Imported SARS-COV-2 Variants of Concern Drove Spread of Infections Across Kenya During the Second Year of the Pandemic

Characterization of SARS-CoV-2 intrahost genetic evolution in vaccinated and non-vaccinated patients from the Kenyan population

Vaccination is a key control measure of coronavirus disease 2019 by preventing severe effects of disease outcomes, reducing hospitalization rates and death, and increasing immunity. However, vaccination can affect the evolution and adaptation of SARS-CoV-2 largely through vaccine-induced immune pressure. Here, we investigated intrahost recombination and single nucleotide variations (iSNVs) on the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome in non-vaccinated and vaccinated sequences from the Kenyan population to profile intrahost viral genetic evolution and adaptations driven by vaccine-induced immune pressure. We identified recombination hotspots in the S, N, and ORF1a/b genes and showed the genetic evolution landscape of SARS-CoV-2 by comparing within- and inter-wave recombination events from the beginning of the pandemic (June 2020 to December 2022) in Kenya. We further reveal differential expression of recombinant RNA species between vaccinated and non-vaccinated individuals and perform an in-depth analysis of iSNVs to identify and characterize the functional properties of non-synonymous mutations found in ORF-1 a/b, S, and N genes. Lastly, we detected a minority variant in non-vaccinated patients in Kenya, with an immune escape mutation S255F of the spike gene, and showed differential recombinant RNA species. Overall, this work identified unique in vivo mutations and intrahost recombination patterns in SARS-CoV-2, which could have significant implications for virus evolution, virulence, and immune escape.IMPORTANCEThe impact of vaccination on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversity in Kenya and much of Africa remains unknown. This can be attributed to lower sequencing rates; however, this information is relevant to improvement in vaccine and antiviral research. In this study, we investigated how vaccination and SARS-CoV-2 transmission waves affect intrahost non-homologous recombination and single nucleotide variations (iSNVs). We identified unique in vivo mutations and intrahost recombination patterns in SARS-CoV-2, which could have significant implications for virus evolution, virulence, and immune escape. We also demonstrate a methodology for studying genetic changes in a pathogen by a simultaneous analysis of both intrahost single nucleotide variations and recombination events. The study reveals the diversity of SARS-CoV-2 in Kenya and highlights the need for sustained genomic surveillance in Kenya and Africa to better understand how the virus evolves. Such surveillance ensures detection of drifts in evolution, allowing information for updates in vaccines, policy making, and containment of future variants of SARS-CoV-2.

Characterization of SARS-CoV-2 intrahost genetic evolution in vaccinated and non-vaccinated patients from the Kenyan population

Vaccination is a key control measure of COVID-19 by preventing severe effects of disease outcomes, reducing hospitalization rates and death, and increasing immunity. However, vaccination can affect the evolution and adaptation of SARS-CoV-2, largely through vaccine-induced immune pressure. Here we investigated intrahost recombination and single nucleotide variations (iSNVs) on the SARS-CoV-2 genome in non-vaccinated and vaccinated sequences from the Kenyan population to profile intrahost viral genetic evolution and adaptations driven by vaccine-induced immune pressure. We identified recombination hotspots in the S, N, and ORF1a/b genes and showed the genetic evolution landscape of SARS-CoV-2 by comparing within-wave and inter-wave recombination events from the beginning of the pandemic (June 2020) to (December 2022) in Kenya. We further reveal differential expression of recombinant RNA species between vaccinated and non-vaccinated individuals and perform an in-depth analysis of iSNVs to identify and characterize the functional properties of non-synonymous mutations found in ORF-1 a/b, S, and N genes. Lastly, we detected a minority variant in non-vaccinated patients in Kenya, with an immune escape mutation S255F of the spike gene and showed differential recombinant RNA species. Overall, this work identified unique in vivo mutations and intrahost recombination patterns in SARS-CoV-2 which could have significant implications for virus evolution, virulence, and immune escape.

Characterization of SARS-CoV-2 genetic evolution in vaccinated and non-vaccinated patients from the Kenyan population

Vaccination is a key control measure of COVID-19 by preventing severe effects of disease outcomes, reducing hospitalization rates and death, and increasing herd immunity. However, vaccination can affect the evolution and adaptation of SARS-CoV-2, largely through vaccine-induced immune pressure. Here we investigated the recombination events and single nucleotide polymorphisms (SNPs) on SARS-CoV-2 genome in non-vaccinated and vaccinated patients in the Kenyan population. We identified recombination hotspots in the S, N, and ORF1a/b genes and showed the genetic evolution landscape of SARS-CoV-2 by comparing within-wave and inter-wave recombination events from the beginning of the pandemic (June 2020) to (October 2022) in Kenya. An in-depth analysis of (SNPs) on the S, ORf1a/b, and N genes identified previously unreported mutations. We detected a minority variant in non-vaccinated patients in Kenya, that contained immune escape mutation S255F of the spike gene and showing a differential recombination pattern within the non-vaccinated patients. Detailed analysis of recombination between waves suggested an association between increased population immunity and declining risk of emergence of variants of concern. Overall, this work identified unique mutations in SARS-CoV-2 which could have significant implications for virus evolution, virulence, and immune escape.

