Molecular Epidemiology Of HIV-1 Research Articles

User experience with HIV molecular epidemiology in research, surveillance, and cluster detection and response: a needs assessment

Objective HIV molecular epidemiology (HIV ME) is a tool that aims to improve HIV research, surveillance, and cluster detection and response. HIV ME is a core pillar of the U.S. initiative to End the HIV Epidemic but faces some challenges and criticisms from stakeholders. We sought to assess user experience to identify the current needs for HIV ME. Methods Users of HIV ME, including researchers and public health practitioners, were engaged via a structured survey. Needs were assessed via open-ended questions about HIV ME. Data were analyzed using reflexive thematic analysis; the concordance of results was assessed semi-quantitatively. Results Of 90 possible HIV-ME end-users, 57 completed the survey (response rate = 63%), which included users engaged in research (n = 29) and public health (n = 28). Respondents identified current imperatives, challenges, and strategies to improve HIV ME. Imperatives included characterization of the virus, identification of HIV hotspots, and tailoring of HIV interventions. Challenges encompassed technological issues, ethical concerns, and implementation difficulties. Strategies to improve HIV ME involved improving data access and analysis, enhancing implementation guidance and resources, and fostering community engagement and support. Researchers and public health practitioners prioritized different imperatives, but similarly emphasized the ethical concerns with HIV ME. Conclusion The imperatives identified by users underscore the necessity of HIV ME, while the challenges highlight the hurdles to be overcome, including ethical concerns which emerged as a shared emphasis across user groups. The strategies outlined offer a roadmap for overcoming these challenges. These insights, drawn from user experience, present a valuable opportunity to inform the development of guidelines for the ethical application of HIV ME in research, surveillance, and cluster detection and response.

Human Immunodeficiency Virus Type-1 Genetic Diversity and Drugs Resistance Mutations among People Living with HIV in Karachi, Pakistan.

The human immunodeficiency virus type-1 epidemic in Pakistan has significantly increased over the last two decades. In Karachi, Pakistan, there is a lack of updated information on the complexity of HIV-1 genetic diversity and the burden of drug resistance mutations (DRMs) that can contribute to ART failure and poor treatment outcomes. This study aimed to determine HIV-1 genetic diversity and identify drug-resistance mutations among people living with HIV in Karachi. A total of 364 HIV-positive individuals, with a median age of 36 years, were enrolled in the study. The HIV-1 partial pol gene was successfully sequenced from 268 individuals. The sequences were used to generate phylogenetic trees to determine clade diversity and also to assess the burden of DRMs. Based on the partial pol sequences, 13 distinct HIV-1 subtypes and recombinant forms were identified. Subtype A1 was the most common clade (40%), followed by CRF02_AG (33.2%). Acquired DRMs were found in 30.6% of the ART-experienced patients, of whom 70.7%, 20.7%, and 8.5% were associated with resistance to NNRTIs, NRTIs, and PIs, respectively. Transmitted DRMs were found in 5.6% of the ART-naïve patients, of whom 93% were associated with resistance against NNRTIs and 7% to PIs. The high prevalence of DRMs in ART-experienced patients poses significant challenges to the long-term benefits and sustainability of the ART program. This study emphasizes the importance of continuous HIV molecular epidemiology and drug resistance surveillance to support evidence-based HIV prevention, precise ART, and targeted AIDS care.

Prioritization of ethical concerns regarding HIV molecular epidemiology by public health practitioners and researchers

