute febrile illness.
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Affiliation(s)
- Matthew L Robinson
- Division of Infectious Disease, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Yukari C Manabe
- Division of Infectious Disease, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
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33
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Amarasinghe GK, Bào Y, Basler CF, Bavari S, Beer M, Bejerman N, Blasdell KR, Bochnowski A, Briese T, Bukreyev A, Calisher CH, Chandran K, Collins PL, Dietzgen RG, Dolnik O, Dürrwald R, Dye JM, Easton AJ, Ebihara H, Fang Q, Formenty P, Fouchier RAM, Ghedin E, Harding RM, Hewson R, Higgins CM, Hong J, Horie M, James AP, Jiāng D, Kobinger GP, Kondo H, Kurath G, Lamb RA, Lee B, Leroy EM, Li M, Maisner A, Mühlberger E, Netesov SV, Nowotny N, Patterson JL, Payne SL, Paweska JT, Pearson MN, Randall RE, Revill PA, Rima BK, Rota P, Rubbenstroth D, Schwemmle M, Smither SJ, Song Q, Stone DM, Takada A, Terregino C, Tesh RB, Tomonaga K, Tordo N, Towner JS, Vasilakis N, Volchkov VE, Wahl-Jensen V, Walker PJ, Wang B, Wang D, Wang F, Wang LF, Werren JH, Whitfield AE, Yan Z, Ye G, Kuhn JH. Taxonomy of the order Mononegavirales: update 2017. Arch Virol 2017; 162:2493-2504. [PMID: 28389807 PMCID: PMC5831667 DOI: 10.1007/s00705-017-3311-7] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 02/26/2017] [Indexed: 12/11/2022]
Abstract
In 2017, the order Mononegavirales was expanded by the inclusion of a total of 69 novel species. Five new rhabdovirus genera and one new nyamivirus genus were established to harbor 41 of these species, whereas the remaining new species were assigned to already established genera. Furthermore, non-Latinized binomial species names replaced all paramyxovirus and pneumovirus species names, thereby accomplishing application of binomial species names throughout the entire order. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).
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Affiliation(s)
- Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Yīmíng Bào
- Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Sina Bavari
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Nicolás Bejerman
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Kim R Blasdell
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Alisa Bochnowski
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Alexander Bukreyev
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Charles H Calisher
- Arthropod-Borne and Infectious Diseases Laboratory, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Peter L Collins
- Respiratory Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Olga Dolnik
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | | | - John M Dye
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Andrew J Easton
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Hideki Ebihara
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Qi Fang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhèjiāng University, Hángzhōu, China
| | | | - Ron A M Fouchier
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Elodie Ghedin
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Robert M Harding
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Roger Hewson
- Public Health England, Porton Down, Wiltshire, Salisbury, UK
| | - Colleen M Higgins
- Institute of Applied Ecology, School of Science, Auckland University of Technology, Auckland, New Zealand
- AUT Roche Diagnostic Laboratory, Auckland University of Technology, Auckland, New Zealand
| | - Jian Hong
- Analysis Center of Agrobiology and Environmental Sciences and Institute of Agrobiology and Environmental Sciences, Zhèjiāng University, Hángzhōu, China
| | - Masayuki Horie
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
| | - Anthony P James
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Dàohóng Jiāng
- State Key Laboratory of Agricultural Microbiology, The Provincial Key Lab of Plant Pathology of Húběi Province, College of Plant Science and Technology, Huázhōng Agricultural University, Wǔhàn, China
| | - Gary P Kobinger
- Department of Microbiology, Immunology and Infectious Diseases Université Laval, Quebec City, Canada
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Gael Kurath
- US Geological Survey Western Fisheries Research Center, Seattle, Washington, USA
| | - Robert A Lamb
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Howard Hughes Medical Institute, Northwestern University, Evanston, IL, USA
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric M Leroy
- Centre International de Recherches Médicales de Franceville, Institut de Recherche pour le Développement, Franceville, Gabon
| | - Ming Li
- Institute of Applied Ecology, School of Science, Auckland University of Technology, Auckland, New Zealand
- AUT Roche Diagnostic Laboratory, Auckland University of Technology, Auckland, New Zealand
| | - Andrea Maisner
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Elke Mühlberger
- Department of Microbiology and, National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Sergey V Netesov
- Novosibirsk State University, Novosibirsk, Novosibirsk Oblast, Russia
| | - Norbert Nowotny
- Institute of Virology, University of Veterinary Medicine, Vienna, Austria
- Department of Basic Medical Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Jean L Patterson
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Susan L Payne
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Janusz T Paweska
- Center for Emerging and Zoonotic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham, Johannesburg, Gauteng, South Africa
| | - Michael N Pearson
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Rick E Randall
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, Scotland, UK
| | - Peter A Revill
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
- Victorian Infectious Diseases Reference Laboratory, Doherty Institute of Infection and Immunity, Melbourne, Victoria, Australia
| | - Bertus K Rima
