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

Abstract

Background: The first SARS-CoV-2 case in Kenya was reported in March 2020, resulting in waves driven by B.1 and B.1.1 strains. VOC's emerged in 2021, with three additional waves. The first case within Laikipia County was reported in May 2020, variants undetermined.Nationally, 42% to 92% of cases were symptomatic. However, the association between VOCs and specific clinical symptoms remained unclear due to a limited capacity for genomic surveillance. We aimed to describe the temporal-molecular epidemiology of SARS-CoV-2 lineages, and understand the associated symptoms and outcomes. Methods: A retrospective analysis was done on convenience specimen from 97 patients, drawn from either Nanyuki Teaching & Referral Hospital, or targeted through community surveillance.NP/OP swabs, collected between May and December 2021, were screened using antigen tests, followed by a confirmatory RT-PCR, whole genome sequencing and construction of sequencing libraries. Clinical symptoms were compared, across the identified VOCs, using the Fisher's exact test. Results: The sequences (n= 97) fell into 10 Pango lineages across three VOCs; Alpha (1 lineage; {n=8}), Delta (7 lineages; {n=52}) and Omicron (2 lineages; {n=37}), with an estimated 75 independent introductions.Alpha and Delta were common in persons 31 to 45 years, 50.0% and 30.8% respectively. Omicron was common in persons 16 to 30 years (51.4%). Delta, relative to all other VOC, was more associated with moderate to severe lower-respiratory tract symptoms, including chest pain (OR 43.71; 95% CI 2.54 – 753.1, p<0.001) and shortness of breath (OR 26.8; 95% CI 3.89 – 1158.14, p<0.001), and non-specific symptoms such as muscular pain (OR 27.0; 95% CI 1.55 – 471.8, p=0.001), general weakness (OR 20.85; 95% CI 3.0 – 908.78) and fever (OR 6.11; 95% CI 1.57 – 35.35, p= 0.004). Omicron was more associated with mild to moderate upper-respiratory tract symptoms, including cough (OR 3.78; 95% CI 1.1 – 16.74, p= 0.026) and sore throat (OR 22.42; 95% CI 7.11 – 81.40, p<0.001).Delayed neurological complications were suspected in four Delta patients; neuralgia, neuritis, peripheral neuropathy, numbness of hand and tinnitus. Discussion: Sequential VOC replacement from Alpha to Delta, then to Omicron was observed over the period. Severe symptoms and mortality declined significantly with the Omicron wave, as had been reported in Malawi and South Africa. Further, no gastrointestinal symptoms were observed across all VOC, consistent with other findings, making it unlikely for COVID-19 to be an attributable cause in relevant scenario.Understanding the sequelae of neurological complications, including the possibility of delayed autoimmune responses, to inform treatment strategies, is research dependent. Conclusion: The emergence of a new wave of severe COVID-19, to an extent that would strain the existing healthcare infrastructure, is unlikely, as evidenced by declining symptom severity across VOC's, high recovery rates and increased vaccine coverage.