BackgroundHIV molecular epidemiology (HIV ME) can support the early detection of emerging clusters of new HIV infections by combining HIV sequence data routinely obtained during the clinical treatment of people living with HIV with behavioral, geographic, and sociodemographic information. While information about emerging clusters promises to facilitate HIV prevention and treatment efforts, the use of this data also raises several ethical concerns. We sought to assess how those working on the frontlines of HIV ME, specifically public health practitioners (PHPs) and researchers, prioritized these issues.MethodsEthical issues were identified through literature review, qualitative in-depth interviews, and stakeholder engagement. PHPs and researchers using HIV ME prioritized the issues using best–worst scaling (BWS). A balanced incomplete block design was used to generate 11 choice tasks each consisting of a sub-set of 5 ethical concerns. In each task, respondents were asked to assess the most and least concerning issue. Data were analyzed using conditional logit, with a Swait-Louviere test of poolability. Latent class analysis was then used to explore preference heterogeneity.ResultsIn total, 57 respondents completed the BWS experiment May–June 2023 with the Swait-Louviere test indicating that researchers and PHPs could be pooled (p = 0.512). Latent class analysis identified two classes, those highlighting “Harms” (n = 29) (prioritizing concerns about potential risk of legal prosecution, individual harm, and group stigma) and those highlighting “Utility” (n = 28) (prioritizing concerns about limited evidence, resource allocation, non-disclosure of data use for HIV ME, and the potential to infer the directionality of HIV transmission). There were no differences in the characteristics of members across classes.ConclusionsThe ethical issues of HIV ME vary in importance among stakeholders, reflecting different perspectives on the potential impact and usefulness of the data. Knowing these differences exist can directly inform the focus of future deliberations about the policies and practices of HIV ME in the United States.

HBV and HCV Co-Infection in Chinese Newly Diagnosed HIV+ Subjects in 2015 and 2023: A Cross-Sectional Study.

With shared routes of transmission, HBV and HCV co-infection are estimated to occur more in subjects with HIV. This study aimed to characterize and describe the prevalence of HBV and HCV co-infections in a cohort of newly diagnosed HIV+ subjects living in China. We conducted a cross-sectional study among newly diagnosed HIV+ subjects aged 18-100 who participated in surveys on the national HIV molecular epidemiology in 2015 and 2023. (The epidemiological table survey is located in the national database alongside serologic testing). The chi-square test was used to identify changes in infections between the studying populations in 2015 and 2023, and conditional logistic regression models were fit to identify risk factors for each co-infection. Among the 11,024 newly diagnosed HIV+ subjects who were surveyed (n = 4501 in 2015; n = 6523 in 2023), the prevalence of HBV, HCV, and HBV/HCV in 2023 was lower than that in 2015, respectively. No decrease was observed in HCV co-infection in men who had sex with men (MSM) in North China, Northeast China, and East China. Increasing recognition among those at high risk of heterosexual transmission and those with low educational backgrounds is paramount to the prevention and control of HIV/HBV/HCV infections.

Molecular epidemiology of HIV among people who inject drugs after the HIV-outbreak in Athens, Greece: Evidence for a ‘slow burn’ outbreak

BackgroundNew diagnoses of HIV-1 infection among people who inject drugs (PWID) in Athens, Greece, saw a significant increase in 2011 and a subsequent decline after 2013. Despite this, ongoing HIV-1 transmission persisted from 2014 to 2020 within this population. Our objective was to estimate the time of infection for PWID in Athens following the HIV-1 outbreak, explore the patterns of HIV-1 dispersal over time, and determine the duration from infection to diagnosis. MethodsTime from HIV-1 infection to diagnosis was estimated for 844 individuals infected within 4 PWID-specific clusters and for 8 PWID infected with sub-subtype A6 diagnosed during 2010–2019. Phylogeny reconstruction was performed using the maximum-likelihood method. HIV-1 infection dates were based on molecular clock calculations. ResultsIn total 86 of 92 (93.5%) sequences from PWID diagnosed during 2016–2019 were either related to the previously identified PWID-specific clusters (n = 81) or belonged to a new A6 cluster (n = 5). The median time between infection and diagnosis was 0.42 years during the outbreak period and 0.70 years during 2016–2019 (p < 0.001). The proportion of clustered sequences from PWID was very low at 5.3% during the pre-outbreak period (1998–2009), saw an increase to 41.7% one year before the outbreak in 2010, and consistently remained high during the whole period after 2011, spanning the post-outbreak period (2016–2019) with a range from 92.9% to 100%. ConclusionsThe substantial proportion of clustered infections (93.5%) during 2016–2019 implies a persistent ‘slow burn’ HIV outbreak among PWID in Athens, suggesting that the outbreak was not successfully eliminated. The consistently high proportion of clustered sequences since the onset of the outbreak suggests the persistence of ongoing HIV-1 transmission attributed to injection practices. Our findings underscore the importance of targeted interventions among PWID, considering the ongoing transmission rate and prolonged time from infection to diagnosis.