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, The Queen's University of Belfast, Belfast, Northern Ireland, UK
| | - Paul Rota
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Dennis Rubbenstroth
- Institute for Virology, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Martin Schwemmle
- Institute for Virology, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sophie J Smither
- CBR Division, Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire, UK
| | - Qisheng Song
- Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, Missouri, USA
| | - David M Stone
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | - Ayato Takada
- Division of Global Epidemiology, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Calogero Terregino
- Istituto Zooprofilattico Sperimentale delle Venezie, Department of Comparative Biomedical Sciences, National/OIE Reference Laboratory for Newcastle Disease and Avian Influenza, FAO Reference Centre for Animal Influenza and Newcastle Disease, OIE Collaborating Centre for Diseases at the Human-Animal Interface, Legnaro, Padova, Italy
| | - Robert B Tesh
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Keizo Tomonaga
- Institute for Frontier Life and Medical Sciences (inFront), Kyoto University, Kyoto, Japan
| | - Noël Tordo
- Institut Pasteur, Unité des Stratégies Antivirales, WHO Collaborative Centre for Viral Haemorrhagic Fevers and Arboviruses, OIE Reference Laboratory for RVFV and CCHFV, Paris, France
- Institut Pasteur de Guinée, Conakry, Guinea
| | - Jonathan S Towner
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Nikos Vasilakis
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Viktor E Volchkov
- Molecular Basis of Viral Pathogenicity, CIRIINSERM U1111 - CNRS UMR5308, Université de Lyon, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Victoria Wahl-Jensen
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD, USA
| | - Peter J Walker
- School of Biological Sciences, University of Queensland, St. Lucia, QLD, Australia
| | - Beibei Wang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhèjiāng University, Hángzhōu, China
| | - David Wang
- Departments of Molecular Microbiology and Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Fei Wang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhèjiāng University, Hángzhōu, China
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY, USA
| | | | - Zhichao Yan
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhèjiāng University, Hángzhōu, China
| | - Gongyin Ye
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhèjiāng University, Hángzhōu, China
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA.
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Rascovan N, Duraisamy R, Desnues C. Metagenomics and the Human Virome in Asymptomatic Individuals. Annu Rev Microbiol 2017; 70:125-41. [PMID: 27607550 DOI: 10.1146/annurev-micro-102215-095431] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
High-throughput sequencing technologies have revolutionized how we think about viruses. Investigators can now go beyond pathogenic viruses and have access to the thousands of viruses that inhabit our bodies without causing clinical symptoms. By studying their interactions with each other, with other microbes, and with host genetics and immune systems, we can learn how they affect health and disease. This article reviews current knowledge of the composition and diversity of the human virome in physiologically healthy individuals. It focuses on recent results from metagenomics studies and discusses the contribution of bacteriophages and eukaryotic viruses to human health.
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Affiliation(s)
- Nicolás Rascovan
- Faculté de Médecine, Aix Marseille Université, 13385 Marseille, France.,URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 13385 Marseille, France;
| | - Raja Duraisamy
- Faculté de Médecine, Aix Marseille Université, 13385 Marseille, France.,URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 13385 Marseille, France;
| | - Christelle Desnues
- Faculté de Médecine, Aix Marseille Université, 13385 Marseille, France.,URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 13385 Marseille, France;
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35
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Goldberg TL, Bennett AJ, Kityo R, Kuhn JH, Chapman CA. Kanyawara Virus: A Novel Rhabdovirus Infecting Newly Discovered Nycteribiid Bat Flies Infesting Previously Unknown Pteropodid Bats in Uganda. Sci Rep 2017; 7:5287. [PMID: 28706276 PMCID: PMC5509700 DOI: 10.1038/s41598-017-05236-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 05/25/2017] [Indexed: 12/21/2022] Open
Abstract
Bats are natural reservoir hosts of highly virulent pathogens such as Marburg virus, Nipah virus, and SARS coronavirus. However, little is known about the role of bat ectoparasites in transmitting and maintaining such viruses. The intricate relationship between bats and their ectoparasites suggests that ectoparasites might serve as viral vectors, but evidence to date is scant. Bat flies, in particular, are highly specialized obligate hematophagous ectoparasites that incidentally bite humans. Using next-generation sequencing, we discovered a novel ledantevirus (mononegaviral family Rhabdoviridae, genus Ledantevirus) in nycteribiid bat flies infesting pteropodid bats in western Uganda. Mitochondrial DNA analyses revealed that both the bat flies and their bat hosts belong to putative new species. The coding-complete genome of the new virus, named Kanyawara virus (KYAV), is only distantly related to that of its closest known relative, Mount Elgon bat virus, and was found at high titers in bat flies but not in blood or on mucosal surfaces of host bats. Viral genome analysis indicates unusually low CpG dinucleotide depletion in KYAV compared to other ledanteviruses and rhabdovirus groups, with KYAV displaying values similar to rhabdoviruses of arthropods. Our findings highlight the possibility of a yet-to-be-discovered diversity of potentially pathogenic viruses in bat ectoparasites.
