Genomic epidemiology of SARS-CoV-2 in Sudan: A retrospective analysis 2020-2022 (preprint)

SARS-CoV-2 was first detected in Sudan on 13th March 2020. Here, we describe the genomic epidemiology of SARS-CoV-2 in Sudan between May 2020 and April 2022 to understand the introduction and transmission of SARS-CoV-2 variants in the country. A total of 667 SARS-CoV-2 positive samples were successfully sequenced using the nCoV-19 Artic protocol on the Oxford Nanopore Technology ([≥]70% genome completeness). The genomes were compared with a select contemporaneous global dataset to determine genetic relatedness and estimate import/export events. The genomes were classified into 37 Pango lineages within the ancestral strain (107 isolates across 13 Pango lineages), Eta variant of interest (VOI) (78 isolates in 1 lineage), Alpha variant of concern (VOC) (10 isolates in 2 lineages), Beta VOC (26 isolates in 1 lineage), Delta VOC (171 isolates across 8 lineages) and Omicron VOC (242 isolates across 12 lineages). We estimated a total of 144 introductions of the observed variants from different countries across the globe. Multiple introductions of the Eta VOI, Beta VOC and Omicron VOC were observed in Sudan mainly from Europe and Africa. These findings suggest a need for continuous genomic surveillance of SARS-CoV-2 to monitor their introduction and spread consequently inform public health measures to combat SARS-CoV-2 transmission.

Temporal changes in the positivity rate of common enteric viruses among paediatric admissions in coastal Kenya, in the period spanning the COVID-19 pandemic, 2019-2022 (preprint)

Abstract Background The non-pharmaceutical interventions (NPIs) implemented to curb the spread of SARS_CoV_2 early in the COVID_19 pandemic years, disrupted the activity of other respiratory viruses. There is limited data from low and middle income countries (LMICs) to determine whether COVID_19 NPIs also impacted the epidemiology of enteric viruses. We investigated the changes in infection patterns of common enteric viruses among hospitalised children who presented with diarrhoea to a referral hospital in coastal Kenya, in the period spanning the COVID_19 pandemic. Methods A total of 870 stool samples from children under 13 years of age admitted to Kilifi County Hospital between January 2019, and December 2022 were screened for rotavirus group A (RVA), norovirus genogroup II (GII), astrovirus, sapovirus, and adenovirus type F40/41 using realtime reverse transcription polymerase chain reaction. The proportions positive across the four years were compared using the chi-squared test statistic. Results One or more of the five virus targets were detected in 282 (32.4%) cases. A reduction in the positivity rate of RVA cases was observed from 2019 (12.1%, 95% confidence interval (CI) 8.7% to 16.2%) to 2020 (1.7%, 95% CI 0.2% to 6.0%; p < 0.001). However, in the 2022, RVA positivity rate rebounded to 23.5% (95% CI 18.2% to 29.4%). For norovirus GII, the positivity rate fluctuated over the four years with its highest positivity rate observed in 2020 (16.2%; 95% C.I, 10.0% to 24.1%). No astrovirus cases were detected in 2020 and 2021, but the positivity rate in 2022 was similar to that in 2019 (3.1% (95% CI 1.5% to 5.7%) vs 3.3% (95% CI 1.4% to 6.5%)). A higher case fatality rate was observed in 2021 (9.0%) compared to the 2019 (3.2%), 2020 (6.8%) and 2022 (2.1%) (p <0.001). Conclusion Our study finds that in 2020 the transmission of common enteric viruses, especially RVA and astrovirus, in Kilifi Kenya may have been disrupted due to the COVID_19 NPIs. After 2020, local enteric virus transmission patterns appeared to return to prepandemic levels coinciding with the removal of most of the government COVID_19 NPIs.

A new Omicron lineage with Spike Y451H mutation that dominated a new COVID-19 wave in Kilifi, Coastal Kenya: March-May 2023 (preprint)

We report a newly emerged SARS-CoV-2 Omicron lineage, named FY.4, that has two unique mutations; spike:Y451H and ORF3a:P42L. FY.4 emergence has coincided with increased SARS-CoV-2 cases in coastal Kenya, April-May 2023. We demonstrate the value of continued SARS-CoV-2 genomic surveillance in the post-acute pandemic era in understanding new COVID-19 outbreaks.

