High frequency of HIV-1 infections with multiple HIV-1 strains in men having sex with men (MSM) in Senegal

Men Who Have Sex with Both Men and Women in West Africa: Factors Associated with a High Behavioral Risk of Acquiring HIV from Male Partners and Transmission to Women (CohMSM ANRS 12324-Expertise France)

HIV is highly prevalent in men who have sex with men (MSM) in West Africa. Many MSM in the region also have sex with women (MSMW). Accordingly, they are a potential bridge subpopulation for HIV transmission to women. We aimed to evaluate the proportions and characteristics of West African MSMW at high behavioral risk of acquiring HIV from male partners and transmitting it to female partners (HBRMF). The cohort ANRS-12324 CohMSM Study included 630 HIV-negative MSM in Burkina Faso, Cote d'Ivoire, Mali, and Togo. Among MSMW (i.e., with ≥ 1 female partner) in the cohort, HBRMF was identified using trajectory models based on seven at-risk sexual practices with male and female partners, including inconsistent condom use, multiple partnerships, and receptive same-sex anal intercourse. To assess the relevance of using trajectory models, we compared the proportions of participants who seroconverted during the cohort follow-up among those at HBRMF and those not at HBRMF. Factors associated with HBRMF were identified using a generalized estimation equation logistic regression model accounting for longitudinal data. Approximately half (47%) of the 304 MSMW (22% of all CohMSM study participants) were at HBRMF. This group accounted for 75% of the 28 HIV seroconversions observed during follow-up (p = 0.001). HBRMF was positively associated with being aged < 25 years (aOR 95% CI 1.67 [1.23-2.27]), being sexually attracted only to men (1.97 [1.38-2.78]), feelings of loneliness (1.92 [1.38-2.65]), and homonegative violence score (1.22 [1.05-1.41]). HBRMF was negatively associated with having had both stable and casual female partners in the previous 6 months (0.34 [0.20-0.60] vs. only a stable female partner). HBRMF tended to be negatively associated with having ≥ 4 sexual intercourses with female partners in the previous four weeks (0.54 [0.27-1.06] vs. no intercourse). Establishing official relationships with women might be a strategy for young and/or stigmatized MSMW to comply with social pressure to display a heterosexual lifestyle. However, this seems to increase the risk of HIV transmission to female partners. In the present study, almost half of MSMW were at HBRMF. This result stresses the need to adapt HIV research and prevention to MSMW and their female partners.

Multiple Infection and Human Immunodeficiency Virus Superinfection Among Persons who Inject Drugs in Indonesia and Ukraine

BACKGROUND

The HIV Prevention Trials Network (HPTN) 074 study evaluated an integrated human immunodeficiency virus (HIV) treatment and prevention strategy among persons who inject drugs (PWID) in Indonesia, Ukraine, and Vietnam. We previously detected multiple HIV infection in 3 of 7 (43%) of seroconverters with 3-8 HIV strains per person. In this report, we analyzed multiple HIV infection and HIV superinfection (SI) in the HPTN 074 cohort.

METHODS

We analyzed samples from 70 participants in Indonesia and Ukraine who had viral load >400 copies/mL at enrollment and the final study visit (median follow-up, 2.5 years). HIV was characterized with Sanger sequencing, next-generation sequencing, and phylogenetic analysis. Additional methods were used to characterize a rare case of triple-variant SI.

RESULTS

At enrollment, multiple infection was detected in only 3 of 58 (5.2%) participants with env sequence data. SI was detected in only 1 of 70 participants over 172.3 person-years of follow-up (SI incidence, 0.58/100 person-years [95% confidence interval, .015-3.2]). The SI case involved acquisition of 3 HIV strains with rapid selection of a strain with a single pol region cluster.

CONCLUSIONS

These data from a large cohort of PWID suggest that intrahost viral selection and other factors may lead to underestimation of the frequency of multiple HIV infection and SI events.

The Role of Phylogenetics in Discerning HIV-1 Mixing among Vulnerable Populations and Geographic Regions in Sub-Saharan Africa: A Systematic Review

To reduce global HIV-1 incidence, there is a need to understand and disentangle HIV-1 transmission dynamics and to determine the geographic areas and populations that act as hubs or drivers of HIV-1 spread. In Sub-Saharan Africa (sSA), the region with the highest HIV-1 burden, information about such transmission dynamics is sparse. Phylogenetic inference is a powerful method for the study of HIV-1 transmission networks and source attribution. In this review, we assessed available phylogenetic data on mixing between HIV-1 hotspots (geographic areas and populations with high HIV-1 incidence and prevalence) and areas or populations with lower HIV-1 burden in sSA. We searched PubMed and identified and reviewed 64 studies on HIV-1 transmission dynamics within and between risk groups and geographic locations in sSA (published 1995-2021). We describe HIV-1 transmission from both a geographic and a risk group perspective in sSA. Finally, we discuss the challenges facing phylogenetic inference in mixed epidemics in sSA and offer our perspectives and potential solutions to the identified challenges.