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Affiliation(s)
- Tony L Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.
- Global Health Institute, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.
- Department of Zoology, Makerere University, Kampala, Uganda.
| | - Andrew J Bennett
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Robert Kityo
- Department of Zoology, Makerere University, Kampala, Uganda
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, 21702, USA
| | - Colin A Chapman
- Department of Zoology, Makerere University, Kampala, Uganda
- Department of Anthropology and School of Environment, McGill University, Montreal, Quebec, H3A 2T7, Canada
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36
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Gubala A, Walsh S, McAllister J, Weir R, Davis S, Melville L, Mitchell I, Bulach D, Gauci P, Skvortsov A, Boyle D. Identification of very small open reading frames in the genomes of Holmes Jungle virus, Ord River virus, and Wongabel virus of the genus Hapavirus, family Rhabdoviridae. Evol Bioinform Online 2017; 13:1176934317713484. [PMID: 28747815 PMCID: PMC5510769 DOI: 10.1177/1176934317713484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 05/05/2017] [Indexed: 12/11/2022] Open
Abstract
Viruses of the family Rhabdoviridae infect a broad range of hosts from a variety of ecological and geographical niches, including vertebrates, arthropods, and plants. The arthropod-transmitted members of this family display considerable genetic diversity and remarkable genomic flexibility that enable coding for various accessory proteins in different locations of the genome. Here, we describe the genome of Holmes Jungle virus, isolated from Culex annulirostris mosquitoes collected in northern Australia, and make detailed comparisons with the closely related Ord River and Wongabel viruses, with a focus on identifying very small open reading frames (smORFs) in their genomes. This is the first systematic prediction of smORFs in rhabdoviruses, emphasising the intricacy of the rhabdovirus genome and the knowledge gaps. We speculate that these smORFs may be of importance to the life cycle of the virus in the arthropod vector.
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Affiliation(s)
- Aneta Gubala
- Land Division, Defence Science and Technology Group, Fishermans Bend, VIC, Australia
| | - Susan Walsh
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Northern Territory Government, Berrimah, NT, Australia
| | - Jane McAllister
- Land Division, Defence Science and Technology Group, Fishermans Bend, VIC, Australia
| | - Richard Weir
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Northern Territory Government, Berrimah, NT, Australia
| | - Steven Davis
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Northern Territory Government, Berrimah, NT, Australia
| | - Lorna Melville
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Northern Territory Government, Berrimah, NT, Australia
| | - Ian Mitchell
- Land Division, Defence Science and Technology Group, Fishermans Bend, VIC, Australia
| | - Dieter Bulach
- Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC, Australia
| | - Penny Gauci
- Land Division, Defence Science and Technology Group, Fishermans Bend, VIC, Australia
| | - Alex Skvortsov
- Land Division, Defence Science and Technology Group, Fishermans Bend, VIC, Australia
| | - David Boyle
- Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC, Australia
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37
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Sauvage V, Gomez J, Boizeau L, Laperche S. The potential of viral metagenomics in blood transfusion safety. Transfus Clin Biol 2017; 24:218-222. [PMID: 28694025 DOI: 10.1016/j.tracli.2017.06.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 06/13/2017] [Indexed: 02/08/2023]
Abstract
Thanks to the significant advent of high throughput sequencing in the last ten years, it is now possible via metagenomics to define the spectrum of the microbial sequences present in human blood samples. Therefore, metagenomics sequencing appears as a promising approach for the identification and global surveillance of new, emerging and/or unexpected viruses that could impair blood transfusion safety. However, despite considerable advantages compared to the traditional methods of pathogen identification, this non-targeted approach presents several drawbacks including a lack of sensitivity and sequence contaminant issues. With further improvements, especially to increase sensitivity, metagenomics sequencing should become in a near future an additional diagnostic tool in infectious disease field and especially in blood transfusion safety.
