Advanced molecular surveillance approaches for characterization of blood borne hepatitis viruses.
Defining genetic diversity of viral infections directly from patient specimens is the ultimate goal of surveillance. Simple tools that can provide full-length sequence information on blood borne viral hepatitis viruses: hepatitis C, hepatitis B and hepatitis D viruses (HCV, HBV and HDV) remain elusi...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2020-01-01
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| Series: | PLoS ONE |
| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0236046&type=printable |
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| author | Michael G Berg Ana Olivo Kenn Forberg Barbara J Harris Julie Yamaguchi Rachel Shirazi Yael Gozlan Silvia Sauleda Lazare Kaptue Mary A Rodgers Orna Mor Gavin A Cloherty |
| author_facet | Michael G Berg Ana Olivo Kenn Forberg Barbara J Harris Julie Yamaguchi Rachel Shirazi Yael Gozlan Silvia Sauleda Lazare Kaptue Mary A Rodgers Orna Mor Gavin A Cloherty |
| author_sort | Michael G Berg |
| collection | DOAJ |
| description | Defining genetic diversity of viral infections directly from patient specimens is the ultimate goal of surveillance. Simple tools that can provide full-length sequence information on blood borne viral hepatitis viruses: hepatitis C, hepatitis B and hepatitis D viruses (HCV, HBV and HDV) remain elusive. Here, an unbiased metagenomic next generation sequencing approach (mNGS) was used for molecular characterization of HCV infections (n = 99) from Israel which yielded full-length HCV sequences in 89% of samples, with 7 partial sequences sufficient for classification. HCV genotypes were primarily 1b (68%) and 1a (19%), with minor representation of genotypes 2c (1%) and 3a (8%). HBV/HDV coinfections were characterized by suppressed HBV viral loads, resulting in sparse mNGS coverage. A probe-based enrichment approach (xGen) aiming to increase HBV and HDV coverage was validated on a panel of diverse genotypes, geography and titers. The method extended HBV genome coverage a median 61% (range 8-84%) and provided orders of magnitude boosts in reads and sequence depth for both viruses. When HBV-xGen was applied to Israeli samples, coverage was improved by 28-73% in 4 samples and identified HBV genotype A1, A2, D1 specimens and a dual B/D infection. Abundant HDV reads in mNGS libraries yielded 18/26 (69%) full genomes and 8 partial sequences, with HDV-xGen only providing minimal extension (3-11%) of what were all genotype 1 genomes. Advanced molecular approaches coupled to virus-specific capture probes promise to enhance surveillance of viral infections and aid in monitoring the spread of local subtypes. |
| format | Article |
| id | doaj-art-e0bac11290554c258f2bf2dc9268f58b |
| institution | OA Journals |
| issn | 1932-6203 |
| language | English |
| publishDate | 2020-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-e0bac11290554c258f2bf2dc9268f58b2025-08-20T02:00:42ZengPublic Library of Science (PLoS)PLoS ONE1932-62032020-01-01157e023604610.1371/journal.pone.0236046Advanced molecular surveillance approaches for characterization of blood borne hepatitis viruses.Michael G BergAna OlivoKenn ForbergBarbara J HarrisJulie YamaguchiRachel ShiraziYael GozlanSilvia SauledaLazare KaptueMary A RodgersOrna MorGavin A ClohertyDefining genetic diversity of viral infections directly from patient specimens is the ultimate goal of surveillance. Simple tools that can provide full-length sequence information on blood borne viral hepatitis viruses: hepatitis C, hepatitis B and hepatitis D viruses (HCV, HBV and HDV) remain elusive. Here, an unbiased metagenomic next generation sequencing approach (mNGS) was used for molecular characterization of HCV infections (n = 99) from Israel which yielded full-length HCV sequences in 89% of samples, with 7 partial sequences sufficient for classification. HCV genotypes were primarily 1b (68%) and 1a (19%), with minor representation of genotypes 2c (1%) and 3a (8%). HBV/HDV coinfections were characterized by suppressed HBV viral loads, resulting in sparse mNGS coverage. A probe-based enrichment approach (xGen) aiming to increase HBV and HDV coverage was validated on a panel of diverse genotypes, geography and titers. The method extended HBV genome coverage a median 61% (range 8-84%) and provided orders of magnitude boosts in reads and sequence depth for both viruses. When HBV-xGen was applied to Israeli samples, coverage was improved by 28-73% in 4 samples and identified HBV genotype A1, A2, D1 specimens and a dual B/D infection. Abundant HDV reads in mNGS libraries yielded 18/26 (69%) full genomes and 8 partial sequences, with HDV-xGen only providing minimal extension (3-11%) of what were all genotype 1 genomes. Advanced molecular approaches coupled to virus-specific capture probes promise to enhance surveillance of viral infections and aid in monitoring the spread of local subtypes.https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0236046&type=printable |
| spellingShingle | Michael G Berg Ana Olivo Kenn Forberg Barbara J Harris Julie Yamaguchi Rachel Shirazi Yael Gozlan Silvia Sauleda Lazare Kaptue Mary A Rodgers Orna Mor Gavin A Cloherty Advanced molecular surveillance approaches for characterization of blood borne hepatitis viruses. PLoS ONE |
| title | Advanced molecular surveillance approaches for characterization of blood borne hepatitis viruses. |
| title_full | Advanced molecular surveillance approaches for characterization of blood borne hepatitis viruses. |
| title_fullStr | Advanced molecular surveillance approaches for characterization of blood borne hepatitis viruses. |
| title_full_unstemmed | Advanced molecular surveillance approaches for characterization of blood borne hepatitis viruses. |
| title_short | Advanced molecular surveillance approaches for characterization of blood borne hepatitis viruses. |
| title_sort | advanced molecular surveillance approaches for characterization of blood borne hepatitis viruses |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0236046&type=printable |
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