Haploflow: Strain-resolved de novo assembly of viral genomes

In viral infections often multiple related viral strains are present, due to coinfection or within-host evolution. We describe Haploflow, a de Bruijn graph-based assembler for de novo genome assembly of viral strains from mixed sequence samples using a novel flow algorithm. We assessed Haploflow across multiple benchmark data sets of increasing complexity, showing that Haploflow is faster and more accurate than viral haplotype assemblers and generic metagenome assemblers not aiming to reconstruct strains. Haplotype reconstructed high-quality strain-resolved assemblies from clinical HCMV samples and SARS-CoV-2 genomes from wastewater metagenomes identical to genomes from clinical isolates.

High HIV burden and recent transmission chains in rural forest areas in southern Cameroon, where ancestors of HIV-1 have been identified in ape populations

We studied HIV prevalence and genetic diversity in rural forest areas in Cameroon, where chimpanzee and gorilla populations infected with the ancestors of the different HIV-1 groups have been identified and transmitted to humans during the 20th century. A total of 2812 individuals were studied, 924 from south-central, 1116 from south-east and 772 from south-west Cameroon. Of 208 (7.4%) samples that were confirmed for HIV-1 infection all belong to HIV-1 group M. In all sites and in all age categories, HIV-1 prevalence was higher in women (160/1599 (10.0%)) as compared to men (48/1213 (4.0%)) with the highest prevalence in women aged between 25 and 34 years (>17%). For 188/208 (92.3%) HIV-1 positive individuals, a fragment of the pol gene was successfully amplified and sequenced. Phylogenetic analysis showed predominance of CRF02_AG (58%), a large diversity of subtypes (A, D, F2 and G), nine different CRFs and more than 12% URFs. Interestingly, 35/188 (18.6%) HIV-1 strains form 12 recent transmission chains. The majority of the clusters are composed of two (n = 8) or three (n = 3) sequences but one cluster included ten HIV-1 strains from women living in four different villages on a major road for logging concessions in the south-east (60 km distance). In the three regions of Cameroon where the ancestors of the four HIV-1 groups have been transmitted to humans, we observed a high HIV prevalence, especially in the southeast where HIV-1 M originated. Many factors allowing rapid establishment in the human population and subsequent rapid spread to urban areas of a new retrovirus or other pathogens of zoonotic origin are now present. Our study shows clearly that some rural areas should also be considered as hot-spots for HIV infection. Prevention efforts together with growing access to HIV diagnosis and antiretroviral treatment are urgently needed in these remote areas.

A case report of HIV-1 superinfection in an HIV controller leading to loss of viremia control: a retrospective of 10 years of follow-up

Background

HIV controllers (HICs) are a rare group of HIV-1-infected individuals able to naturally control viral replication. Several studies have identified the occurrence of HIV dual infections in seropositive individuals leading to disease progression. In HICs, however, dual infections with divergent outcomes in pathogenesis have been described.

Case presentation

Here, we present a case report of a HIC diagnosed in late 1999 who displayed stable CD4⁺ T cell levels and low plasmatic viral load across 12 years of follow-up. In early 2013, the patient started to present an increase in viral load, reaching a peak of 10,000 copies/ml in early 2014, followed by an oscillation of viremia at moderate levels in the following years. The genetic diversity of env proviral quasispecies from peripheral blood mononuclear cells (PBMCs) was studied by single genome amplification (SGA) at six timepoints across 2009–2017. Phylogenetic analyses of env sequences from 2009 and 2010 samples showed the presence of a single subtype B variant (called B₁). Analyses of sequences from 2011 and after revealed an additional subtype B variant (called B₂) and a subsequent dominance shift in the proviral quasispecies frequencies, with the B₂ variant becoming the most frequent from 2014 onwards. Latent syphilis related to unprotected sexual intercourse was diagnosed a year before the first detection of B_2, evidencing risk behavior and supporting the superinfection hypothesis. Immunologic analyses revealed an increase in CD8⁺ and CD4⁺ T cell immune activation following viremia increase and minor T cell subset alterations during follow-up. HIV-specific T cell responses remained low throughout the follow-up period.