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Affiliation(s)
- V Sauvage
- Département d'études des agents transmissibles par le sang, Institut national de la transfusion sanguine (INTS), Centre national de référence risques infectieux transfusionnels, 75015 Paris, France.
| | - J Gomez
- Département d'études des agents transmissibles par le sang, Institut national de la transfusion sanguine (INTS), Centre national de référence risques infectieux transfusionnels, 75015 Paris, France
| | - L Boizeau
- Département d'études des agents transmissibles par le sang, Institut national de la transfusion sanguine (INTS), Centre national de référence risques infectieux transfusionnels, 75015 Paris, France
| | - S Laperche
- Département d'études des agents transmissibles par le sang, Institut national de la transfusion sanguine (INTS), Centre national de référence risques infectieux transfusionnels, 75015 Paris, France
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38
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Kandathil AJ, Breitwieser FP, Sachithanandham J, Robinson M, Mehta SH, Timp W, Salzberg SL, Thomas DL, Balagopal A. Presence of Human Hepegivirus-1 in a Cohort of People Who Inject Drugs. Ann Intern Med 2017; 167:1-7. [PMID: 28586923 PMCID: PMC5721525 DOI: 10.7326/m17-0085] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Next-generation metagenomic sequencing (NGMS) has opened new frontiers in microbial discovery but has been clinically characterized in only a few settings. OBJECTIVE To explore the plasma virome of persons who inject drugs and to characterize the sensitivity and accuracy of NGMS compared with quantitative clinical standards. DESIGN Longitudinal and cross-sectional studies. SETTING A clinical trial (ClinicalTrials.gov: NCT01285050) and a well-characterized cohort study of persons who have injected drugs. PARTICIPANTS Persons co-infected with hepatitis C virus (HCV) and HIV. MEASUREMENTS Viral nucleic acid in plasma by NGMS and quantitative polymerase chain reaction (PCR). RESULTS Next-generation metagenomic sequencing generated a total of 600 million reads, which included the expected HIV and HCV RNA sequences. HIV and HCV reads were consistently identified only when samples contained more than 10 000 copies/mL or IU/mL, respectively, as determined by quantitative PCR. A novel RNA virus, human hepegivirus-1 (HHpgV-1), was also detected by NGMS in 4 samples from 2 persons in the clinical trial. Through use of a quantitative PCR assay for HHpgV-1, infection was also detected in 17 (10.9%) of 156 members of a cohort of persons who injected drugs. In these persons, HHpgV-1 viremia persisted for a median of at least 4538 days and was associated with detection of other bloodborne viruses, such as HCV RNA and SEN virus D. LIMITATION The medical importance of HHpgV-1 infection is unknown. CONCLUSION Although NGMS is insensitive for detection of viruses with relatively low plasma nucleic acid concentrations, it may have broad potential for discovery of new viral infections of possible medical importance, such as HHpgV-1. PRIMARY FUNDING SOURCE National Institutes of Health.
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Affiliation(s)
- Abraham J Kandathil
- From Johns Hopkins University and Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Florian P Breitwieser
- From Johns Hopkins University and Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | - Matthew Robinson
- From Johns Hopkins University and Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Shruti H Mehta
- From Johns Hopkins University and Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Winston Timp
- From Johns Hopkins University and Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Steven L Salzberg
- From Johns Hopkins University and Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - David L Thomas
- From Johns Hopkins University and Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Ashwin Balagopal
- From Johns Hopkins University and Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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39
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Buchko GW, Clifton MC, Wallace EG, Atkins KA, Myler PJ. Backbone chemical shift assignments and secondary structure analysis of the U1 protein from the Bas-Congo virus. BIOMOLECULAR NMR ASSIGNMENTS 2017; 11:51-56. [PMID: 27981424 PMCID: PMC8457264 DOI: 10.1007/s12104-016-9719-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 11/30/2016] [Indexed: 06/06/2023]
Abstract
The Bas-Congo virus (BASV) is the first rhabdovirus associated with a human outbreak of acute hemorrhagic fever. The single-stranded, negative-sense RNA genome of BASV contains the five core genes present in all rhabdoviral genomes plus an additional three genes, annotated U1, U2, and U3, with weak (<21%) sequence similarity only to a handful of genes observed in a few other rhabdoviral genomes. The function of the rhabdoviral U proteins is unknown, but, they are hypothesized to play a role in viral infection or replication. To better understand this unique family of proteins, a construct containing residues 27-203 of the 216-residue U1 protein (BASV-U1*) was prepared. By collecting data in 0.5 M urea it was possible to eliminate transient association enough to enable the assignment of most of the observable 1HN, 1Hα, 15N, 13Cα, 13Cβ, and 13C´ chemical shifts for BASV-U1* that will provide a foundation to study its solution properties. The analyses of these chemical shifts along with 15N-edited NOESY data enabled the identification of the elements of secondary structure present in BASV-U1*.
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Affiliation(s)
- Garry W Buchko
- Seattle Structural Genomics Center for Infectious Disease, Seattle, USA.
