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Hepatitis C Virus Transmission Bottlenecks Analyzed by Deep Sequencing
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| Zeitschriftentitel: | Journal of Virology |
|---|---|
| Personen und Körperschaften: | , , , , |
| In: | Journal of Virology, 84, 2010, 12, S. 6218-6228 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
American Society for Microbiology
|
| Schlagwörter: |
| author_facet |
Wang, Gary P. Sherrill-Mix, Scott A. Chang, Kyong-Mi Quince, Chris Bushman, Frederic D. Wang, Gary P. Sherrill-Mix, Scott A. Chang, Kyong-Mi Quince, Chris Bushman, Frederic D. |
|---|---|
| author |
Wang, Gary P. Sherrill-Mix, Scott A. Chang, Kyong-Mi Quince, Chris Bushman, Frederic D. |
| spellingShingle |
Wang, Gary P. Sherrill-Mix, Scott A. Chang, Kyong-Mi Quince, Chris Bushman, Frederic D. Journal of Virology Hepatitis C Virus Transmission Bottlenecks Analyzed by Deep Sequencing Virology Insect Science Immunology Microbiology |
| author_sort |
wang, gary p. |
| spelling |
Wang, Gary P. Sherrill-Mix, Scott A. Chang, Kyong-Mi Quince, Chris Bushman, Frederic D. 0022-538X 1098-5514 American Society for Microbiology Virology Insect Science Immunology Microbiology http://dx.doi.org/10.1128/jvi.02271-09 <jats:title>ABSTRACT</jats:title> <jats:p>Hepatitis C virus (HCV) replication in infected patients produces large and diverse viral populations, which give rise to drug-resistant and immune escape variants. Here, we analyzed HCV populations during transmission and diversification in longitudinal and cross-sectional samples using 454/Roche pyrosequencing, in total analyzing 174,185 sequence reads. To sample diversity, four locations in the HCV genome were analyzed, ranging from high diversity (the envelope hypervariable region 1 [HVR1]) to almost no diversity (the 5′ untranslated region [UTR]). For three longitudinal samples for which early time points were available, we found that only 1 to 4 viral variants were present, suggesting that productive infection was initiated by a very small number of HCV particles. Sequence diversity accumulated subsequently, with the 5′ UTR showing almost no diversification while the envelope HVR1 showed >100 variants in some subjects. Calculation of the transmission probability for only a single variant, taking into account the measured population structure within patients, confirmed initial infection by one or a few viral particles. These findings provide the most detailed sequence-based analysis of HCV transmission bottlenecks to date. The analytical methods described here are broadly applicable to studies of viral diversity using deep sequencing.</jats:p> Hepatitis C Virus Transmission Bottlenecks Analyzed by Deep Sequencing Journal of Virology |
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| title |
Hepatitis C Virus Transmission Bottlenecks Analyzed by Deep Sequencing |
| title_unstemmed |
Hepatitis C Virus Transmission Bottlenecks Analyzed by Deep Sequencing |
| title_full |
Hepatitis C Virus Transmission Bottlenecks Analyzed by Deep Sequencing |
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Hepatitis C Virus Transmission Bottlenecks Analyzed by Deep Sequencing |
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Hepatitis C Virus Transmission Bottlenecks Analyzed by Deep Sequencing |
| title_short |
Hepatitis C Virus Transmission Bottlenecks Analyzed by Deep Sequencing |
| title_sort |
hepatitis c virus transmission bottlenecks analyzed by deep sequencing |
| topic |
Virology Insect Science Immunology Microbiology |
| url |
http://dx.doi.org/10.1128/jvi.02271-09 |
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2010 |
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6218-6228 |
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<jats:title>ABSTRACT</jats:title>
<jats:p>Hepatitis C virus (HCV) replication in infected patients produces large and diverse viral populations, which give rise to drug-resistant and immune escape variants. Here, we analyzed HCV populations during transmission and diversification in longitudinal and cross-sectional samples using 454/Roche pyrosequencing, in total analyzing 174,185 sequence reads. To sample diversity, four locations in the HCV genome were analyzed, ranging from high diversity (the envelope hypervariable region 1 [HVR1]) to almost no diversity (the 5′ untranslated region [UTR]). For three longitudinal samples for which early time points were available, we found that only 1 to 4 viral variants were present, suggesting that productive infection was initiated by a very small number of HCV particles. Sequence diversity accumulated subsequently, with the 5′ UTR showing almost no diversification while the envelope HVR1 showed >100 variants in some subjects. Calculation of the transmission probability for only a single variant, taking into account the measured population structure within patients, confirmed initial infection by one or a few viral particles. These findings provide the most detailed sequence-based analysis of HCV transmission bottlenecks to date. The analytical methods described here are broadly applicable to studies of viral diversity using deep sequencing.</jats:p> |