Assessing transmission attribution risk from simulated sequencing data in HIV molecular epidemiology.

HIV molecular epidemiology (ME) is the analysis of sequence data together with individual-level clinical, demographic, and behavioral data to understand HIV epidemiology. The use of ME has raised concerns regarding identification of the putative source in direct transmission events. This could result in harm ranging from stigma to criminal prosecution in some jurisdictions. Here we assessed the risks of ME using simulated HIV genetic sequencing data. We simulated social networks of men-who-have-sex-with-men, calibrating the simulations to data from San Diego. We used these networks to simulate consensus and next-generation sequence (NGS) data to evaluate the risks of identifying direct transmissions using different HIV sequence lengths, and population sampling depths. To identify the source of transmissions, we calculated infector probability and used phyloscanner software for the analysis of consensus and NGS data, respectively. Consensus sequence analyses showed that the risk of correctly inferring the source (direct transmission) within identified transmission pairs was very small and independent of sampling depth. Alternatively, NGS analyses showed that identification of the source of a transmission was very accurate, but only for 6.5% of inferred pairs. False positive transmissions were also observed, where one or more unobserved intermediaries were present when compared to the true network. Source attribution using consensus sequences rarely infers direct transmission pairs with high confidence but is still useful for population studies. In contrast, source attribution using NGS data was much more accurate in identifying direct transmission pairs, but for only a small percentage of transmission pairs analyzed.

Distinct genetic clusters in HIV-1 CRF01_AE-infected patients induced variable degrees of CD4+ T-cell loss.

Retroviruses swiftly adapt, employing error-prone enzymes for genetic and phenotypic evolution, optimizing survival strategies, and enhancing virulence levels. HIV-1 CRF01_AE has persistently undergone adaptive selection, and cluster 1 and 2 infections display lower counts and fast loss of CD4+ T cells than other HIV-1 sub-types and CRF01_AE clusters. Its mechanisms are associated with increased CXCR4 tropism due to an envelope structure change favoring a tropism shift from CCR5 to CXCR4, thereby shaping viral phenotype features and impacting pathogenicity. This underscores the significance of consistently monitoring HIV-1 genetic evolution and phenotypic transfer to see whether selection bias across risk groups alters the delicate balance of transmissible versus toxic trade-offs, since virulent strains such as CRF01_AE clusters 1 and 2 could seriously compromise the efficacy of antiviral treatment. Only through such early warning and diagnostic services can precise antiviral treatments be administered to those infected with more virulent HIV-1 strains.

Developing a next level integrated genomic surveillance: Advances in the molecular epidemiology of HIV in Germany

Advances in the molecular epidemiological studies of the Human Immunodeficiency Virus (HIV) at the Robert Koch Institute (RKI) by laboratory and bioinformatic automation should allow the processing of larger numbers of samples and more comprehensive and faster data analysis in order to provide a higher resolution of the current HIV infection situation in near real-time and a better understanding of the dynamic of the German HIV epidemic. The early detection of the emergence and transmission of new HIV variants is important for the adaption of diagnostics and treatment guidelines. Likewise, the molecular epidemiological detection and characterization of spatially limited HIV outbreaks or rapidly growing sub-epidemics is of great importance in order to interrupt the transmission pathways by regionally adapting prevention strategies. These aims are becoming even more important in the context of the SARS-CoV2 pandemic and the Ukrainian refugee movement, which both have effects on the German HIV epidemic that should be monitored to identify starting points for targeted public health measures in a timely manner. To this end, a next level integrated genomic surveillance of HIV is to be established.

Identification of new circulating recombinant form of HIV-1 CRF139_02B in Japan, and search for the origin.