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Matthew C Clifton
- Seattle Structural Genomics Center for Infectious Disease, Seattle, USA
- Beryllium, Bainbridge Island, WA, 97331, USA
- Nurix Inc., San Francisco, CA, 94158, USA
| | - Ellen G Wallace
- Seattle Structural Genomics Center for Infectious Disease, Seattle, USA
- Beryllium, Bainbridge Island, WA, 97331, USA
| | - Kateri A Atkins
- Seattle Structural Genomics Center for Infectious Disease, Seattle, USA
- Beryllium, Bainbridge Island, WA, 97331, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease, Seattle, USA
- Center for Infectious Disease Research, 307 Westlake Ave. N., Seattle, WA, 98109, USA
- Department of Global Health, University of Washington, Seattle, WA, 98165, USA
- Department of Biomedical Informatics and Health Education, University of Washington, Seattle, WA, 98195, USA
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40
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Moustafa A, Xie C, Kirkness E, Biggs W, Wong E, Turpaz Y, Bloom K, Delwart E, Nelson KE, Venter JC, Telenti A. The blood DNA virome in 8,000 humans. PLoS Pathog 2017; 13:e1006292. [PMID: 28328962 PMCID: PMC5378407 DOI: 10.1371/journal.ppat.1006292] [Citation(s) in RCA: 199] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 04/03/2017] [Accepted: 03/14/2017] [Indexed: 02/06/2023] Open
Abstract
The characterization of the blood virome is important for the safety of blood-derived transfusion products, and for the identification of emerging pathogens. We explored non-human sequence data from whole-genome sequencing of blood from 8,240 individuals, none of whom were ascertained for any infectious disease. Viral sequences were extracted from the pool of sequence reads that did not map to the human reference genome. Analyses sifted through close to 1 Petabyte of sequence data and performed 0.5 trillion similarity searches. With a lower bound for identification of 2 viral genomes/100,000 cells, we mapped sequences to 94 different viruses, including sequences from 19 human DNA viruses, proviruses and RNA viruses (herpesviruses, anelloviruses, papillomaviruses, three polyomaviruses, adenovirus, HIV, HTLV, hepatitis B, hepatitis C, parvovirus B19, and influenza virus) in 42% of the study participants. Of possible relevance to transfusion medicine, we identified Merkel cell polyomavirus in 49 individuals, papillomavirus in blood of 13 individuals, parvovirus B19 in 6 individuals, and the presence of herpesvirus 8 in 3 individuals. The presence of DNA sequences from two RNA viruses was unexpected: Hepatitis C virus is revealing of an integration event, while the influenza virus sequence resulted from immunization with a DNA vaccine. Age, sex and ancestry contributed significantly to the prevalence of infection. The remaining 75 viruses mostly reflect extensive contamination of commercial reagents and from the environment. These technical problems represent a major challenge for the identification of novel human pathogens. Increasing availability of human whole-genome sequences will contribute substantial amounts of data on the composition of the normal and pathogenic human blood virome. Distinguishing contaminants from real human viruses is challenging. Novel sequencing technologies offer insight into the virome in human samples. Here, we identify the viral DNA sequences in blood of over 8,000 individuals undergoing whole genome sequencing. This approach serves to identify 94 viruses; however, many are shown to reflect widespread DNA contamination of commercial reagents or of environmental origin. While this represents a significant limitation to reliably identify novel viruses infecting humans, we could confidently detect sequences and quantify abundance of 19 human viruses in 42% of individuals. Ancestry, sex, and age were important determinants of viral prevalence. This large study calls attention on the challenge of interpreting next generation sequencing data for the identification of novel viruses. However, it serves to categorize the abundance of human DNA viruses using an unbiased technique.
