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Li H, Marks KM, Talal AH, van Seggelen WO, Akil B, Radix A, Huprikar S, Branch AD, Wang S, Shaw GM, Fierer DS. Assessing routes of hepatitis C transmission in HIV-infected men who have sex with men using single genome sequencing. PLoS One 2020; 15:e0235237. [PMID: 32667919 PMCID: PMC7363067 DOI: 10.1371/journal.pone.0235237] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 06/10/2020] [Indexed: 02/07/2023] Open
Abstract
The epidemic of hepatitis C virus (HCV) infection among HIV-infected men who have sex with men (MSM) is in its second decade, but the routes of transmission remain poorly understood. We hypothesized that by pairing single genome sequencing (SGS), to enumerate infecting HCV genomes (viruses), with detailed sexual and drug histories, we could gain insight into the routes of transmission among MSM. We used SGS to analyze blood specimens from eight HIV-infected MSM who had 10 episodes of acute (seronegative) or early HCV infections. Seven of eight men reported condomless receptive anal intercourse (CRAI), six with rectal exposure to semen, and all eight denied rectal trauma or bleeding. Of the 10 HCV infections, eight resulted from transmission of a single virus; one infection resulted from transmission of either one or a few (three or four) closely-related viruses; and one infection resulted from transmission of >10 distinct viruses. The participant infected by >10 viruses reported sharing injection equipment for methamphetamine during sex. Two other participants also injected methamphetamine during sex but they did not share injection equipment and were infected by a single virus. Conclusions: Most HCV infections of HIV-infected MSM without a history of either rectal trauma or bleeding or shared injection equipment were caused by a single virus. Intra-rectal exposure to semen during CRAI is therefore likely sufficient for HCV transmission among MSM. Conversely, rectal trauma or bleeding or shared injection equipment are not necessary for HCV transmission among MSM. These results help clarify routes of HCV transmission among MSM and can therefore help guide the design of much-needed behavioral and other interventions to prevent HCV transmission among MSM.
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Affiliation(s)
- Hui Li
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Kristen M. Marks
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Andrew H. Talal
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Wouter O. van Seggelen
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Bisher Akil
- Chelsea Village Medical, New York, New York, United States of America
| | - Asa Radix
- Callen-Lorde Community Health Center, New York, New York, United States of America
| | - Shirish Huprikar
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Andrea D. Branch
- Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Shuyi Wang
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - George M. Shaw
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Daniel S. Fierer
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
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King B, Tarr AW. How have retrovirus pseudotypes contributed to our understanding of viral entry? Future Virol 2017. [DOI: 10.2217/fvl-2017-0062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Study of virus entry into host cells is important for understanding viral tropism and pathogenesis. Studying the entry of in vitro cultured viruses is not always practicable. Study of highly pathogenic viruses, viruses that do not grow in culture, and viruses that rapidly change phenotype in vitro can all benefit from alternative models of entry. Retrovirus particles can be engineered to display the envelope proteins of heterologous enveloped viruses. This approach, broadly termed ‘pseudotyping’, is an important technique for interrogating virus entry. In this perspective we consider how retrovirus pseudotypes have addressed these challenges and improved our understanding of the entry pathways of diverse virus species, including Ebolavirus, human immunodeficiency virus and hepatitis C virus.
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Affiliation(s)
- Barnabas King
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust & the University of Nottingham, Nottingham, UK
- School of Life Sciences, Faculty of Medicine & Health Sciences, University of Nottingham, Nottingham, UK
| | - Alexander W Tarr
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust & the University of Nottingham, Nottingham, UK
- School of Life Sciences, Faculty of Medicine & Health Sciences, University of Nottingham, Nottingham, UK
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Guinoiseau T, Moreau A, Hohnadel G, Ngo-Giang-Huong N, Brulard C, Vourc’h P, Goudeau A, Gaudy-Graffin C. Deep sequencing is an appropriate tool for the selection of unique Hepatitis C virus (HCV) variants after single genomic amplification. PLoS One 2017; 12:e0174852. [PMID: 28362878 PMCID: PMC5376297 DOI: 10.1371/journal.pone.0174852] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 03/16/2017] [Indexed: 01/19/2023] Open
Abstract
Hepatitis C virus (HCV) evolves rapidly in a single host and circulates as a quasispecies wich is a complex mixture of genetically distinct virus’s but closely related namely variants. To identify intra-individual diversity and investigate their functional properties in vitro, it is necessary to define their quasispecies composition and isolate the HCV variants. This is possible using single genome amplification (SGA). This technique, based on serially diluted cDNA to amplify a single cDNA molecule (clonal amplicon), has already been used to determine individual HCV diversity. In these studies, positive PCR reactions from SGA were directly sequenced using Sanger technology. The detection of non-clonal amplicons is necessary for excluding them to facilitate further functional analysis. Here, we compared Next Generation Sequencing (NGS) with De Novo assembly and Sanger sequencing for their ability to distinguish clonal and non-clonal amplicons after SGA on one plasma specimen. All amplicons (n = 42) classified as clonal by NGS were also classified as clonal by Sanger sequencing. No double peaks were seen on electropherograms for non-clonal amplicons with position-specific nucleotide variation below 15% by NGS. Altogether, NGS circumvented many of the difficulties encountered when using Sanger sequencing after SGA and is an appropriate tool to reliability select clonal amplicons for further functional studies.
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Affiliation(s)
- Thibault Guinoiseau
- INSERM U966, Université François Rabelais and CHRU de Tours, Tours, France
- * E-mail:
| | - Alain Moreau
- INSERM U966, Université François Rabelais and CHRU de Tours, Tours, France
| | - Guillaume Hohnadel
- INSERM U966, Université François Rabelais and CHRU de Tours, Tours, France
| | - Nicole Ngo-Giang-Huong
- Institut de Recherche pour le Développement (IRD) UMI 174 PHPT-Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Celine Brulard
- UMR INSERM U930, Université François Rabelais, Tours, France
| | - Patrick Vourc’h
- UMR INSERM U930, Université François Rabelais, Tours, France
| | - Alain Goudeau
- INSERM U966, Université François Rabelais and CHRU de Tours, Tours, France
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