Many circulating recombinant forms (CRFs) of HIV-1 have been reported, resulting in complex molecular epidemiology of HIV-1 infection. In this study, we newly identified CRF139_02B in Japan from 4 cases of anti-retroviral therapy naïve people living with HIV. Near full-length genome sequences of CRF139_02B were determined using Illumina MiSeq. Basic Local Alignment Search Tool (BLAST) revealed that there were several sequences having the same breakpoints as CRF139_02B in the UK and Nepal, though its full-length genome sequences were not available. Maximum clade credibility tree analysis using the region of protease and reverse transcriptase of HIV- 1 estimated that the time to the most recent common ancestor of CRF139_02B variants found in Japan was 2017.6 (95% highest posterior density interval: 2015.9-2019.3), and that among the UK, Nepal, and Japan was 2010.4 (2007.8- 2012.5). These results suggested that CRF139_02B circulated in Japan recently and domestically. Furthermore, the origin of CRF139_02B could be in the UK. Because there is a possibility that further international circulation of CRF139_02B may be observed in the near future, continuous monitoring of HIV-1 molecular epidemiology will be needed.

The molecular epidemiology of HIV-1 in Sweden 1996 to 2022, and the influence of migration from Ukraine.

BackgroundThe global distribution of HIV-1 subtypes is evolving, which is reflected in the Swedish HIV cohort. The subtype HIV-1A6, which may be prone to developing resistance to cabotegravir, is the most common subtype in Ukraine.AimWe aimed to examine trends in HIV-1 subtype distribution in Sweden, with a special focus on HIV-1A6, and to describe the virology, demography and treatment of Ukrainian people living with HIV (PLWH) who migrated to Sweden in 2022.MethodsData about PLWH in Sweden are included in a national database (InfCareHIV). We used the online tool COMET to establish HIV-1 subtypes and the Stanford database to define drug resistance mutations. We investigated the relation between virological characteristics and demographic data.ResultsThe early epidemic was predominated by HIV-1 subtype B infections in people born in Sweden. After 1990, the majority of new PLWH in Sweden were PLWH migrating to Sweden, resulting in an increasingly diverse epidemic. In 2022, HIV-1A6 had become the sixth most common subtype in Sweden and 98 of the 431 new PLWH that were registered in Sweden came from Ukraine. We detected HIV RNA in plasma of 32 Ukrainian patients (34%), of whom 17 were previously undiagnosed, 10 had interrupted therapy and five were previously diagnosed but not treated. We found HIV-1A6 in 23 of 24 sequenced patients.ConclusionThe molecular HIV epidemiology in Sweden continues to diversify and PLWH unaware of their HIV status and predominance of HIV-1A6 should be considered when arranging care directed at PLWH from Ukraine.

2899. Integrating HIV Partner Services and Molecular Epidemiology Data to Enhance HIV Transmission Disruption in Rhode Island: Findings from a Public Health-Academic Partnership

Abstract Background HIV remains a significant public health concern. Both contact tracing (identifying and notifying partners of people diagnosed with HIV) and molecular epidemiology (phylogenetic inference and cluster detection), are used to disrupt transmission. Integration of both modalities may be synergistic, though it is not evaluated or implemented routinely. Methods To assess whether integrating HIV contact tracing and molecular epidemiology data are more informative for public health than using each separately, we evaluated concordance between a statewide public health contact tracing database (CTDB) collected in 2008-2021 and handled by the Rhode Island Department of Health, and a statewide individual-level HIV-1 pol sequence database (SDB) collected in 2004-2021 by Brown University investigators. Molecular clusters were identified using at least one of seven common phylogenetic methods. Concordance (overlap in persons appearing in both databases) was evaluated using the Jaccard Similarity Coefficient (JSC). Results The CTDB included disease intervention specialist interview data from 2469 unique persons (2468 newly diagnosed; 1458 named partners) and the SDB included sequences from 3266 persons. There were 920 persons who appeared in both databases, while 2346/3266 (72%) appeared in the SDB but not CTDB, and 1549/2469 (63%) appeared in the CTDB but not SDB. Of the 351 molecular clusters identified, 156 (44%) consisted of persons also in the CTDB. The JSC between the SDB and CTDB was 0.19. Of the 920 persons in both databases, 509 newly diagnosed persons provided partner data and 63% (320/509) of those clustered phylogenetically. Of the 156 named partners of these 509, 76% (118/156) clustered phylogenetically. Cluster sizes ranged from 2-31 (mean = 3.4), of which a mean of 0.20 partners were named in the CTDB. Conclusion Integration between molecular epidemiology and contact tracing data may be synergistic to disrupt HIV transmission given the only moderate concordance between them. The existing concordance between the databases allows better characterization of the local HIV epidemic, while the discordance suggests data incompleteness in both databases, informing public health towards investigations to disrupt transmission. Disclosures All Authors: No reported disclosures

High Diversity and Transmission Dynamics of HIV-1 Non-C Subtypes in Bangladesh.