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Affiliation(s)
- Ahmed Moustafa
- Human Longevity Inc., San Diego, California, United States of America
| | - Chao Xie
- Human Longevity Singapore Pte. Ltd., Singapore
| | - Ewen Kirkness
- Human Longevity Inc., San Diego, California, United States of America
| | - William Biggs
- Human Longevity Inc., San Diego, California, United States of America
| | - Emily Wong
- Human Longevity Inc., San Diego, California, United States of America
| | | | - Kenneth Bloom
- Human Longevity Inc., San Diego, California, United States of America
| | - Eric Delwart
- Blood Systems Research Institute, Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Karen E. Nelson
- J. Craig Venter Institute, La Jolla, California, United States of America
| | - J. Craig Venter
- Human Longevity Inc., San Diego, California, United States of America
- J. Craig Venter Institute, La Jolla, California, United States of America
- * E-mail: (JCV); (AT)
| | - Amalio Telenti
- Human Longevity Inc., San Diego, California, United States of America
- J. Craig Venter Institute, La Jolla, California, United States of America
- * E-mail: (JCV); (AT)
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41
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Ergünay K, Brinkmann A, Litzba N, Günay F, Kar S, Öter K, Örsten S, Sarıkaya Y, Alten B, Nitsche A, Linton YM. A novel rhabdovirus, related to Merida virus, in field-collected mosquitoes from Anatolia and Thrace. Arch Virol 2017; 162:1903-1911. [PMID: 28283817 DOI: 10.1007/s00705-017-3314-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 02/21/2017] [Indexed: 01/26/2023]
Abstract
Next-generation sequencing technologies have significantly facilitated the discovery of novel viruses, and metagenomic surveillance of arthropods has enabled exploration of the diversity of novel or known viral agents. We have identified a novel rhabdovirus that is genetically related to the recently described Merida virus via next-generation sequencing in a mosquito pool from Thrace. The complete viral genome contains 11,798 nucleotides with 83% genome-wide nucleotide sequence similarity to Merida virus. Five major putative open reading frames that follow the canonical rhabdovirus genome organization were identified. A total of 1380 mosquitoes comprising 13 species, collected from Thrace and the Mediterranean and Aegean regions of Anatolia were screened for the novel virus using primers based on the N and L genes of the prototype genome. Eight positive pools (6.2%) exclusively comprised Culex pipiens sensu lato specimens originating from all study regions. Infections were observed in pools with female as well as male or mixed-sex individuals. The overall and Cx. pipiens-specific minimal infection rates were calculated to be 5.7 and 14.8, respectively. Sequencing of the PCR products revealed marked diversity within a portion of the N gene, with up to 4% divergence and distinct amino acid substitutions that were unrelated to the collection site. Phylogenetic analysis of the complete and partial viral polymerase (L gene) amino acid sequences placed the novel virus and Merida virus in a distinct group, indicating that these strains are closely related. The strain is tentatively named "Merida-like virus Turkey". Studies are underway to isolate and further explore the host range and distribution of this new strain.
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Affiliation(s)
- Koray Ergünay
- Virology Unit, Department of Medical Microbiology, Hacettepe University Faculty of Medicine, Morphology Building 3rd Floor, Sihhiye, 06100, Ankara, Turkey. .,Center for Biological Threats and Special Pathogens 1 (ZBS-1), Robert Koch Institute, Berlin, Germany.
| | - Annika Brinkmann
- Center for Biological Threats and Special Pathogens 1 (ZBS-1), Robert Koch Institute, Berlin, Germany
| | - Nadine Litzba
- Center for Biological Threats and Special Pathogens 1 (ZBS-1), Robert Koch Institute, Berlin, Germany
| | - Filiz Günay
- Division of Ecology, Department of Biology, Faculty of Sciences, Hacettepe University, Ankara, Turkey
| | - Sırrı Kar
- Department of Biology, Faculty of Arts and Sciences, Namık Kemal University, Tekirdağ, Turkey
| | - Kerem Öter
- Department of Parasitology, Faculty of Veterinary Medicine, Istanbul University, Istanbul, Turkey
| | - Serra Örsten
- Virology Unit, Department of Medical Microbiology, Hacettepe University Faculty of Medicine, Morphology Building 3rd Floor, Sihhiye, 06100, Ankara, Turkey
| | - Yasemen Sarıkaya
- Division of Ecology, Department of Biology, Faculty of Sciences, Hacettepe University, Ankara, Turkey
| | - Bülent Alten
- Division of Ecology, Department of Biology, Faculty of Sciences, Hacettepe University, Ankara, Turkey
| | - Andreas Nitsche
- Center for Biological Threats and Special Pathogens 1 (ZBS-1), Robert Koch Institute, Berlin, Germany
| | - Yvonne-Marie Linton
- Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Suitland, MD, USA.,Department of Entomology, Walter Reed Army Institute of Research, Silver Spring, MD, USA.,Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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42
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Wiley MR, Prieto K, Blasdell KR, Caì Y, Campos Lawson C, Walker PJ, Chiu CY, Palacios G, Kuhn JH. Beatrice Hill Virus Represents a Novel Species in the Genus Tibrovirus (Mononegavirales: Rhabdoviridae). GENOME ANNOUNCEMENTS 2017; 5:e01485-16. [PMID: 28126935 PMCID: PMC5270694 DOI: 10.1128/genomea.01485-16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 11/22/2016] [Indexed: 11/20/2022]
Abstract
The rhabdoviral genus Tibrovirus currently has three official members assigned to two species: Bivens Arm virus and Tibrogargan virus (species Tibrogargan tibrovirus) and Coastal Plains virus (species Coastal Plains tibrovirus). Here, we report the complete genome sequence of a new putative member of this genus, Beatrice Hill virus. Although relatively closely related to the three classified viruses, Beatrice Hill virus represents a novel Tibrovirus species.