Immunogenicity and safety of mixed COVID-19 vaccine regimens in patients with immune-mediated inflammatory diseases: a single-centre prospective cohort study.

OBJECTIVE: Among persons with immune-mediated inflammatory diseases (IMIDs) who received SARS-CoV-2 vaccines, we compared postvaccine antibody responses and IMID disease activity/states. DESIGN: Single-centre prospective cohort study. SETTING: Specialty ambulatory clinics in central Canada. PARTICIPANTS: People with inflammatory arthritis (n=78; 77% rheumatoid arthritis), systemic autoimmune rheumatic diseases (n=84; 57% lupus), inflammatory bowel disease (n=93; 43% Crohn's) and multiple sclerosis (n=72; 71% relapsing-remitting) (female 79.4%, white 84.7%, mean (SD) age 56.0 (14.3) years) received COVID-19 vaccinations between March 2021 and September 2022. PRIMARY OUTCOME: Postvaccination anti-spike, anti-receptor binding domain (anti-RBD) and anti-nucleocapsid (anti-NC) IgG antibodies tested by multiplex immunoassays compared across vaccine regimens and with responses in 370 age-matched and sex-matched vaccinated controls. SECONDARY OUTCOMES: COVID-19 infection and self-reported IMID disease activity/state. RESULTS: Most (216/327, 66.1%) received homologous messenger RNA (mRNA) (BNT162b2 or mRNA1273) vaccines, 2.4% received homologous ChAdOx1 and 30.6% received heterologous vaccines (23.9% ChAdOx1/mRNA, 6.4% heterologous mRNA) for their first two vaccines (V1, V2). Seroconversion rates were 52.0% (91/175) for post-V1 anti-spike and 58.9% (103/175) for anti-RBD; 91.5% (214/234) for post-V2 anti-spike and 90.2% (211/234) for anti-RBD; and were lower than controls (post-V2 anti-spike 98.1% (360/370), p<0.0001). Antibody titres decreased 3 months after V2 but increased 1 month after the third vaccine (V3) and 1 month after the fourth vaccine (V4) (BAU/mL median (IQR), anti-spike 1835 (2448) 1 month post-V2, 629.1 (883.4) 3 months post-V2, 4757.5 (7033.1) 1 month post-V3 and 4356.0 (9393.4) 1 month post-V4; anti-RBD 1686.8 (2199.44) 1 month post-V2, 555.8 (809.3) 3 months post-V2, 4280.3 (6380.6) 1 month post-V3 and 4792.2 (11 673.78) 1 month post-V4). If primed with a vector vaccine, an mRNA vaccine increased antibody titres to those comparable to homologous mRNA vaccines. Anti-RBD and anti-spike titres were higher in anti-NC seropositive (n=31; 25 participants) versus seronegative samples (BAU/mL median (IQR) anti-RBD 11 755.3 (20 373.1) vs 1248.0 (53 278.7); anti-spike 11 254.4 (15 352.6) vs 1313.1 (3106.6); both p<0.001). IMID disease activity/state and rates of self-reported moderate or severe IMID flare were similar across vaccinations. CONCLUSION: Heterologous COVID-19 vaccination improves seroconversion rates following a vector vaccine and does not lead to IMID disease flare. IMIDs benefit from at least three vaccines.

Adverse Events and Serological Responses After SARS-CoV-2 Vaccination in Individuals With Inflammatory Bowel Disease.

INTRODUCTION: We determined adverse events after 4 doses of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) vaccine in those with inflammatory bowel disease (IBD), associations between antibodies and injection site reactions (ISR), and risk of IBD flare. METHODS: Individuals with IBD were interviewed for adverse events to SARS-CoV-2 vaccine. Multivariable linear regression assessed the association between antibody titers and ISR. RESULTS: Severe adverse events occurred in 0.03%. ISR were significantly associated with antibody levels after the fourth dose (geometric mean ratio = 2.56; 95% confidence interval 1.18-5.57). No cases of IBD flare occurred. DISCUSSION: SARS-CoV-2 vaccines are safe for those with IBD. ISR after the fourth dose may indicate increased antibodies.