Genetic diversity and molecular epidemiology of HIV are directly relevant to HIV transmission. We report here the genetic diversity and transmission dynamics of non-C subtypes of HIV-1 strains detected in Bangladeshi key populations. Sequence analysis of gag gene revealed four subtypes A1, B, D, G, and nine CRFs (01_AE, 02_AG, 09_cpx, 10_CD, 15_AE/B, 13_cpx, 14_BG, 22_01_A1, and 25_AGU). Most of these non-C strains were detected in returnee migrant workers from different parts of the world. Phylogenetic analysis showed that the Bangladeshi HIV-1 strains detected in migrant workers and their wives and local sex workers shared common ancestries. The identification of the multiple subtypes indicates high diversity of non-C HIV-1 variants circulating in Bangladesh which might have been imported by migrant workers from multiple geographical areas.

High-Level Drug-Resistant Mutations among HIV-1 Subtype A6 and CRF02_AG in Kazakhstan.

HIV incidence in Kazakhstan increased by 73% between 2010 and 2020, with an estimated 35,000 people living with HIV (PLHIV) in 2020. The development of antiretroviral drug resistance is a major threat to effective antiretroviral therapy (ART), yet studies on the prevalence of drug resistance in Kazakhstan are sparse. In this study on the molecular epidemiology of HIV in Kazakhstan, we analyzed 968 partial HIV-1 pol sequences that were collected between 2017 and 2020 from PLHIV across all regions of Kazakhstan, covering almost 3% of PLHIV in 2020. Sequences predominantly represented subtypes A6 (57%) and CRF02_AG (41%), with 32% of sequences exhibiting high-level drug resistance. We further identified distinct drug-resistant mutations (DRMs) in the two subtypes: subtype A6 showed a propensity for DRMs A62V, G190S, K101E, and D67N, while CRF02_AG showed a propensity for K103N and V179E. Codon usage analysis revealed that different mutational pathways for the two subtypes may explain the difference in G190S and V179E frequencies. Phylogenetic analysis highlighted differences in the timing and geographic spread of both subtypes within the country, with A62V-harboring subtype A6 sequences clustering on the phylogeny, indicative of sustained transmission of the mutation. Our findings suggest an HIV epidemic characterized by high levels of drug resistance and differential DRM frequencies between subtypes. This emphasizes the importance of drug resistance monitoring within Kazakhstan, together with DRM and subtype screening at diagnosis, to tailor drug regimens and provide effective, virally suppressive ART.

Brief Report: Challenges in Obtaining the Informed Perspectives of Stakeholders Regarding HIV Molecular Epidemiology.

HIV molecular epidemiology (HIV-ME) is now being used in a variety of ways, including molecular HIV surveillance to help identify and respond to emerging HIV transmission clusters as specified in the Ending the HIV Epidemic in the U.S. initiative. However, HIV-ME in general, and its use for cluster detection and response, in particular, raises significant ethical and social concerns, which have spurred vigorous debates. Nevertheless, there is a paucity of information regarding how these potential benefits and concerns are perceived among people living with HIV and people without HIV at an increased risk. Virtual engagement with US participants. We rigorously developed a brief informational video about HIV-ME and conducted a series of in-depth interviews with people living with HIV and people without HIV at an increased risk. Through extensive stakeholder engagement during the video development process and subsequent in-depth interviews (N = 24), several preliminary findings surfaced. In contrast to the high level of concern raised by some critics of HIV-ME, our data appear to show broad support for it. In addition, we observed conflation of perspectives about HIV-ME with concerns about HIV public health surveillance more generally. Our experiences reveal substantial communication challenges related to the nature of HIV-ME that need to be overcome to ensure that it is properly understood, which is necessary for meaningfully engaging stakeholders in discussions about its use. Moreover, ongoing, responsive, engagement efforts are critical. Additional systematic data are needed to help inform policy making and practice regarding HIV-ME.

