Streamlined Subpopulation, Subtype, and Recombination Analysis of HIV-1 Half-Genome Sequences Generated by High-Throughput Sequencing

ABSTRACT High-throughput sequencing (HTS) has been widely used to characterize HIV-1 genome sequences. There are no algorithms currently that can directly determine genotype and quasispecies population using short HTS reads generated from long genome sequences without additional software. To establi...

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Autores principales:	Bhavna Hora, Naila Gulzar, Yue Chen, Konstantinos Karagiannis, Fangping Cai, Chang Su, Krista Smith, Vahan Simonyan, Sharaf Ali Shah, Manzoor Ahmed, Ana M. Sanchez, Mars Stone, Myron S. Cohen, Thomas N. Denny, Raja Mazumder, Feng Gao
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	HIV-1 genetic recombination quasispecies sequencing Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/ad53339e65e5434399222e31b258226c
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spelling	oai:doaj.org-article:ad53339e65e5434399222e31b258226c2021-11-15T15:30:58ZStreamlined Subpopulation, Subtype, and Recombination Analysis of HIV-1 Half-Genome Sequences Generated by High-Throughput Sequencing10.1128/mSphere.00551-202379-5042https://doaj.org/article/ad53339e65e5434399222e31b258226c2020-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00551-20https://doaj.org/toc/2379-5042ABSTRACT High-throughput sequencing (HTS) has been widely used to characterize HIV-1 genome sequences. There are no algorithms currently that can directly determine genotype and quasispecies population using short HTS reads generated from long genome sequences without additional software. To establish a robust subpopulation, subtype, and recombination analysis workflow, we amplified the HIV-1 3′-half genome from plasma samples of 65 HIV-1-infected individuals and sequenced the entire amplicon (∼4,500 bp) by HTS. With direct analysis of raw reads using HIVE-hexahedron, we showed that 48% of samples harbored 2 to 13 subpopulations. We identified various subtypes (17 A1s, 4 Bs, 27 Cs, 6 CRF02_AGs, and 11 unique recombinant forms) and defined recombinant breakpoints of 10 recombinants. These results were validated with viral genome sequences generated by single genome sequencing (SGS) or the analysis of consensus sequence of the HTS reads. The HIVE-hexahedron workflow is more sensitive and accurate than just evaluating the consensus sequence and also more cost-effective than SGS. IMPORTANCE The highly recombinogenic nature of human immunodeficiency virus type 1 (HIV-1) leads to recombination and emergence of quasispecies. It is important to reliably identify subpopulations to understand the complexity of a viral population for drug resistance surveillance and vaccine development. High-throughput sequencing (HTS) provides improved resolution over Sanger sequencing for the analysis of heterogeneous viral subpopulations. However, current methods of analysis of HTS reads are unable to fully address accurate population reconstruction. Hence, there is a dire need for a more sensitive, accurate, user-friendly, and cost-effective method to analyze viral quasispecies. For this purpose, we have improved the HIVE-hexahedron algorithm that we previously developed with in silico short sequences to analyze raw HTS short reads. The significance of this study is that our standalone algorithm enables a streamlined analysis of quasispecies, subtype, and recombination patterns from long HIV-1 genome regions without the need of additional sequence analysis tools. Distinct viral populations and recombination patterns identified by HIVE-hexahedron are further validated by comparison with sequences obtained by single genome sequencing (SGS).Bhavna HoraNaila GulzarYue ChenKonstantinos KaragiannisFangping CaiChang SuKrista SmithVahan SimonyanSharaf Ali ShahManzoor AhmedAna M. SanchezMars StoneMyron S. CohenThomas N. DennyRaja MazumderFeng GaoAmerican Society for MicrobiologyarticleHIV-1genetic recombinationquasispeciessequencingMicrobiologyQR1-502ENmSphere, Vol 5, Iss 5 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	HIV-1 genetic recombination quasispecies sequencing Microbiology QR1-502