Conclusions

Altogether, these results show that loss of viremia control in the HIC was associated with superinfection. These data alert to the negative consequences of reinfection on HIV pathogenesis, even in patients with a long history of viremia control and an absence of disease progression, reinforcing the need for continued use of adequate prevention strategies.

HIV controllers suppress viral replication and evolution and prevent disease progression following intersubtype HIV-1 superinfection

OBJECTIVE

The aim of this study was to investigate the impact of intersubtype HIV-1 superinfection on viremia, reservoir reseeding, viral evolution and disease progression in HIV controllers (HIC).

DESIGN

A longitudinal analysis of two Brazilian HIC individuals (EEC09 and VC32) previously identified as dually infected with subtypes B and F1 viruses.

METHODS

Changes in plasma viremia, total HIV-1 DNA levels, CD4+ T-cell counts and HIV-1 quasispecies composition were measured over time. HIV-1 env diversity in peripheral blood mononuclear cell (PBMC) and plasma samples was accessed by single genome amplification and next-generation sequencing approaches, respectively. Viral evolution was evaluated by estimating nucleotide diversity and divergence.

RESULTS

Individual EEC09 was probably initially infected with a CCR5-tropic subtype B strain and sequentially superinfected with a CXCR4-tropic subtype B strain and with a subtype F1 variant. Individual VC32 was infected with a subtype B strain and superinfected with a subtype F1 variant. The intersubtype superinfection events lead to a moderate increase in viremia and extensive turnover of viral population in plasma but exhibited divergent impact on the size and composition of cell-associated HIV DNA population. Both individuals maintained virologic control (<2000 copies/ml) and presented no evidence of viral evolution or immunologic progression for at least 2 years after the intersubtype superinfection event.

CONCLUSION

These data revealed that some HIC are able to repeatedly limit replication and evolution of superinfecting viral strains of a different subtype with no signs of disease progression.

Genetic diversity and transmission networks of HIV-1 strains among men having sex with men (MSM) in Lomé, Togo

Understanding the HIV epidemic in key populations is important. Today only scarce information is available on HIV-1 strains that circulate in men having sex with men (MSM) in sub-Saharan Africa. Here, we studied for the first time the genetic diversity of HIV-1 strains circulating in the MSM population in Lomé, the capital city from Togo. The overall subtype/CRF distribution in pol (protease and/or partial reverse transcriptase (RT)) among the 79 HIV-1 strains from MSM was as follows: CRF02_AG (72%, n=57), subtype G (2.5%, n=2), sub-subtype A3 (1.3%, n=1), and unique recombinant forms (URF) (24%, n=19). Among the 19 URFs four different mosaic structures were observed, annotated as URF1 to URF4. Fifteen sequences (URF1) had the same mosaic structure in pol (G/CRF02_AG) and could represent a new circulating recombinant form (CRF). Phylogenetic analysis of the RT sequences showed that there were several introductions of CRF02_AG strains in the MSM population, however half of the CRF02_AG and all URF1 strains formed a separate, well-supported cluster suggesting one major introduction of CRF02_AG in the MSM population followed by efficient transmission and emergence of a possible new CRF. At least 40% of the strains fell into recent transmission chains involving two to seven MSM. Comparison with >950 HIV-1 sequences from previous studies in Togo showed intermixing of the HIV-1 epidemics between MSM and the general population. Moreover, an HIV-1 strain from a recently HIV-1 infected male patient from Germany, fell within a cluster of HIV-1 strains from MSM from Togo, illustrating recent exchange between MSM from Africa and people from other geographic regions. With growing evidence of the importance of MSM in the dynamic of the HIV epidemic in Africa there is an urgent need for appropriate interventions to limit HIV transmission in this population group.

Phage and Yeast Display

Despite the availability of antimicrobial drugs, the continued development of microbial resistance--established through escape mutations and the emergence of resistant strains--limits their clinical utility. The discovery of novel, therapeutic, monoclonal antibodies (mAbs) offers viable clinical alternatives in the treatment and prophylaxis of infectious diseases. Human mAb-based therapies are typically nontoxic in patients and demonstrate high specificity for the intended microbial target. This specificity prevents negative impacts on the patient microbiome and avoids driving the resistance of nontarget species. The in vitro selection of human antibody fragment libraries displayed on phage or yeast surfaces represents a group of well-established technologies capable of generating human mAbs. The advantage of these forms of microbial display is the large repertoire of human antibody fragments present during a single selection campaign. Furthermore, the in vitro selection environments of microbial surface display allow for the rapid isolation of antibodies--and their encoding genes--against infectious pathogens and their toxins that are impractical within in vivo systems, such as murine hybridomas. This article focuses on the technologies of phage display and yeast display, as these strategies relate to the discovery of human mAbs for the treatment and vaccine development of infectious diseases.

