Chemistry and Bioinformatics Considerations in Using Next-Generation Sequencing Technologies to Inferring HIV Proviral DNA Genome-Intactness
HIV persists via integration of the viral DNA into the human genome. The HIV DNA pool within an infected individual is a complex population that comprises both intact and defective viral genomes, each with a distinct integration site, in addition to a unique repertoire of viral quasi-species. Obtain...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-09-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/13/9/1874 |
| _version_ | 1797516960325435392 |
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| author | Guinevere Q. Lee |
| author_facet | Guinevere Q. Lee |
| author_sort | Guinevere Q. Lee |
| collection | DOAJ |
| description | HIV persists via integration of the viral DNA into the human genome. The HIV DNA pool within an infected individual is a complex population that comprises both intact and defective viral genomes, each with a distinct integration site, in addition to a unique repertoire of viral quasi-species. Obtaining an accurate profile of the viral DNA pool is critical to understanding viral persistence and resolving interhost differences. Recent advances in next-generation deep sequencing (NGS) technologies have enabled the development of two sequencing assays to capture viral near-full- genome sequences at single molecule resolution (FLIP-seq) or to co-capture full-length viral genome sequences in conjunction with its associated viral integration site (MIP-seq). This commentary aims to provide an overview on both FLIP-seq and MIP-seq, discuss their strengths and limitations, and outline specific chemistry and bioinformatics concerns when using these assays to study HIV persistence. |
| first_indexed | 2024-03-10T07:08:09Z |
| format | Article |
| id | doaj.art-e8ddab36fc4443b59f903609e4f6285c |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T07:08:09Z |
| publishDate | 2021-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-e8ddab36fc4443b59f903609e4f6285c2023-11-22T15:39:18ZengMDPI AGViruses1999-49152021-09-01139187410.3390/v13091874Chemistry and Bioinformatics Considerations in Using Next-Generation Sequencing Technologies to Inferring HIV Proviral DNA Genome-IntactnessGuinevere Q. Lee0Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USAHIV persists via integration of the viral DNA into the human genome. The HIV DNA pool within an infected individual is a complex population that comprises both intact and defective viral genomes, each with a distinct integration site, in addition to a unique repertoire of viral quasi-species. Obtaining an accurate profile of the viral DNA pool is critical to understanding viral persistence and resolving interhost differences. Recent advances in next-generation deep sequencing (NGS) technologies have enabled the development of two sequencing assays to capture viral near-full- genome sequences at single molecule resolution (FLIP-seq) or to co-capture full-length viral genome sequences in conjunction with its associated viral integration site (MIP-seq). This commentary aims to provide an overview on both FLIP-seq and MIP-seq, discuss their strengths and limitations, and outline specific chemistry and bioinformatics concerns when using these assays to study HIV persistence.https://www.mdpi.com/1999-4915/13/9/1874HIV genomesHIV persistencedeep sequencing |
| spellingShingle | Guinevere Q. Lee Chemistry and Bioinformatics Considerations in Using Next-Generation Sequencing Technologies to Inferring HIV Proviral DNA Genome-Intactness Viruses HIV genomes HIV persistence deep sequencing |
| title | Chemistry and Bioinformatics Considerations in Using Next-Generation Sequencing Technologies to Inferring HIV Proviral DNA Genome-Intactness |
| title_full | Chemistry and Bioinformatics Considerations in Using Next-Generation Sequencing Technologies to Inferring HIV Proviral DNA Genome-Intactness |
| title_fullStr | Chemistry and Bioinformatics Considerations in Using Next-Generation Sequencing Technologies to Inferring HIV Proviral DNA Genome-Intactness |
| title_full_unstemmed | Chemistry and Bioinformatics Considerations in Using Next-Generation Sequencing Technologies to Inferring HIV Proviral DNA Genome-Intactness |
| title_short | Chemistry and Bioinformatics Considerations in Using Next-Generation Sequencing Technologies to Inferring HIV Proviral DNA Genome-Intactness |
| title_sort | chemistry and bioinformatics considerations in using next generation sequencing technologies to inferring hiv proviral dna genome intactness |
| topic | HIV genomes HIV persistence deep sequencing |
| url | https://www.mdpi.com/1999-4915/13/9/1874 |
| work_keys_str_mv | AT guinevereqlee chemistryandbioinformaticsconsiderationsinusingnextgenerationsequencingtechnologiestoinferringhivproviraldnagenomeintactness |