CROI 2016 Abstract eBook

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Poster Abstracts

gp41, gag , and/or pol -integrase sequences from 415 HIV-1 group M specimens, CRF02_AG accounted for 62.6% of HIV infections; 6 subtypes, 11 CRFs and 21 URFs were found. From 2010-2015, the prevalence of HTLV was 1% (95% confidence interval: 0.70-1.33) in the study population, with no significant effect of HIV co-infection. Sequence classification of the tat and/or gag region identified HTLV-1 (n=32), HTLV-2 (n=5), and HTLV-3 (n=1) infections. Conclusions: Our findings confirm that South Cameroon has a high burden of HIV infections and indicate a high level of HIV-1 and HTLV strain diversity in the region. Only 4 previous HTLV-3 infections have been reported, making our identification and sequencing of a new HTLV-3 infection of great significance. Likewise, the 2 HIV-1 group N infections we report are 9% of the 22 total group N infections reported and add to the limited sequence information available. Continued HIV/HTLV surveillance in South Cameroon will be essential to ensure diagnostic tests and HIV research keep pace with these rapidly evolving viruses. 213 Complete Genomes Reveal Complex HIV-1 Diversity in the Democratic Republic of Congo Mary A. Rodgers 1 ; Ana S.Vallari 1 ; Barbara Harris 1 ; Carole McArthur 2 ; Larry Sthreshley 3 ; Catherine Brennan 1 1 Abbott Lab, Abbott Park, IL, USA; 2 Univ of Missouri-Kansas City, Kansas City, MO, USA; 3 Presbyterian Church (USA), Kinshasa, Democratic Republic of Congo, Louisville, KY, USA Background: Surveillance of human immunodeficiency virus-1 (HIV-1) strain diversity is fundamental to collective efforts towards the prevention, diagnosis, and treatment of HIV-1 infections globally. However, limited surveillance has been conducted in the Democratic Republic of Congo (DRC), where a high level of strain diversity and intersubtype recombination has been reported. Since partial sequences may underrepresent recombination and diversity, complete genome sequencing is essential to improving HIV surveillance in the DRC. In this study we have sequenced the complete genomes of rare variant HIV-1 specimens from the DRC to meet neglected surveillance needs and to examine HIV-1 diversity. Methods: HIV-1 specimens were collected at two rural hospitals in the DRC between 2001-2003. Out of 172 HIV-1 specimens classified by phylogenetic analysis of the envelope immunodominant region sequence, 18 rare and unclassified subtypes were selected for next generation sequencing (NGS) using an established HIV-specific primer approach. The viral load for 9 of these specimens was less than 5 log 10 copies/ml, and NGS library preparation conditions were further optimized for these specimens. Genomes were assembled by aligning reads to references and de novo assembly using CLC Bio software. Strain classification was determined by phylogenetic and recombination analysis. Results: For low viral load specimens, the highest genome coverage was obtained by concentrating the total nucleic acid extract before reverse transcription at 42 o C using a SMART cDNA kit (Clontech). Genome sequences with >99.5% genome coverage, an average read depth of >10, and a sequence length of >9500 nucleotides were obtained for 14 HIV-1 specimens. The remaining four genomes had coverage of >60%. Phylogenetic and recombination analysis of the 14 complete genomes identified pure subtypes D (n=1), H (n=3), and CRF25 (n=1). The remaining genomes were simple recombinants of a single subtype with unclassified or CRF sequence (n=6), or complex recombinants of 4 or more subtypes, including A, G, H, K, and unclassified (n=3). Two of these complex recombinants shared 97% sequence identity. Conclusions: The sequence complexity of the reported genomes demonstrates a high level of diversity in HIV-1 strains circulating in the DRC. These complete genomes are a valuable contribution towards HIV-1 surveillance, and the complex recombinants will be useful for modeling the history of HIV-1 in the DRC. 214 HIV-2 Group A in France Displayed 2 Clades With Distinct Geographical Origins Benoit Visseaux 1 ; Charlotte Charpentier 1 ; Mélanie Bertine 1 ; Amel Besseghir 2 ; Catherine Fagard 3 ; Florence Damond 4 ; Sophie Matheron 4 ; Stephane Hue 5 ; Diane Descamps 4 ; for the ANRS CO5 HIV-2 cohort 1 INSERM UMR 1137, Paris, France; 2 Univ de Bordeaux, Bordeaux, France; 3 CMG-EC INSERM U897, Bordeaux, France; 4 Hosp Bichat-Claude Bernard, Paris, France; 5 London Sch of Hygiene & Trop Med, London, UK;

Background: Damond et al. 2000 showed that HIV-2 group A can be divided in two distinct genotypes. We analysed all the HIV-2 pol , env and vif sequences available in France to better characterise genetic variations between these two genotypes, analyse their relative prevalence in France and to explore a potential link with patient’s country of birth. Methods: Maximum likelihood phylogenetic trees were reconstructed from 446 HIV-2 partial pol (PR and RT; 1350 nt), 155 vif (655 nt) and 154 partial env (525 nt) sequences sampled from 386 patients followed up in France, using FastTree 2.1 under the GTR evolutionary model. Publically available sequences sampled outside of France were included for pol and vif fragments (207 and 22 sequences, respectively). Recombination analyses were conducted with the RDP4 software. Patients’ country of birth was retrieved for the patients included in the French ANRS CO5 HIV-2 cohort (n=272). Results: The group A formed two distinct and strongly supported clusters, herein called A1 and A2, in all trees (cf. Figure 1), suggestive of a past founder effect. Overall, 72% and 28% of the group A sequences belonged to cluster A1 and A2 respectively, with 20% of the latter being sampled in France. Among the 193 HIV-2 A sequences obtained from public databases 19 (10%) belong to clade A2. Inter-cluster median genetic distances were 0.12 [IQR=0.11-0.14], 0.12 [0.11-0.13] and 0.15 [0.12-0.18] substitutions/site for pol , vif and env , respectively. For the 163 viruses with more than one genetic region available, 17 (10%) presented inconsistent clade assignments across trees, suggesting potential recombination events. A1 viruses were most prevalent amongst patients born in coastal Western African countries (i.e. Senegal, Gambia, Guinea Bissau and Guinea) with 40 A1- and 8 A2-infected patients. Inversely, A2 strains were predominantly found among patients originating from inland Western countries such as Mali and Burkina Faso with 8 A1- and 29 A2-infected patients, suggesting distinct origins of the two clades. Sequences issued from patients born in Ivory-coast displayed a balanced prevalence of these clades with 13 A1- and 16 A2-infected patients). Conclusions: This study provides an enhanced understanding of the geographical and genetic diversity of HIV-2 group A. It highlights the co-circulation of two distinct clades in France that likely appeared from an ancient divergent event, followed by a founder effect explaining the distinct geographical patterns in Western Africa.

Poster Abstracts

82

CROI 2016