Clinical epidemiology of COVID-19 among hospitalized children in rural western Kenya

The epidemiology of pediatric COVID-19 in sub-Saharan Africa and the role of fecal-oral transmission in SARS-CoV-2 are poorly understood. Among children and adolescents in Kenya, we identify correlates of COVID-19 infection, document the clinical outcomes of infection, and evaluate the prevalence and viability of SARS-CoV-2 in stool. We recruited a prospective cohort of hospitalized children aged two months to 15 years in western Kenya between March 1 and June 30 2021. Children with SARS-CoV-2 were followed monthly for 180-days after hospital discharge. Bivariable logistic regression analysis was used to identify the clinical and sociodemographics correlates of SARS-CoV-2 infection. We also calculated the prevalence of SARS-CoV-2 detection in stool of confirmed cases. Of 355 systematically tested children, 55 (15.5%) were positive and were included in the cohort. The commonest clinical features among COVID-19 cases were fever (42/55, 76%), cough (19/55, 35%), nausea and vomiting (19/55, 35%), and lethargy (19/55, 35%). There were no statistically significant difference in baseline sociodemographic and clinical characteristics between SARS-CoV-2 positive and negative participants. Among positive participants, 8/55 (14.5%, 95%CI: 5.3%-23.9%) died; seven during the inpatient period. Forty-nine children with COVID-19 had stool samples or rectal swabs available at baseline, 9 (17%) had PCR-positive stool or rectal swabs, but none had SARS-CoV-2 detected by culture. Syndromic identification of COVID-19 is particularly challenging among children as the presenting symptoms and signs mirror other common pediatric diseases. Mortality among children hospitalized with COVID-19 was high in this cohort but was comparable to mortality seen with other common illnesses in this setting. Among this small set of children with COVID-19 we detected SARS-CoV-2 DNA, but were not able to culture viable SARs-CoV-2 virus, in stool. This suggests that fecal transmission may not be a substantial risk in children recently diagnosed and hospitalized with COVID-19 infection.

Mudhune G, M. Morobe J, Said Mohammed K, O. Makori T, Ndwiga L, W. Mburu M, O. Moraa E, Musyoki J, Murunga N, N. Waliaula I, K. Mumelo A, Bejon P, Isabella Ochola-Oyier L, Githinji G, Nokes J, Agoti C. 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

Background: Understanding the molecular epidemiology and clinical presentation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) in rural-urban populations in Kenya is important for informing future public health responses and clinical care. Methods: We undertook a retrospective analysis of the clinical presentation and phylogenetic relatedness of specimens from 97 SARS-CoV-2 cases collected between 24th April and 31st December 2021 in Laikipia county, Kenya. VOC were related to observed symptoms. Phylogenetic analyses included contemporaneous sequences from across Kenya and the globe, to contextualise local transmission dynamics. Results: These sequences fell into three VOC; Alpha (n=8), Delta (n=52) and Omicron (n=37). We estimated 75 independent SARS-CoV-2 introductions into the county. The Alpha and Delta VOC were commonly detected in persons aged 31 to 45 years, 50.0% and 30.8%, respectively. The Omicron VOC was mostly detected in 16 to 30-year-olds (51.4%). Whereas relative to the other VOCs, Omicron was associated with mild upper-respiratory tract symptoms (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), Delta was associated with moderate to severe lower-respiratory tract symptoms (shortness of breath, OR 26.8; 95% CI 3.89 – 1158.14, p<0.001) and fever (OR 6.11; 95% CI 1.57 – 35.35, p= 0.004). Post-acute phase neurological complications were suspected in four Delta infected cases (neuralgia, neuritis, peripheral neuropathy, numbness of hand and tinnitus). Conclusion: We highlight the distinctive clinical characteristics of SARS-CoV-2 VOCs, as observed in Laikipia, Kenya, to support evidence-based clinical decisions. Multiple introductions of the VOCs were recorded despite the public health measures that were in place questioning their effectiveness during the study period.

COVID-19 vaccination refusal trends in Kenya over 2021

BACKGROUND

Vaccination refusal exacerbates global COVID-19 vaccination inequities. No studies in East Africa have examined temporal trends in vaccination refusal, precluding addressing refusal. We assessed vaccine refusal over time in Kenya, and characterized factors associated with changes in vaccination refusal.

METHODS

We analyzed data from the Kenya Rapid Response Phone Survey (RRPS), a household cohort survey representative of the Kenyan population including refugees. Vaccination refusal (defined as the respondent stating they would not receive the vaccine if offered to them at no cost) was measured in February and October 2021. Proportions of vaccination refusal were plotted over time. We analyzed factors in vaccination refusal using a weighted multivariable logistic regression including interactions for time.