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| author | Wang, Gary P., Sherrill-Mix, Scott A., Chang, Kyong-Mi, Quince, Chris, Bushman, Frederic D. |
| author_facet | Wang, Gary P., Sherrill-Mix, Scott A., Chang, Kyong-Mi, Quince, Chris, Bushman, Frederic D., Wang, Gary P., Sherrill-Mix, Scott A., Chang, Kyong-Mi, Quince, Chris, Bushman, Frederic D. |
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| description | <jats:title>ABSTRACT</jats:title> <jats:p>Hepatitis C virus (HCV) replication in infected patients produces large and diverse viral populations, which give rise to drug-resistant and immune escape variants. Here, we analyzed HCV populations during transmission and diversification in longitudinal and cross-sectional samples using 454/Roche pyrosequencing, in total analyzing 174,185 sequence reads. To sample diversity, four locations in the HCV genome were analyzed, ranging from high diversity (the envelope hypervariable region 1 [HVR1]) to almost no diversity (the 5′ untranslated region [UTR]). For three longitudinal samples for which early time points were available, we found that only 1 to 4 viral variants were present, suggesting that productive infection was initiated by a very small number of HCV particles. Sequence diversity accumulated subsequently, with the 5′ UTR showing almost no diversification while the envelope HVR1 showed >100 variants in some subjects. Calculation of the transmission probability for only a single variant, taking into account the measured population structure within patients, confirmed initial infection by one or a few viral particles. These findings provide the most detailed sequence-based analysis of HCV transmission bottlenecks to date. The analytical methods described here are broadly applicable to studies of viral diversity using deep sequencing.</jats:p> |
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| spelling | Wang, Gary P. Sherrill-Mix, Scott A. Chang, Kyong-Mi Quince, Chris Bushman, Frederic D. 0022-538X 1098-5514 American Society for Microbiology Virology Insect Science Immunology Microbiology http://dx.doi.org/10.1128/jvi.02271-09 <jats:title>ABSTRACT</jats:title> <jats:p>Hepatitis C virus (HCV) replication in infected patients produces large and diverse viral populations, which give rise to drug-resistant and immune escape variants. Here, we analyzed HCV populations during transmission and diversification in longitudinal and cross-sectional samples using 454/Roche pyrosequencing, in total analyzing 174,185 sequence reads. To sample diversity, four locations in the HCV genome were analyzed, ranging from high diversity (the envelope hypervariable region 1 [HVR1]) to almost no diversity (the 5′ untranslated region [UTR]). For three longitudinal samples for which early time points were available, we found that only 1 to 4 viral variants were present, suggesting that productive infection was initiated by a very small number of HCV particles. Sequence diversity accumulated subsequently, with the 5′ UTR showing almost no diversification while the envelope HVR1 showed >100 variants in some subjects. Calculation of the transmission probability for only a single variant, taking into account the measured population structure within patients, confirmed initial infection by one or a few viral particles. These findings provide the most detailed sequence-based analysis of HCV transmission bottlenecks to date. The analytical methods described here are broadly applicable to studies of viral diversity using deep sequencing.</jats:p> Hepatitis C Virus Transmission Bottlenecks Analyzed by Deep Sequencing Journal of Virology |
| spellingShingle | Wang, Gary P., Sherrill-Mix, Scott A., Chang, Kyong-Mi, Quince, Chris, Bushman, Frederic D., Journal of Virology, Hepatitis C Virus Transmission Bottlenecks Analyzed by Deep Sequencing, Virology, Insect Science, Immunology, Microbiology |
| title | Hepatitis C Virus Transmission Bottlenecks Analyzed by Deep Sequencing |
| title_full | Hepatitis C Virus Transmission Bottlenecks Analyzed by Deep Sequencing |
| title_fullStr | Hepatitis C Virus Transmission Bottlenecks Analyzed by Deep Sequencing |
| title_full_unstemmed | Hepatitis C Virus Transmission Bottlenecks Analyzed by Deep Sequencing |
| title_short | Hepatitis C Virus Transmission Bottlenecks Analyzed by Deep Sequencing |
| title_sort | hepatitis c virus transmission bottlenecks analyzed by deep sequencing |
| title_unstemmed | Hepatitis C Virus Transmission Bottlenecks Analyzed by Deep Sequencing |
| topic | Virology, Insect Science, Immunology, Microbiology |
| url | http://dx.doi.org/10.1128/jvi.02271-09 |