ABSTRACT
Background: Despite increased social vulnerability and barriers to care, there has been a paucity of data on SARS-CoV-2 incidence among key populations in sub-Saharan Africa. We seek to characterize active infections and define transmission dynamics of SARS-CoV-2 among people who inject drugs (PWID) and their sexual and injecting partners from Nairobi and the coastal region in Kenya. Method(s): This was a nested cross-sectional study of SARS-CoV-2 infection from April to July 2021 within a cohort study of assisted partner services for PWID in Kenya. A total of 1000 PWID and their partners (500 living with and 500 living without HIV) were recruited for SARS-CoV-2 antibody testing, of whom 440 were randomly selected to provide self-collected nasal swabs for real-time PCR testing. Whole genome sequencing (WGS) was completed on a limited subset of samples (N=23) with cycle threshold values 32.0. Phylogenetic tree construction and analysis was performed using the Nextstrain pipeline and compared with publicly available SARS-CoV-2 sequences from GenBank. Result(s): A total of 438 (99.5%) participants provided samples for SARS-CoV-2 PCR testing. Median age was 37 (IQR 32-42);128 (29.2%) were female;and 222 (50.7%) were living with HIV. The overall prevalence of SARS-CoV-2 infection identified by RT-PCR was 86 (19.6%). In univariate analyses, there was no increased relative risk of SARSCoV- 2 infection related to positive HIV status, frequenting an injection den, methadone treatment, unstable housing, report of any high-risk exposure, or having a sexual or injecting partner diagnosed with COVID-19 or who died from COVID-19 or flu-like illness. Eight samples were successfully sequenced via WGS and classified as WHO variants of concern: 3 Delta, 3 Alpha, and 2 Beta. Seven were classified into clades predominantly circulating in Kenya during 2021. Notably, two sequences were identical and matched identically to another Kenyan sequence, which is consistent with, though not indictive of, a transmission linkage. Conclusion(s): Overall, the risk of SARS-CoV-2 infection in this population of PWID and their partners was not significantly associated with risk factors related to injection drug use. At a genomic level, the SARS-CoV-2 strains in this study were consistent with contemporary Kenyan lineages circulating during the time and not unique to PWID. Prevention efforts, therefore, must also focus on marginalized groups for control given the substantial amount of mixing that likely occurs between populations.
ABSTRACT
Background: In sub-Saharan Africa many persons who inject drugs (PWID) are living with undiagnosed or untreated HIV and experience high levels of poverty, housing instability, and co morbid conditions that contribute to worse outcomes from SARS-CoV-2. We sought to determine SARS-CoV-2 antibody prevalence and risk factors for PWID and their sexual and injecting partners in Kenya. Identifying the burden of infection in marginalized populations like PWID may contribute to controlling the pandemic in LMIC Methods: In a nested cross-sectional study, we recruited PWID living with HIV and their injecting and/or sexual partners in Nairobi, Kilifi, and Mombasa counties at needle and syringe programs (NSP). Blood samples were collected from consenting participants at enrollment to determine SARS-CoV-2 antibodies using a Platellia BioRad SARS-CoV-2 total antibody enzyme-linked immunosorbent assay. Baseline data was collected on HIV status, antiretroviral therapy (ART) and methadone adherence. Logistic regression was used to identify factors associated with antibody positivity Results: In total,1000 participants were enrolled in the study between April and July 2021, of whom 323 (32.3%) were women and 677 (67.7%) were men. Median age of participants was 36 years (Interquartile range [IQR]: 30, 42). SARS-CoV-2 positivity was reported in 309 (30.9%) of the participants. Of the participants who tested positive for SARS-CoV-2 antibodies, 39.5% did not report any symptoms at any time during the last 3 months. Men were significantly less likely than women to have SARS-CoV-2 antibodies (Odds ratio [OR] 0.70, 95% confidence interval [CI] 0.52, 0.94;p<0.016). Participants from the Coast region had lower odds of SARS-CoV-2 antibody positivity compared to the Nairobi region (OR 0.72, 95% CI, 0.54, 0.95;p<0.019) and participants who had a sexual or injecting partner diagnosed with COVID-19 were more likely to have SARS-CoV-2 antibodies detected (OR 2.12, 95% CI 1.02, 4.39;p<0.042). Living with HIV was not significantly associated with presence of SARS-CoV-2 antibodies Conclusion: SARS-CoV-2 antibody was detected in 30.9% of participants in this cohort of PWID and their partners, suggesting high transmission rates within this key population. SARS-CoV-2 seroprevalence was similar for people living with and without HIV;no increase in risk was found for those living with HIV. This cohort represents an at-risk population that should be considered for COVID-19 vaccination, surveillance and other targeted public health measures.
ABSTRACT
Background: The first confirmed case of SARS-CoV-2 in North America was identified in Washington state (WA) on January 21, 2020. By October 1, 2020, there were 89,974 confirmed cases of SARS-CoV-2 in WA. To understand the role of epidemic seeding events, we estimated the number and timing of introductions of SARS-CoV-2 lineages in WA using phylogenetic methods. Methods: Our analysis used full genome SARS-CoV-2 sequences from GISAID sampled between December 2019 and September 2020. In order to incorporate phylogenetic uncertainty into our estimates, we generated 25 samples of sequences each with 5 random polytomy resolutions. Each sample contained 4918 high quality WA sequences and 6504 non-WA sequences, including 5056 non-WA sequences that were closest to WA sequences based on the raw number of mutations and a time-stratified random sample of 1448 additional non-WA sequences. Sequences were aligned using MAFFT and phylogenetic trees were reconstructed by lineage (GISAID clades S, L/V, G/GH and GR) using IQTREE. We then time-calibrated each phylogeny using the treedater algorithm assuming a strict molecular clock and used maximum parsimony ancestral state reconstruction to estimate the state (WA or non-WA) of each node. Internal node date for the MRCA of each subclade of two or more sequences or the date of sampling for singletons was assumed to be the date of SARS-CoV-2 introduction. Results: We estimated a median of 287 separate introductions (range 244-320) and 204 exported lineages (range 188-227) of SARS-CoV-2 into and out of WA through September 2020. Introductions began in mid-January 2020 and peaked in number on March 29, 2020 (Figure). Approximately 73% of introductions occurred prior to May 1, 2020. The majority of introductions were lineage G/ GH (72%), followed by lineage GR (16%), S (5%) and L/V (7%). The resulting WA subclades ranged in size from 1-2193 sequences: 71% included just one sampled sequence, 9% included 2 WA sequences, 12% included 3-10 WA sequences, 4% included 11-50 sequences, and 4% were large subclades that included more than 50 WA sequences and were suggestive of extended local transmission chains. Conclusion: We found phylogenetic evidence that the SARS-CoV-2 epidemic in WA was seeded by multiple ongoing introductions, although due to incomplete sampling our estimates underestimate the true number of introductions. In addition, lineages with the Spike 614G variant accounted for the majority (88%) of introductions.