FINDINGS

Among 11,569 households, vaccination refusal in Kenya decreased from 24 % in February 2021 to 9 % in October 2021. Vaccination refusal was associated with having education beyond the primary level (-4.1[-0.7,-8.9] percentage point difference (ppd)); living with somebody who had symptoms of COVID-19 in the past 14 days (-13.72[-8.9,-18.6]ppd); having symptoms of COVID-19 in the past 14 days (11.0[5.1,16.9]ppd); and distrusting the government in responding to COVID-19 (14.7[7.1,22.4]ppd). There were significant interactions with time and: refugee status and geography, living with somebody with symptoms of COVID-19, having symptoms of COVID-19, and believing in misinformation.

INTERPRETATION

The temporal reduction in vaccination refusal in Kenya likely represents substantial strides by the Kenyan vaccination program and possible learnt lessons which require examination. Going forward, there are still several groups which need specific targeting to decrease vaccination refusal and improve vaccination equity, including those with lower levels of education, those with recent COVID-19 symptoms, those who do not practice personal COVID-19 mitigation measures, refugees in urban settings, and those who do not trust the government. Policy and program should focus on decreasing vaccination refusal in these populations, and research focus on understanding barriers and motivators for vaccination.

Mudhune G, M. Morobe J, Said Mohammed K, O. Makori T, Ndwiga L, W. Mburu M, O. Moraa E, Musyoki J, Murunga N, N. Waliaula I, K. Mumelo A, Bejon P, Isabella Ochola-Oyier L, Githinji G, Nokes J, Agoti C. 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

Background: Understanding the molecular epidemiology and clinical presentation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) in rural-urban populations in Kenya is important for informing future public health responses and clinical care. Methods: We undertook a retrospective analysis of the clinical presentation and phylogenetic relatedness of specimens from 97 SARS-CoV-2 cases collected between 24th April and 31st December 2021 in Laikipia county, Kenya. VOC were related to observed symptoms. Phylogenetic analyses included contemporaneous sequences from across Kenya and the globe, to contextualise local transmission dynamics. Results: These sequences fell into three VOC; Alpha (n=8), Delta (n=52) and Omicron (n=37). We estimated 75 independent SARS-CoV-2 introductions into the county. The Alpha and Delta VOC were commonly detected in persons aged 31 to 45 years, 50.0% and 30.8%, respectively. The Omicron VOC was mostly detected in 16 to 30-year-olds (51.4%). Whereas relative to the other VOCs, Omicron was associated with mild upper-respiratory tract symptoms (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), Delta was associated with moderate to severe lower-respiratory tract symptoms (shortness of breath, OR 26.8; 95% CI 3.89 – 1158.14, p<0.001) and fever (OR 6.11; 95% CI 1.57 – 35.35, p= 0.004). Post-acute phase neurological complications were suspected in four Delta infected cases (neuralgia, neuritis, peripheral neuropathy, numbness of hand and tinnitus). Conclusion: We highlight the distinctive clinical characteristics of SARS-CoV-2 VOCs, as observed in Laikipia, Kenya, to support evidence-based clinical decisions. Multiple introductions of the VOCs were recorded despite the public health measures that were in place questioning their effectiveness during the study period.

Informing healthcare operations with integrated pathology, clinical, and epidemiology data: Lessons from a single institution in Kenya during COVID-19 waves

Pathology, clinical care teams, and public health experts often operate in silos. We hypothesized that large data sets from laboratories when integrated with other healthcare data can provide evidence that can be used to optimize planning for healthcare needs, often driven by health-seeking or delivery behavior. From the hospital information system, we extracted raw data from tests performed from 2019 to 2021, prescription drug usage, and admission patterns from pharmacy and nursing departments during the COVID-19 pandemic in Kenya (March 2020 to December 2021). Proportions and rates were calculated. Regression models were created, and a t-test for differences between means was applied for monthly or yearly clustered data compared to pre-COVID-19 data. Tests for malaria parasite, Mycobacterium tuberculosis, rifampicin resistance, blood group, blood count, and histology showed a statistically significant decrease in 2020, followed by a partial recovery in 2021. This pattern was attributed to restrictions implemented to control the spread of COVID-19. On the contrary, D-dimer, fibrinogen, CRP, and HbA1c showed a statistically significant increase (p-value <0.001). This pattern was attributed to increased utilization related to the clinical management of COVID-19. Prescription drug utilization revealed a non-linear relationship to the COVID-19 positivity rate. The results from this study reveal the expected scenario in the event of similar outbreaks. They also reveal the need for increased efforts at diabetes and cancer screening, follow-up of HIV, and tuberculosis patients. To realize a broader healthcare impact, pathology departments in Africa should invest in integrated data analytics, for non-communicable diseases as well.