spellingShingle	HIV-1 genetic recombination quasispecies sequencing Microbiology QR1-502 Bhavna Hora Naila Gulzar Yue Chen Konstantinos Karagiannis Fangping Cai Chang Su Krista Smith Vahan Simonyan Sharaf Ali Shah Manzoor Ahmed Ana M. Sanchez Mars Stone Myron S. Cohen Thomas N. Denny Raja Mazumder Feng Gao Streamlined Subpopulation, Subtype, and Recombination Analysis of HIV-1 Half-Genome Sequences Generated by High-Throughput Sequencing
description	ABSTRACT High-throughput sequencing (HTS) has been widely used to characterize HIV-1 genome sequences. There are no algorithms currently that can directly determine genotype and quasispecies population using short HTS reads generated from long genome sequences without additional software. To establish a robust subpopulation, subtype, and recombination analysis workflow, we amplified the HIV-1 3′-half genome from plasma samples of 65 HIV-1-infected individuals and sequenced the entire amplicon (∼4,500 bp) by HTS. With direct analysis of raw reads using HIVE-hexahedron, we showed that 48% of samples harbored 2 to 13 subpopulations. We identified various subtypes (17 A1s, 4 Bs, 27 Cs, 6 CRF02_AGs, and 11 unique recombinant forms) and defined recombinant breakpoints of 10 recombinants. These results were validated with viral genome sequences generated by single genome sequencing (SGS) or the analysis of consensus sequence of the HTS reads. The HIVE-hexahedron workflow is more sensitive and accurate than just evaluating the consensus sequence and also more cost-effective than SGS. IMPORTANCE The highly recombinogenic nature of human immunodeficiency virus type 1 (HIV-1) leads to recombination and emergence of quasispecies. It is important to reliably identify subpopulations to understand the complexity of a viral population for drug resistance surveillance and vaccine development. High-throughput sequencing (HTS) provides improved resolution over Sanger sequencing for the analysis of heterogeneous viral subpopulations. However, current methods of analysis of HTS reads are unable to fully address accurate population reconstruction. Hence, there is a dire need for a more sensitive, accurate, user-friendly, and cost-effective method to analyze viral quasispecies. For this purpose, we have improved the HIVE-hexahedron algorithm that we previously developed with in silico short sequences to analyze raw HTS short reads. The significance of this study is that our standalone algorithm enables a streamlined analysis of quasispecies, subtype, and recombination patterns from long HIV-1 genome regions without the need of additional sequence analysis tools. Distinct viral populations and recombination patterns identified by HIVE-hexahedron are further validated by comparison with sequences obtained by single genome sequencing (SGS).
format	article
author	Bhavna Hora Naila Gulzar Yue Chen Konstantinos Karagiannis Fangping Cai Chang Su Krista Smith Vahan Simonyan Sharaf Ali Shah Manzoor Ahmed Ana M. Sanchez Mars Stone Myron S. Cohen Thomas N. Denny Raja Mazumder Feng Gao
author_facet	Bhavna Hora Naila Gulzar Yue Chen Konstantinos Karagiannis Fangping Cai Chang Su Krista Smith Vahan Simonyan Sharaf Ali Shah Manzoor Ahmed Ana M. Sanchez Mars Stone Myron S. Cohen Thomas N. Denny Raja Mazumder Feng Gao
author_sort	Bhavna Hora
title	Streamlined Subpopulation, Subtype, and Recombination Analysis of HIV-1 Half-Genome Sequences Generated by High-Throughput Sequencing
title_short	Streamlined Subpopulation, Subtype, and Recombination Analysis of HIV-1 Half-Genome Sequences Generated by High-Throughput Sequencing
title_full	Streamlined Subpopulation, Subtype, and Recombination Analysis of HIV-1 Half-Genome Sequences Generated by High-Throughput Sequencing
title_fullStr	Streamlined Subpopulation, Subtype, and Recombination Analysis of HIV-1 Half-Genome Sequences Generated by High-Throughput Sequencing
title_full_unstemmed	Streamlined Subpopulation, Subtype, and Recombination Analysis of HIV-1 Half-Genome Sequences Generated by High-Throughput Sequencing
title_sort	streamlined subpopulation, subtype, and recombination analysis of hiv-1 half-genome sequences generated by high-throughput sequencing
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/ad53339e65e5434399222e31b258226c
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Streamlined Subpopulation, Subtype, and Recombination Analysis of HIV-1 Half-Genome Sequences Generated by High-Throughput Sequencing

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