Temporal trends and transmission dynamics of pre-treatment HIV-1 drug resistance within and between risk groups in Kenya, 1986-2020.

BACKGROUND: Evidence on the distribution of pre-treatment HIV-1 drug resistance (HIVDR) among risk groups is limited in Africa. We assessed the prevalence, trends and transmission dynamics of pre-treatment HIVDR within and between MSM, people who inject drugs (PWID), female sex workers (FSWs), heterosexuals (HETs) and perinatally infected children in Kenya. METHODS: HIV-1 partial pol sequences from antiretroviral-naive individuals collected from multiple sources between 1986 and 2020 were used. Pre-treatment reverse transcriptase inhibitor (RTI), PI and integrase inhibitor (INSTI) mutations were assessed using the Stanford HIVDR database. Phylogenetic methods were used to determine and date transmission clusters. RESULTS: Of 3567 sequences analysed, 550 (15.4%, 95% CI: 14.2-16.6) had at least one pre-treatment HIVDR mutation, which was most prevalent amongst children (41.3%), followed by PWID (31.0%), MSM (19.9%), FSWs (15.1%) and HETs (13.9%). Overall, pre-treatment HIVDR increased consistently, from 6.9% (before 2005) to 24.2% (2016-20). Among HETs, pre-treatment HIVDR increased from 6.6% (before 2005) to 20.2% (2011-15), but dropped to 6.5% (2016-20). Additionally, 32 clusters with shared pre-treatment HIVDR mutations were identified. The majority of clusters had R0 ≥ 1.0, indicating ongoing transmissions. The largest was a K103N cluster involving 16 MSM sequences sampled between 2010 and 2017, with an estimated time to the most recent common ancestor (tMRCA) of 2005 [95% higher posterior density (HPD), 2000-08], indicating propagation over 12 years. CONCLUSIONS: Compared to HETs, children and key populations had higher levels of pre-treatment HIVDR. Introduction of INSTIs after 2017 may have abrogated the increase in pre-treatment RTI mutations, albeit in the HET population only. Taken together, our findings underscore the need for targeted efforts towards equitable access to ART for children and key populations in Kenya.

Prevention of mother-to-child transmission of HIV in Kenya: challenges to implementation.

BACKGROUND: The prevention of mother-to-child transmission of human immunodeficiency virus (HIV) is lauded as one of the more successful HIV prevention measures. However, despite some gains in the prevention of mother-to-child transmission of HIV (PMTCT) in sub-Saharan Africa, mother-to-child transmission rates are still high. In Kenya, mother-to-child transmission is considered one of the greatest health challenges and scaling up PMTCT services is crucial to its elimination by 2015. However, guideline implementation faces barriers that challenge scale-up of services. The objective of this paper is to identify barriers to PMTCT implementation in the context of a randomized control trial on the use of structured mobile phone messages in PMTCT. METHODS: The preliminary analysis presented here is based on survey data collected during enrolment in PMTCT services at one of two health facilities in Nairobi, Kenya, with overall number of antenatal care (ANC) visits determined from 48 hour follow up data. RESULTS: Data was collected for 503 women. Despite significant differences in the type of facility and sample characteristics between sites, all women presented to care at 20 weeks gestation or later and 88.8% attended less than four ANC visits. PMTCT counselling at first visit had high coverage (86%), however less than a third of women (31.34%) reported receiving contraception counselling. Although 60.8% of women had reportedly disclosed their status to their partners, only 40% were aware of their partner's status. Very few women had been tested for TB (10%) or received single dose nevirapine during their first antenatal care appointment (20%). CONCLUSION: Revised PMTCT guidelines aim to reduce the inequity between PMTCT services in high and low resource settings in efforts to eliminate mother-to-child transmission. However, guideline implementation in low resource settings continues to be confronted with challenges related to late presentation, less than four ANC visits, low screening rates for opportunistic infections, and limited contraception counselling. These challenges are further complicated by lack of disclosure to partners. Effective scale up and implementation of PMTCT services requires that such ongoing program challenges be identified and appropriately addressed within the local context.

Quantifying rates of HIV-1 flow between risk groups and geographic locations in Kenya: A country-wide phylogenetic study.

In Kenya, HIV-1 key populations including men having sex with men (MSM), people who inject drugs (PWID) and female sex workers (FSW) are thought to significantly contribute to HIV-1 transmission in the wider, mostly heterosexual (HET) HIV-1 transmission network. However, clear data on HIV-1 transmission dynamics within and between these groups are limited. We aimed to empirically quantify rates of HIV-1 flow between key populations and the HET population, as well as between different geographic regions to determine HIV-1 'hotspots' and their contribution to HIV-1 transmission in Kenya. We used maximum-likelihood phylogenetic and Bayesian inference to analyse 4058 HIV-1 pol sequences (representing 0.3 per cent of the epidemic in Kenya) sampled 1986-2019 from individuals of different risk groups and regions in Kenya. We found 89 per cent within-risk group transmission and 11 per cent mixing between risk groups, cyclic HIV-1 exchange between adjoining geographic provinces and strong evidence of HIV-1 dissemination from (i) West-to-East (i.e. higher-to-lower HIV-1 prevalence regions), and (ii) heterosexual-to-key populations. Low HIV-1 prevalence regions and key populations are sinks rather than major sources of HIV-1 transmission in Kenya. Targeting key populations in Kenya needs to occur concurrently with strengthening interventions in the general epidemic.