Phylodynamics and migration data help describe HIV transmission dynamics in internally displaced people who inject drugs in Ukraine.

Internally displaced persons are often excluded from HIV molecular epidemiology surveillance due to structural, behavioral, and social barriers in access to treatment. We test a field-based molecular epidemiology framework to study HIV transmission dynamics in a hard-to-reach and highly stigmatized group, internally displaced people who inject drugs (IDPWIDs). We inform the framework by Nanopore generated HIV pol sequences and IDPWID migration history. In June-September 2020, we recruited 164 IDPWID in Odesa, Ukraine, and obtained 34 HIV sequences from HIV-infected participants. We aligned them to publicly available sequences (N = 359) from Odesa and IDPWID regions of origin and identified 7 phylogenetic clusters with at least 1 IDPWID. Using times to the most recent common ancestors of the identified clusters and times of IDPWID relocation to Odesa, we infer potential post-displacement transmission window when infections likely to happen to be between 10 and 21 months, not exceeding 4 years. Phylogeographic analysis of the sequence data shows that local people in Odesa disproportionally transmit HIV to the IDPWID community. Rapid transmissions post-displacement in the IDPWID community might be associated with slow progression along the HIV continuum of care: only 63% of IDPWID were aware of their status, 40% of those were in antiviral treatment, and 43% of those were virally suppressed. Such HIV molecular epidemiology investigations are feasible in transient and hard-to-reach communities and can help indicate best times for HIV preventive interventions. Our findings highlight the need to rapidly integrate Ukrainian IDPWID into prevention and treatment services following the dramatic escalation of the war in 2022.

Community Insights in Phylogenetic HIV Research: The CIPHR Project Protocol

ABSTRACT Inferring HIV transmission networks from HIV sequences is gaining popularity in the field of HIV molecular epidemiology. However, HIV sequences are often analyzed at distance from those affected by HIV epidemics, namely without the involvement of communities most affected by HIV. These remote analyses often mean that knowledge is generated in absence of lived experiences and socio-economic realities that could inform the ethical application of network-derived information in ‘real world’ programmes. Procedures to engage communities are noticeably absent from the HIV molecular epidemiology literature. Here we present our team’s protocol for engaging community activists living in Nairobi, Kenya in a knowledge exchange process – The CIPHR Project (Community Insights in Phylogenetic HIV Research). Drawing upon a community-based participatory approach, our team will (1) explore the possibilities and limitations of HIV molecular epidemiology for key population programmes, (2) pilot a community-based HIV molecular study, and (3) co-develop policy guidelines on conducting ethically safe HIV molecular epidemiology. Critical dialogue with activist communities will offer insight into the potential uses and abuses of using such information to sharpen HIV prevention programmes. The outcome of this process holds importance to the development of policy frameworks that will guide the next generation of the global response.

Molecular epidemiology of HIV-1 among adult female sex workers at the Guatemala-Mexico border

ABSTRACT Sex workers have been demonstrated to have increased vulnerabilities to HIV and a high population prevalence of the disease. Despite their increased risk, sex workers have been underrepresented in molecular epidemiology studies assessing HIV in Mesoamerica. This study aims to describe the sociodemographic characteristics and phylogenetic profile of HIV-1 within a cohort of HIV-positive female sex workers (FSW) situated at the Guatemala-Mexico border. HIV viral sequences were collected from a cohort of FSW ≥18 years of age from San Marcos, Guatemala (n = 6) and compared to viral sequences collected as part of the Mesoamerican Drug Resistance Monitoring Programme to assess HIV viral diversity in Mexico and Guatemala (n = 3956). All of the FSW sampled were determined to have genetically unrelated HIV infections, suggesting multiple introductions of the virus and/or the potential existence of populations not captured by current surveillance efforts. Many reported numerous vulnerabilities that may have heightened their risk of acquiring and transmitting HIV through sex work activities. Our phylogenetic analysis indicated that national surveillance programmes may not fully capture the viral diversity among FSW and their clients within this region. Additional research is needed to fully capture HIV diversity and transmission in Mesoamerica, especially in the Guatemala-Mexico border region.

