ABSTRACT
ObjectivesThis study assesses the cumulative incidence of SARS-CoV-2 infection among healthcare workers (HCWs) during South Africas first wave and examines the associated demographic, health-related, and occupational risk factors for infection. MethodsMulti-stage cluster sampling was used in a cross-sectional study to recruit 1,309 HCWs from two academic hospitals in the Eastern Cape, South Africa over six weeks in November and December 2020. Prior test results for SARS-CoV-2 polymerase chain reaction (PCR) and participants characteristics were recorded while a blood sample was drawn for detection of IgG antibodies against SARS-CoV-2 nucleocapsid protein. The primary outcome measure was the SARS-CoV-2 cumulative incidence rate, defined as the combined total of positive results for either PCR or IgG antibodies, divided by the total sample. The secondary outcome was significant risk factors associated with infection. ResultsOf the total participants included in the analysis (N=1295), the majority were female (81.5%), of black race (78.7%) and nurses (44.8%). A total of 390 (30.1%) HCWs had a positive SARS-CoV-2 PCR result and SARS-CoV-2 antibodies were detected in 488 (37.7%), yielding a cumulative incidence of 47.2% (n = 611). In the adjusted logistic regression model, being overweight (Adjusted odds ratio (AOR) = 2.15, 95% CI 1.44-3.20), obese (AOR = 1.37, 95% CI 1.02-1.85) and living with HIV (AOR = 1.78, 95% CI 1.38-were independently associated with SARS-CoV-2 infection. There was no significant difference in infection rates between high, medium and low COVID-19 exposure working environments. ConclusionsThe high SARS-CoV-2 cumulative incidence in the cohort was surprising this early in the epidemic and probably related to exposure both in and outside the hospitals. To mitigate the impact of SARS-CoV-2 among HCWs, infection prevention and control (IPC) strategies should target community transmission in addition to screening for HIV and metabolic conditions. Strengths and limitations of this studyO_LIThis is a large representative sample of the total workforce of the two hospitals, with a good spectrum of staff category. C_LIO_LICombining the historical SARS-CoV-2 PCR results with the Nucleocapsid IgG enabled capturing of some of the asymptomatic and missed SARS-CoV-2 infections. C_LIO_LIThis is one of the first studies to look at SARS-CoV-2 infection risk factors in a high exposure environment in Africa. C_LIO_LIA limitation is that HIV ELISA and CD4 counts were not tested, but relied on self-report, which may likely underestimate the burden of HIV in the cohort. C_LI
ABSTRACT
Continued uncontrolled transmission of the severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) in many parts of the world is creating the conditions for significant virus evolution. Here, we describe a new SARS-CoV-2 lineage (501Y.V2) characterised by eight lineage-defining mutations in the spike protein, including three at important residues in the receptor-binding domain (K417N, E484K and N501Y) that may have functional significance. This lineage emerged in South Africa after the first epidemic wave in a severely affected metropolitan area, Nelson Mandela Bay, located on the coast of the Eastern Cape Province. This lineage spread rapidly, becoming within weeks the dominant lineage in the Eastern Cape and Western Cape Provinces. Whilst the full significance of the mutations is yet to be determined, the genomic data, showing the rapid displacement of other lineages, suggest that this lineage may be associated with increased transmissibility.