Navigating Coronavirus Disease 2019 Vaccination and Uveitis: Identifying the Rates and Risk of Recurrent Uveitis after Coronavirus Disease Vaccination.

PURPOSE: To identify rates of uveitis reactivation both before and after the coronavirus disease (COVID) 2019 vaccine in subjects with a previous diagnosis of uveitis. DESIGN: Retrospective study. PARTICIPANTS: Subjects were identified from the Inflammatory Eye Disease Registry at Auckland District Health Board diagnosed with uveitis between January 1, 2010, and December 31, 2020. METHODS: Date of COVID vaccination was determined from the patient clinical record. Rate of flare was calculated for 3 months before vaccination and 3 months after each vaccination. MAIN OUTCOME MEASURE: Uveitis flare was defined as the presence of new uveitis activity or increased activity that required a change in uveitis treatment. RESULTS: A total of 4184 eyes of 3008 patients were included in the study with a total of 8474 vaccinations given during the study period. Median age was 54.8 years, and 1474 (49.0%) were female. Noninfectious etiology was most common, occurring in 2296 patients (76.3%) and infectious etiology occurring in 712 patients (23.7%). Rate of uveitis flare was 12.3 per 1000 patient-months at baseline, 20.7 after the first dose, 15.0 after the second dose, 12.8 after the third dose, and 23.9 after the fourth dose. The median period of quiescence before flare was 3.9 years. An increase in uveitis flare was seen in both infectious uveitis (baseline 13.1 compared with 20.2 after first dose, 154% increase) and noninfectious uveitis (baseline 12.4 compared with 20.9 after first dose, 169% increase). Risk factors for uveitis flare were identified to be recurrent uveitis, chronic uveitis, shorter period of quiescence, and first dose of vaccine. Median time to uveitis flare was 0.53 months after the first vaccination, 1.74 months after the second vaccination, and 1.35 months after the third vaccination. CONCLUSIONS: The current study demonstrates an increased risk of uveitis flare after the first dose of COVID vaccination. This risk was highest in those with previous recurrences, chronic uveitis, and shorter period of quiescence. FINANCIAL DISCLOSURE(S): Proprietary or commercial disclosure may be found after the references.

SARS-CoV-2 seroprevalence in three Kenyan health and demographic surveillance sites, December 2020-May 2021

Background Most of the studies that have informed the public health response to the COVID-19 pandemic in Kenya have relied on samples that are not representative of the general population. We conducted population-based serosurveys at three Health and Demographic Surveillance Systems (HDSSs) to determine the cumulative incidence of infection with SARS-CoV-2. Methods We selected random age-stratified population-based samples at HDSSs in Kisumu, Nairobi and Kilifi, in Kenya. Blood samples were collected from participants between 01 Dec 2020 and 27 May 2021. No participant had received a COVID-19 vaccine. We tested for IgG antibodies to SARS-CoV-2 spike protein using ELISA. Locally-validated assay sensitivity and specificity were 93% (95% CI 88–96%) and 99% (95% CI 98–99.5%), respectively. We adjusted prevalence estimates using classical methods and Bayesian modelling to account for the sampling scheme and assay performance. Results We recruited 2,559 individuals from the three HDSS sites, median age (IQR) 27 (10–78) years and 52% were female. Seroprevalence at all three sites rose steadily during the study period. In Kisumu, Nairobi and Kilifi, seroprevalences (95% CI) at the beginning of the study were 36.0% (28.2–44.4%), 32.4% (23.1–42.4%), and 14.5% (9.1–21%), and respectively;at the end they were 42.0% (34.7–50.0%), 50.2% (39.7–61.1%), and 24.7% (17.5–32.6%), respectively. Seroprevalence was substantially lower among children (<16 years) than among adults at all three sites (p≤0.001). Conclusion By May 2021 in three broadly representative populations of unvaccinated individuals in Kenya, seroprevalence of anti-SARS-CoV-2 IgG was 25–50%. There was wide variation in cumulative incidence by location and age.