Molecular Epidemiology of HIV-1 in Ghana: Subtype Distribution, Drug Resistance and Coreceptor Usage.

The greatest HIV-1 genetic diversity is found in West/Central Africa due to the pandemic’s origins in this region, but this diversity remains understudied. We characterized HIV-1 subtype diversity (from both sub-genomic and full-genome viral sequences), drug resistance and coreceptor usage in 103 predominantly (90%) antiretroviral-naive individuals living with HIV-1 in Ghana. Full-genome HIV-1 subtyping confirmed the circulating recombinant form CRF02_AG as the dominant (53.9%) subtype in the region, with the complex recombinant 06_cpx (4%) present as well. Unique recombinants, most of which were mosaics containing CRF02_AG and/or 06_cpx, made up 37% of sequences, while “pure” subtypes were rare (<6%). Pretreatment resistance to at least one drug class was observed in 17% of the cohort, with NNRTI resistance being the most common (12%) and INSTI resistance being relatively rare (2%). CXCR4-using HIV-1 sequences were identified in 23% of participants. Overall, our findings advance our understanding of HIV-1 molecular epidemiology in Ghana. Extensive HIV-1 genetic diversity in the region appears to be fueling the ongoing creation of novel recombinants, the majority CRF02_AG-containing, in the region. The relatively high prevalence of pretreatment NNRTI resistance but low prevalence of INSTI resistance supports the use of INSTI-based first-line regimens in Ghana.

"Everything…Fell Apart Once COVID-19 Hit"-Leveraging the COVID-19 Response to Strengthen Public Health Activities toward Ending the HIV Epidemic: A Qualitative Study.

COVID-19 caused widespread disruption of activities for Ending the HIV Epidemic (EHE). In this study we assessed public health perspectives on leveraging the COVID-19 response to advance the goals of EHE. We conducted a qualitative study with 33 public health partners in the Midwestern and Southern United States from October 2020 to February 2022. Participants were asked how the strategies developed for COVID-19 could be applied to the HIV epidemic. Interviews were recorded, transcribed, and examined using rapid qualitative analysis. Four themes emerged: (1) Rebuilding teams and adapting culture for success in EHE activities; (2) Recognizing and modernizing the role of disease intervention specialists (DIS); (3) Enhanced community awareness of the public health role in disease response and prevention; and (4) Leveraging COVID-19 data systems and infrastructure for EHE activities. The COVID-19 pandemic called attention to the dearth of public health funding and outdated information technology (IT) infrastructure used for HIV activities. It also led to greater public health knowledge, including increased familiarity with partner services and molecular epidemiology of HIV, and opportunities to develop new data systems for surveillance that can be applied to efforts for EHE.

Molecular Epidemiology of HIV-1 among Prisoners in Central Brazil and Evidence of Transmission Clusters.

Higher rates of human immunodeficiency virus (HIV) infection have been detected in prisoners when compared with the general population, but research into HIV molecular epidemiology and its transmission network has been lacking among them. Thus, this study aimed to verify potential HIV molecular transmission networks among prisoners. In addition, we aimed to describe the mutations related to antiretroviral resistance in these isolates. Thus, we conducted a cross-sectional survey from 2013 to 2018 in prisons in Central-Western Brazil, and the final sampling composed of 84 prisoners. Proviral DNA was extracted from each whole blood sample followed by amplification of the partial polymerase gene and sequencing. Forty-nine sequences (58.3%) were classified as subtype B, followed by C (14.3%), D, and F1 (2.4% each). A complex and dynamic HIV-1 epidemic is observed in the prisons, as 25% of the sequences were recombinant forms. We detected 15 HIV transmission clusters composed of at least two sequences, that included not only prisoners but also individuals from the general population from the same State with a variety of risk behaviors. Thirty-two percent (32.0%) of treatment-experienced prisoners had at least one drug resistance mutation (DRM), while transmitted DRMs were found in 5.9% of the prisoners. We highlight the urgent need for routine surveillance of HIV-1 infection including resistance genotypic tests considering the high disease burden, risky behaviors inside prisons, and the dynamic relationship of prisoners with the outside community.