HIV epidemic and needs beyond fast-track cities: a transmission networks analysis to study the dynamic of HIV clusters in a French region near Paris

The Centre-Loire Valley region is a low-density demographic and medical region near the fast-track city of Paris, with persistent elevated rate of positive HIV testing. We investigated the role and characteristics of transmission clusters in the HIV dynamics in this region for appropriate local response. HIV pol gene sequences collected in Centre-Loire Valley over a decade (2010-2020) were included in a phylogenetic analysis combined with epidemiological data. Putative transmission clusters were inferred using HIV TRACE methods. Risk factors of being part of a cluster were studied using multivariate logistic regression models. Of the 1305 participants, 579 (44%) were born out of France, mainly from Sub-Saharan Africa, 494 (38%) were women, 433 (33%) men who have sex with men (MSM), 694 (53%) heterosexuals. Migrants had lower CD4 cell count at diagnosis than those born in France (296 vs 443, p< 0.01), likely due to delayed time to diagnosis. A total of 86 clusters were identified (clu..., Drug resistance genotyping was realized in the two specialized virology laboratories of the CLV region (903 from Tours and 402 from Orléans), by sequencing pol gene encoding HIV-1 reverse transcriptase (RT) and protease from patients’ plasma samples, using Sanger as previously described (Chaix M-L, Descamps D, Harzic M, et al. Stable prevalence of genotypic drug resistance mutations but increase in non-B virus among patients with primary HIV-1 infection in France. AIDS 2003; 17:2635–2643).
, ## HIV epidemic and needs beyond fast-track cities: a transmission networks analysis to study the dynamic of HIV clusters in a French region near Paris

This dataset includes HIV pol sequences isolated from 1305 adults who were followed at one of the hospitals in the Centre-Val de Loire region (France) between 2010 and 2020.
We have submitted our raw data as a fasta file (PHYLOVIH.fasta) and specimen information (PHYLOVIH_Metadata.csv).

## Description of the data and file structure

### PHYLOVIH.fasta

This fasta file includes 1305 Partial pol gene sequences. Each sequence is labeled with the participant's unique identifier.
For example: >VIH-000001 refers to participant 1 of the study.

### PHYLOVIH_Metadata.csv

* Sequence name : unique participant identifier (same identifier used in PHYLOVIH.fasta )
* Sample date : date of the blood sample  (month-year)
* Country : where the sample was taken (all samples from the study )
* Subtype : HIV-subtype determined by uploading sequences indi..., All subjects of this study gave their informed and written consent for the reuse of their anonymized data for research purposes. Metadata only contain sequence features but no identifying information (date of birth, home address or identification number). The clinical data of participants involved in clusters were not disclosed in order to minimise the risk of re-identification and stigmatisation of participants when communicating molecular clusters.