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Affiliation(s)
- Michael R Wiley
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland, USA
| | - Karla Prieto
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland, USA
| | - Kim R Blasdell
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Health and Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Yíngyún Caì
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
| | - Cristine Campos Lawson
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
| | - Peter J Walker
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Health and Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia
- School of Biological Sciences, University of Queensland, St. Lucia, Queensland, Australia
| | - Charles Y Chiu
- University of California, San Francisco, California, USA
| | - Gustavo Palacios
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
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43
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Ngoi CN, Siqueira J, Li L, Deng X, Mugo P, Graham SM, Price MA, Sanders EJ, Delwart E. The plasma virome of febrile adult Kenyans shows frequent parvovirus B19 infections and a novel arbovirus (Kadipiro virus). J Gen Virol 2016; 97:3359-3367. [PMID: 27902331 DOI: 10.1099/jgv.0.000644] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Viral nucleic acids present in the plasma of 498 Kenyan adults with unexplained fever were characterized by metagenomics analysis of 51 sample pools. The highest to lowest fraction of plasma pools was positive for parvovirus B19 (75 %), pegivirus C (GBV-C) (67 %), alpha anellovirus (59 %), gamma anellovirus (55 %), beta anellovirus (41 %), dengue virus genotype 2 (DENV-2) (16 %), human immunodeficiency virus type 1 (6 %), human herpesvirus 6 (6 %), HBV (4 %), rotavirus (4 %), hepatitis B virus (4 %), rhinovirus C (2 %), Merkel cell polyomavirus (MCPyV; 2 %) and Kadipiro virus (2 %). Ranking by overall percentage of viral reads yielded similar results. Characterization of viral nucleic acids in the plasma of a febrile East African population showed a high frequency of parvovirus B19 and DENV infections and detected a reovirus (Kadipiro virus) previously reported only in Asian Culex mosquitoes, providing a baseline to compare with future virome studies to detect emerging viruses in this region.
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Affiliation(s)
- Carolyne N Ngoi
- Centre for Geographic Medicine Research - Coast, Kenya Medical Research Institute, Kilifi, Kenya
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Juliana Siqueira
- Blood Systems Research Institute, San Francisco, CA, USA
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Linlin Li
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Peter Mugo
- Centre for Geographic Medicine Research - Coast, Kenya Medical Research Institute, Kilifi, Kenya
| | - Susan M Graham
- Centre for Geographic Medicine Research - Coast, Kenya Medical Research Institute, Kilifi, Kenya
- University of Washington, Seattle, WA, USA
| | - Matt A Price
- International AIDS Vaccine Initiative, New York, NY, USA
- Department of Epidemiology and Biostatistics, University of California at San Francisco, CA, USA
| | - Eduard J Sanders
- Centre for Geographic Medicine Research - Coast, Kenya Medical Research Institute, Kilifi, Kenya
- Nuffield Department of Medicine, University of Oxford, Headington, UK
| | - Eric Delwart
- Department of Laboratory Medicine, University of California at San Francisco, CA, USA
- Blood Systems Research Institute, San Francisco, CA, USA
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44
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Abstract
Genomic analysis is a powerful tool for understanding viral disease outbreaks. Sequencing of viral samples is now easier and cheaper than ever before and can supplement epidemiological methods by providing nucleotide-level resolution of outbreak-causing pathogens. In this review, we describe methods used to answer crucial questions about outbreaks, such as how they began and how a disease is transmitted. More specifically, we explain current techniques for viral sequencing, phylogenetic analysis, transmission reconstruction, and evolutionary investigation of viral pathogens. By detailing the ways in which genomic data can help us understand viral disease outbreaks, we aim to provide a resource that will facilitate the response to future outbreaks.
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Affiliation(s)
- Shirlee Wohl
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138.,Broad Institute, Cambridge, Massachusetts 02142; ,
| | - Stephen F Schaffner
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138.,Broad Institute, Cambridge, Massachusetts 02142; , .,Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115
| | - Pardis C Sabeti
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138.,Broad Institute, Cambridge, Massachusetts 02142; , .,Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115
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45
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Matranga CB, Gladden-Young A, Qu J, Winnicki S, Nosamiefan D, Levin JZ, Sabeti PC. Unbiased Deep Sequencing of RNA Viruses from Clinical Samples. J Vis Exp 2016. [PMID: 27403729 PMCID: PMC4993327 DOI: 10.3791/54117] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Here we outline a next-generation RNA sequencing protocol that enables de novo assemblies and intra-host variant calls of viral genomes collected from clinical and biological sources. The method is unbiased and universal; it uses random primers for cDNA synthesis and requires no prior knowledge of the viral sequence content. Before library construction, selective RNase H-based digestion is used to deplete unwanted RNA — including poly(rA) carrier and ribosomal RNA — from the viral RNA sample. Selective depletion improves both the data quality and the number of unique reads in viral RNA sequencing libraries. Moreover, a transposase-based 'tagmentation' step is used in the protocol as it reduces overall library construction time. The protocol has enabled rapid deep sequencing of over 600 Lassa and Ebola virus samples-including collections from both blood and tissue isolates-and is broadly applicable to other microbial genomics studies.
