Epidemiology of COVID-19 infections on routine polymerase chain reaction (PCR) and serology testing in Coastal Kenya

Abstract

Background: There are limited studies in Africa describing the epidemiology, clinical characteristics and serostatus of individuals tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We tested routine samples from the Coastal part of Kenya between 17th March 2020 and 30th June 2021. Methods: SARS-CoV-2 infections identified using reverse transcription polymerase chain reaction (RT-PCR) and clinical surveillance data at the point of sample collection were used to classify as either symptomatic or asymptomatic. IgG antibodies were measured in sera samples, using a well validated in-house enzyme-linked immunosorbent assay (ELISA). Results: Mombasa accounted for 56.2% of all the 99,694 naso-pharyngeal/oro-pharyngeal swabs tested, and males constituted the majority tested (73.4%). A total of 7737 (7.7%) individuals were SARS-CoV-2 positive by RT-PCR. The majority (i.e., 92.4%) of the RT-PCR positive individuals were asymptomatic. Testing was dominated by mass screening and travellers, and even at health facility level 91.6% of tests were from individuals without symptoms. Out of the 97,124 tests from asymptomatic individuals 7,149 (7%) were positive and of the 2,568 symptomatic individuals 588 (23%) were positive. In total, 2458 serum samples were submitted with paired naso-pharyngeal/oro-pharyngeal samples and 45% of the RT-PCR positive samples and 20% of the RT-PCR negative samples were paired with positive serum samples. Symptomatic individuals had significantly higher antibody levels than asymptomatic individuals and become RT-PCR negative on repeat testing earlier than asymptomatic individuals. Conclusions: In conclusion, the majority of SARS-CoV-2 infections identified by routine testing in Coastal Kenya were asymptomatic. This reflects the testing practice of health services in Kenya, but also implies that asymptomatic infection is very common in the population. Symptomatic infection may be less common, or it may be that individuals do not present for testing when they have symptoms.

Temporal distribution and clinical characteristics of the Alpha, Delta and Omicron SARS-CoV-2 variants of concern in Laikipia, Kenya: institutional and community-based genomic surveillance

“…Three months into the SARS-CoV-2 outbreak across the county, 184 cases had been confirmed, with a case fatality rate (CFR) of 2.2% 6 . In Kenya, between 42% to 92% of SARS-CoV-2 positive cases, detected mainly through mass screening, were asymptomatic 7,8 . Symptomatic cases frequently reported cough (19.6% -43%), general weakness (4% -13.4%), fever (13.3% -16%), headache (13%), sore throat (10%) and shortness of breath (10.2%) 7,8 .…”

“…In Kenya, between 42% to 92% of SARS-CoV-2 positive cases, detected mainly through mass screening, were asymptomatic 7,8 . Symptomatic cases frequently reported cough (19.6% -43%), general weakness (4% -13.4%), fever (13.3% -16%), headache (13%), sore throat (10%) and shortness of breath (10.2%) 7,8 . In the UK, Alpha VOC cases presented more frequently with cough (odds ratio [OR] 2.…”

Kinetics of naturally induced binding and neutralizing anti-SARS-CoV-2 antibody levels and potencies among Kenyan patients with diverse grades of COVID-19 severity

“…Similar findings were reported from Italy and USA where anti-spike and anti-spike-RBD antibody concentrations were found to be higher among severely than mildly sick COVID-19 patients during acute stages of infection (63)(64). Of note, a recent study on Kenyan COVID-19 patients, found symptomatic COVID-19 patients to have higher spike IgG antibodies as compared to asymptomatic patients (33). Neutralizing antibodies were also higher among severely than mildly sick USA COVID-19 patients (65), and ICU patients compared to non-ICU Chinese patients (66).…”

“…For example in Kenya, approximately 70% of the adult Kenyan population remains unvaccinated with at least two doses , as of September 2022 (31,32). This then provides a unique window to understand naturally acquired immunity to SARS-CoV-2 in our setting, since the majority have acquired immunity through natural infection rather than vaccination (26,(33)(34)(35)(36)(37). Comparing anti-SARS-CoV-2 immune responses between patients with different clinical phenotypes and determining the presence and longevity of antibody neutralization function, may also begin to provide clues for potential correlates of COVID-19 disease severity.…”

Transmission networks of SARS-CoV-2 in Coastal Kenya during the first two waves: A retrospective genomic study

“…The study used residue NP/OP swab samples collected by the Ministry of Health (MoH) County Department of Health rapid response teams (RRTs) for SARS-CoV-2 diagnostic testing ( Agoti et al, 2020 ; Nyagwange et al, 2022 ). The RRTs delivered the NP/OP swabs to the KEMRI-Wellcome Trust Research Programme (KWTRP) laboratories within 48 hr in cool boxes with ice packs.…”