Resolution medicine in cancer, infection, pain and inflammation: are we on track to address the next Pandemic?

Uncontrolled inflammation giving rise to excessive tissue inflammation can lead to chronic inflammation that enhances tissue destruction, amplifying many chronic human pathologies. Normally the acute inflammatory response is protective and should be self-limited returning tissues to functional homeostasis with endogenous programmed resolution via leukocyte vasculature cell-cell interactions and crosstalk that biosynthesize pro-resolving mediators. When failed resolution takes place, as with the use of NSAIDs, tissues undergo chronic inflammation and fibrosis. Herein, we discuss these mechanisms and the role of specialized proresolving mediators, the resolvins, protectins and maresins produced from essential omega-3 fatty acids EPA and DHA, and their contributions via their cognate cell surface receptors, to the resolution response. Harnessing these pathways and their cellular mechanisms can help in providing new therapeutic approaches to many human diseases, infections, organ protection and trauma via resolution medicine to enhance the body's own resilience to challenge.

COVID-19 Vaccination and The Eye.

PURPOSE: To summarize the current evidence on COVID-19 vaccine-associated ocular adverse events. DESIGN: Narrative literature review. METHODS: The literature search was conducted in August 2021 using 4 electronic databases: MEDLINE, EMBASE, PubMed, and the Cochrane Database of Systematic Reviews. Population-based pharmacovigilance surveillance data were retrieved from all governmental agencies participating in the World Health Organization (WHO) Programme for International Drug Monitoring with publicly available online adverse event databases in English. RESULTS: A small number of case reports have documented uveitis flares and acute corneal graft rejection occurring within the first 3 weeks following immunization, while isolated cases of optic neuropathies, retinal conditions, scleritis, and herpetic eye disease have also been highlighted. However, data from population-based pharmacovigilance surveillance systems suggest that the prevalence of vaccination-associated ocular adverse events are very rare. CONCLUSIONS: Vaccination-associated ocular adverse events are rare, and there is currently no substantive evidence to counterweigh the overwhelming benefits of COVID-19 immunization in patients with pre-existing ophthalmic conditions.

Exploring the Impact of Covid-19-Related Perceptions on Psychological Distress and Quality of Life in an International Gastrointestinal Cohort Over Time Guided by the Common Sense Model.

The aim of this longitudinal study was to examine changes in COVID-19 and illness-related perceptions, gastrointestinal symptoms, coping, catastrophising, psychological distress, and QoL during the COVID-19 pandemic. A total of 831 adults with a gastrointestinal condition completed an online questionnaire at baseline (May-October 2020). Of those, 270 (32.5%) participants (85.2% female, mean age = 47.3 years) provided follow-up data (March-May 2021). Repeated-measures multiple analysis of variance and a cross-lagged panel model were used to test the study hypotheses. Gastrointestinal symptoms and COVID-19 perceptions at follow-up were strongly predicted by their baseline values, while illness perceptions were predicted by baseline gastrointestinal symptoms. Cross-lagged relationships indicated a reciprocal relationship between gastrointestinal symptoms and psychological distress. Moreover, gastrointestinal symptoms had substantial predictive utility, strongly predicting future gastrointestinal symptoms, and to a lesser extent, more negative illness perceptions, greater psychological distress, and greater use of adaptive coping strategies across time.