Worldwide Genetic Features of HIV-1 Env α4β7 Binding Motif: The Local Dissemination Impact of the LDI Tripeptide

BACKGROUND

HIV-1 gp120 binds to integrin α4β7, a homing receptor of lymphocytes to gut-associated lymphoid tissues. This interaction is mediated by the LDI/V tripeptide encoded in the V2-loop. This tripeptide mimics similar motifs in mucosal addressin cellular adhesion molecule (MAdCAM) and vascular CAM (VCAM), the natural ligands of α4β7. In this study, we explored the association of V2-loop LDI/V mimotopes with transmission routes and patterns of disease progression in HIV-infected adult and pediatric patients. HIV-1 env sequences available in the Los Alamos HIV Sequence database were included in the analyses.

METHODS

HIV-1 V2-loop sequences generated from infected adults and infants from South and Southeast Brazil, and also retrieved from the Los Alamos database, were assessed for α4β7 binding tripeptide composition. Chi-Square/Fisher Exact test and Mann Whitney U test were used for tripeptide comparisons. Shannon entropy was assessed for conservancy of the α4β7 tripeptide mimotope.

RESULTS

We observed no association between the tripeptide composition or conservation and virus transmission route or disease progression. However, LDI was linked to successful epidemic dissemination of HIV-1 subtype C in South America, and further to other expanding non-B subtypes in Europe and Asia. In Africa, subtypes showing increased LDV prevalence evidenced an ongoing process of selection toward LDI expansion, an observation also extended to subtype B in the Americas and Western Europe.

CONCLUSIONS

The V2-loop LDI mimotope was conserved in HIV-1C from South America and other expanding subtypes across the globe, which suggests that LDI may promote successful dissemination of HIV at local geographic levels by means of increased transmission fitness.

"In the fell clutch of circumstance": HIV and men who have sex with men in sub-Saharan Africa

Men who have sex with men (MSM) in sub-Saharan Africa (SSA) have been repeatedly found to have high risk of HIV infection, and in spite of the differing nature of the HIV epidemic in the general population between East and Southern Africa, and West and Central Africa, MSM are disproportionately affected by HIV across the entire region. Recent research has examined the drivers of HIV risk, and the dynamics of the MSM HIV epidemic in greater detail. However, this growing knowledge has generally not been translated into effective HIV prevention interventions. In part, this is due to the highly stigmatised and frequently criminalised nature of same-sex sexualities in much of the region. Without human-rights-based advocacy targeting governments and interventions aiming to decrease stigma and homophobia, translating research into effective HIV interventions for MSM in SSA at the scale needed to reduce HIV transmission in this population remains highly unlikely.

Short Communication: Investigating a Chain of HIV Transmission Events Due to Homosexual Exposure and Blood Transfusion Based on a Next Generation Sequencing Method

This study investigates a chain of HIV transmission events due to homosexual exposure and blood transfusion in China. The MiSeq platform, a next generation sequencing (NGS) system, was used to obtain genetic details of the HIV-1 env region (336 base pairs). Evolutionary analysis combined with epidemiologic evidence suggests a transmission chain from patient T3 to T2 through homosexual exposure and subsequently to T1 through blood transfusion. More importantly, a phylogenetic study suggested a likely genetic bottleneck for HIV in homosexual transmission from T3 to T2, while T1 inherited the majority of variants from T2. The result from the MiSeq platform is consistent with findings from the epidemiologic survey. The MiSeq platform is a powerful tool for tracing HIV transmissions and intrapersonal evolution.

HIV and STI prevalence and risk factors among male sex workers and other men who have sex with men in Nairobi, Kenya

: Previous surveys of men who have sex with men (MSM) in Africa have not adequately profiled HIV status and risk factors by sex work status. MSM in Nairobi, Kenya, were recruited using respondent-driven sampling, completed a behavioral interview, and were tested for HIV and sexually transmitted infections. Overlapping recruitment among 273 male sex workers and 290 other MSM was common. Sex workers were more likely to report receptive anal sex with multiple partners (65.7% versus 18.0%, P < 0.001) and unprotected receptive anal intercourse (40.0% versus 22.8%, P = 0.005). Male sex workers were also more likely to be HIV infected (26.3% versus 12.2%, P = 0.007).