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Affiliation(s)
| | | | - James Qu
- Broad Institute of MIT and Harvard
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46
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Frey KG, Biser T, Hamilton T, Santos CJ, Pimentel G, Mokashi VP, Bishop-Lilly KA. Bioinformatic Characterization of Mosquito Viromes within the Eastern United States and Puerto Rico: Discovery of Novel Viruses. Evol Bioinform Online 2016; 12:1-12. [PMID: 27346944 PMCID: PMC4912310 DOI: 10.4137/ebo.s38518] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/01/2016] [Accepted: 05/01/2016] [Indexed: 12/14/2022] Open
Abstract
Mosquitoes are efficient, militarily relevant vectors of infectious disease pathogens, including many RNA viruses. The vast majority of all viruses are thought to be undiscovered. Accordingly, recent studies have shown that viruses discovered in insects are very divergent from known pathogens and that many of them lack appropriate reference sequences in the public databases. Given that the majority of viruses are likely still undiscovered, environ mental sampling stands to provide much needed reference samples as well as genetic sequences for comparison. In this study, we sought to determine whether samples of mosquitoes collected from different sites (the Caribbean and locations on the US East Coast) could be differentiated using metagenomic analysis of the RNA viral fraction. We report here distinct virome profiles, even from samples collected short distances apart. In addition to profiling the previously known viruses from these samples, we detected a number of viruses that have been previously undiscovered.
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Affiliation(s)
- Kenneth G Frey
- Naval Medical Research Center - Frederick, Fort Detrick, MD, USA.; Henry M. Jackson Foundation, Bethesda, MD, USA
| | - Tara Biser
- Naval Medical Research Center - Frederick, Fort Detrick, MD, USA.; Hood College, Frederick, MD, USA
| | - Theron Hamilton
- Naval Medical Research Center - Frederick, Fort Detrick, MD, USA
| | | | | | | | - Kimberly A Bishop-Lilly
- Naval Medical Research Center - Frederick, Fort Detrick, MD, USA.; Henry M. Jackson Foundation, Bethesda, MD, USA
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47
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Charles J, Firth AE, Loroño-Pino MA, Garcia-Rejon JE, Farfan-Ale JA, Lipkin WI, Blitvich BJ, Briese T. Merida virus, a putative novel rhabdovirus discovered in Culex and Ochlerotatus spp. mosquitoes in the Yucatan Peninsula of Mexico. J Gen Virol 2016; 97:977-987. [PMID: 26868915 DOI: 10.1099/jgv.0.000424] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sequences corresponding to a putative, novel rhabdovirus [designated Merida virus (MERDV)] were initially detected in a pool of Culex quinquefasciatus collected in the Yucatan Peninsula of Mexico. The entire genome was sequenced, revealing 11 798 nt and five major ORFs, which encode the nucleoprotein (N), phosphoprotein (P), matrix protein (M), glycoprotein (G) and RNA-dependent RNA polymerase (L). The deduced amino acid sequences of the N, G and L proteins have no more than 24, 38 and 43 % identity, respectively, to the corresponding sequences of all other known rhabdoviruses, whereas those of the P and M proteins have no significant identity with any sequences in GenBank and their identity is only suggested based on their genome position. Using specific reverse transcription-PCR assays established from the genome sequence, 27 571 C. quinquefasciatus which had been sorted in 728 pools were screened to assess the prevalence of MERDV in nature and 25 pools were found positive. The minimal infection rate (calculated as the number of positive mosquito pools per 1000 mosquitoes tested) was 0.9, and similar for both females and males. Screening another 140 pools of 5484 mosquitoes belonging to four other genera identified positive pools of Ochlerotatus spp. mosquitoes, indicating that the host range is not restricted to C. quinquefasciatus. Attempts to isolate MERDV in C6/36 and Vero cells were unsuccessful. In summary, we provide evidence that a previously undescribed rhabdovirus occurs in mosquitoes in Mexico.
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Affiliation(s)
- Jermilia Charles
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Andrew E Firth
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Maria A Loroño-Pino
- Laboratorio de Arbovirología, Centro de Investigaciones Regionales Dr Hideyo Noguchi, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Julian E Garcia-Rejon
- Laboratorio de Arbovirología, Centro de Investigaciones Regionales Dr Hideyo Noguchi, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Jose A Farfan-Ale
- Laboratorio de Arbovirología, Centro de Investigaciones Regionales Dr Hideyo Noguchi, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Bradley J Blitvich
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
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