Poonam Gupta, Arvind Rai, Charoo Hans, Mohammad Husain
{"title":"印度HIV-1 vpu快速进展者遗传多样性的观察研究","authors":"Poonam Gupta, Arvind Rai, Charoo Hans, Mohammad Husain","doi":"10.2174/1570162X21666230221152633","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>The genetic diversity in HIV-1 genes affects viral pathogenesis in HIV-1 positive patients. Accessory genes of HIV-1, including <i>vpu</i>, are reported to play a critical role in HIV pathogenesis and disease progression. <i>Vpu</i> has a crucial role in CD4 degradation and virus release. The sequence heterogeneity in the <i>vpu</i> gene may affect disease progression in patients, therefore, the current study was undertaken to identify the role of <i>vpu</i> in patients defined as rapid progressors.</p><p><strong>Objective: </strong>The objective of the study was to identify the viral determinants present on <i>vpu</i> that may be important in disease progression in rapid progressors.</p><p><strong>Methods: </strong>Blood samples were collected from 13 rapid progressors. DNA was isolated from PBMCs and <i>vpu</i> was amplified using nested PCR. Both strands of the gene were sequenced using an automated DNA Sequencer. The characterization and analysis of <i>vpu</i> was done using various bioinformatics tools.</p><p><strong>Results: </strong>The analysis revealed that all sequences had intact ORF and sequence heterogeneity was present across all sequences and distributed all over the gene. The synonymous substitutions, however, were higher than nonsynonymous substitutions. The phylogenetic tree analysis showed an evolutionary relationship with previously published Indian subtype C sequences. Comparatively, the cytoplasmic tail<sub>(77 - 86)</sub> showed the highest degree of variability in these sequences as determined by Entropy- one tool.</p><p><strong>Conclusion: </strong>The study showed that due to the robust nature of the protein, the biological activity of the protein was intact and sequence heterogeneity may promote disease progression in the study population.</p>","PeriodicalId":10911,"journal":{"name":"Current HIV Research","volume":"21 2","pages":"99-108"},"PeriodicalIF":0.8000,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"An Observational Study of Genetic Diversity of HIV-1 <i>vpu</i> in Rapid Progressors in India.\",\"authors\":\"Poonam Gupta, Arvind Rai, Charoo Hans, Mohammad Husain\",\"doi\":\"10.2174/1570162X21666230221152633\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>The genetic diversity in HIV-1 genes affects viral pathogenesis in HIV-1 positive patients. Accessory genes of HIV-1, including <i>vpu</i>, are reported to play a critical role in HIV pathogenesis and disease progression. <i>Vpu</i> has a crucial role in CD4 degradation and virus release. The sequence heterogeneity in the <i>vpu</i> gene may affect disease progression in patients, therefore, the current study was undertaken to identify the role of <i>vpu</i> in patients defined as rapid progressors.</p><p><strong>Objective: </strong>The objective of the study was to identify the viral determinants present on <i>vpu</i> that may be important in disease progression in rapid progressors.</p><p><strong>Methods: </strong>Blood samples were collected from 13 rapid progressors. DNA was isolated from PBMCs and <i>vpu</i> was amplified using nested PCR. Both strands of the gene were sequenced using an automated DNA Sequencer. The characterization and analysis of <i>vpu</i> was done using various bioinformatics tools.</p><p><strong>Results: </strong>The analysis revealed that all sequences had intact ORF and sequence heterogeneity was present across all sequences and distributed all over the gene. The synonymous substitutions, however, were higher than nonsynonymous substitutions. The phylogenetic tree analysis showed an evolutionary relationship with previously published Indian subtype C sequences. Comparatively, the cytoplasmic tail<sub>(77 - 86)</sub> showed the highest degree of variability in these sequences as determined by Entropy- one tool.</p><p><strong>Conclusion: </strong>The study showed that due to the robust nature of the protein, the biological activity of the protein was intact and sequence heterogeneity may promote disease progression in the study population.</p>\",\"PeriodicalId\":10911,\"journal\":{\"name\":\"Current HIV Research\",\"volume\":\"21 2\",\"pages\":\"99-108\"},\"PeriodicalIF\":0.8000,\"publicationDate\":\"2023-01-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Current HIV Research\",\"FirstCategoryId\":\"3\",\"ListUrlMain\":\"https://doi.org/10.2174/1570162X21666230221152633\",\"RegionNum\":4,\"RegionCategory\":\"医学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q4\",\"JCRName\":\"IMMUNOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Current HIV Research","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.2174/1570162X21666230221152633","RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"IMMUNOLOGY","Score":null,"Total":0}
An Observational Study of Genetic Diversity of HIV-1 vpu in Rapid Progressors in India.
Background: The genetic diversity in HIV-1 genes affects viral pathogenesis in HIV-1 positive patients. Accessory genes of HIV-1, including vpu, are reported to play a critical role in HIV pathogenesis and disease progression. Vpu has a crucial role in CD4 degradation and virus release. The sequence heterogeneity in the vpu gene may affect disease progression in patients, therefore, the current study was undertaken to identify the role of vpu in patients defined as rapid progressors.
Objective: The objective of the study was to identify the viral determinants present on vpu that may be important in disease progression in rapid progressors.
Methods: Blood samples were collected from 13 rapid progressors. DNA was isolated from PBMCs and vpu was amplified using nested PCR. Both strands of the gene were sequenced using an automated DNA Sequencer. The characterization and analysis of vpu was done using various bioinformatics tools.
Results: The analysis revealed that all sequences had intact ORF and sequence heterogeneity was present across all sequences and distributed all over the gene. The synonymous substitutions, however, were higher than nonsynonymous substitutions. The phylogenetic tree analysis showed an evolutionary relationship with previously published Indian subtype C sequences. Comparatively, the cytoplasmic tail(77 - 86) showed the highest degree of variability in these sequences as determined by Entropy- one tool.
Conclusion: The study showed that due to the robust nature of the protein, the biological activity of the protein was intact and sequence heterogeneity may promote disease progression in the study population.
期刊介绍：
Current HIV Research covers all the latest and outstanding developments of HIV research by publishing original research, review articles and guest edited thematic issues. The novel pioneering work in the basic and clinical fields on all areas of HIV research covers: virus replication and gene expression, HIV assembly, virus-cell interaction, viral pathogenesis, epidemiology and transmission, anti-retroviral therapy and adherence, drug discovery, the latest developments in HIV/AIDS vaccines and animal models, mechanisms and interactions with AIDS related diseases, social and public health issues related to HIV disease, and prevention of viral infection. Periodically, the journal invites guest editors to devote an issue on a particular area of HIV research of great interest that increases our understanding of the virus and its complex interaction with the host.
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