A Phylogenomic Analysis of HIV Transmission Pattern among High Risk Groups of North-West India

Background Molecular techniques can enhance the power of epidemiological investigations for tracing HIV transmission networks. This information could be useful for developing strategies for prevention of HIV transmission. Hence, we carried out to a study on the transmission patterns among newly diagnosed HIV cases among High-Risk Groups (HRGs) of North-West India using phylogenomic methods. Methods Phylogenomic analysis was carried out among 37 randomly selected samples of recently infected HRGs identified through Recent Infections Testing Algorithm (RITA) using Limiting Antigen Avidity Assay. Amplification of the reverse transcriptase region of pol gene (540 base pairs) and sequencing was done. Reference sequences were extracted from HIV Los Alamos database. Sequences aligned by Clustal W and HIV-1 subtype were determined on the basis of phylogenomic analysis of the pol sequence. Phylogenetic trees were constructed using the MEGA (version 11.0). Results The phylogeny clearly depicts that the study isolates RTFSWCHD and RTFSWPB007 cluster with and are related to the Indian reference sequences AY746371 and EU683781 and a Nepalese sequence KX430115.The other study isolates (RTFSWCHD001, RTFSWPB005, RTFSWCHD002, RTFSWPB006, RTFSWHR008, RTFSWHR 009) clustered uniquely among themselves without any interlinking with other references. One study isolate (RTFSWHP004) clustered closely with Zimbabwian isolate AY998351. The phylogeny shows that the study isolate MSMCHD005 clades separately with the Indian references (DQ838761, EU683781and AY746371), but is also very closely related to the references from China (HG421606, JQ658754), Nepal(JN023039) and Myanmar (N223216, JN223183, KC913773). Other study isolates (MSMCHD003, MSMHP007, MSMCHD004, MSMPB001, MSMPB002, and MSMHR006) are highly interrelated among themselves and form a separate unique clade together. The evolutionary tree shows that all the sequences from current study formed a monophyletic lineage, i.e., sequences from India clustered together more than with sequences from any other country. The study sequences showed relatedness only to the Nepal references KX430115 and JN023035. The South African, UK, Norway, China, and Myanmar references are grouped into aseparate clade. Conclusion Molecular epidemiologic methods were able to reveal transmission networks; hence, phylogenomic methods can be used in HIV Sentinel Surveillance to monitor transmission networks. ### Competing Interest Statement No competing interests ### Funding Statement None ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The study protocol was approved by the Institute Ethics Committee, Postgraduate Institute of Medical Education and Research, Chandigarh (HistoPath/14/2925/525; Date: 07/08/2014). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Yes available upon reasonable request to the authors