Impact du vaccin ARNm BNT162b2 anti-SARS-CoV-2 sur la production d'interféron alpha et l'auto-immunité cellulaire au cours du lupus érythémateux systémique : le projet COVALUS

Alors que la vaccination anti-SARS-CoV-2 est devenue un enjeu important de la prise en charge des patients atteints de maladies auto-immunes systémiques telles que le lupus érythémateux systémique (LES), nous manquons de données sur l'impact de la vaccination par ARN messager sur l'auto-immunité. Notre objectif était de décrire l'impact de la vaccination par ARNm sur la production d'interféron alpha et l'auto-immunité cellulaire au cours du lupus. Nous avons réalisé une étude prospective, observationnelle, monocentrique au cours de laquelle nous avons inclus des patients atteints de LES, éligibles à la vaccination anti-SARS-CoV-2 par le vaccin BNT162b2 selon les recommandations françaises alors en vigueur. Nous avons secondairement exclu les patients non-naïfs vis-à-vis de l'infection par le SARS-CoV-2 à T0 et les patients sous mycophénolate, azathioprine ou rituximab. Les patients étaient évalués juste avant la première dose, puis à 1 mois (M1), à 3 mois (M3) et à 6 mois (M6) de leur première dose. En plus du suivi clinicobiologique habituel de la maladie, nous avons évalué la production d'IFN-alpha par les cellules dendritiques plasmacytoïdes (pDCs) en cytométrie de flux. Nous avons également quantifié l'auto-immunité T en mesurant la proportion de cellules T activées (CD154+ CD69+) après stimulation des cellules sanguines mononucléées périphériques (PBMCs) par des antigènes nucléaires (U1-RNP, histones, SS-A, SS-B). Trente-six patients lupiques et 11 contrôles sains ont été inclus. Les patients lupiques étaient majoritairement des femmes (31/36, 81 %) d'un âge médian de 44 [36–50] ans. Nous avons observé une augmentation significative de la proportion de pDCs produisant spontanément de l'IFN-alpha à M1 (1,27 % [0,6–2,6]) et M3 (1,25 % [0,87–1,83]) comparativement à T0 (0,64 [0,27–1,09] %, respectivement p < 0,001 et p < 0,01) chez les lupiques. Nous avons observé une augmentation similaire dans le groupe contrôle, mais uniquement à M1 (1,46 [0,95–2,12] %) comparativement à T0 (0,25 [0,12–0,47] %, p < 0,02). Par ailleurs, les pDCs des patients lupiques exprimaient à leur surface plus de marqueurs d'activation CD86 et HLA-DR à M3 que à T0. Concernant la proportion de cellules T auto-réactives des patients lupiques, nous avons observé, qu'après une hausse non significative entre T0 et M1, les cellules auto-réactives diminuaient significativement dans le temps (coefficient β d l'effet fixe associé au temps dans le modèle linéaire à effet mixte = −0,00067, p = 0,015). Nous n'avons pas observé une telle tendance chez les contrôles. Au cours du suivi, nous avons observé 2 poussées cliniques de la maladie. À l'exception de ces patients, nous n'avons pas constaté de modification significative du SLEDAI, du taux d'anti-dsDNA, de C3 ou de C4 dans la cohorte. Chez les patients lupiques, la vaccination anti-SARS-CoV-2 par ARNm entraîne (1) une augmentation modeste infra-clinique de la production spontanée d'IFN-alpha par les pDCs et (2) une diminution des cellules T auto-réactives spécifiques des antigènes nucléaires. (French) [ FROM AUTHOR]

Global disparities in SARS-CoV-2 genomic surveillance.

Genomic sequencing is essential to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments, vaccines, and guide public health responses. To investigate the global SARS-CoV-2 genomic surveillance, we used sequences shared via GISAID to estimate the impact of sequencing intensity and turnaround times on variant detection in 189 countries. In the first two years of the pandemic, 78% of high-income countries sequenced >0.5% of their COVID-19 cases, while 42% of low- and middle-income countries reached that mark. Around 25% of the genomes from high income countries were submitted within 21 days, a pattern observed in 5% of the genomes from low- and middle-income countries. We found that sequencing around 0.5% of the cases, with a turnaround time <21 days, could provide a benchmark for SARS-CoV-2 genomic surveillance. Socioeconomic inequalities undermine the global pandemic preparedness, and efforts must be made to support low- and middle-income countries improve their local sequencing capacity.

Sero-surveillance for IgG to SARS-CoV-2 at antenatal care clinics in three Kenyan referral hospitals: Repeated cross-sectional surveys 2020-21.

INTRODUCTION: The high proportion of SARS-CoV-2 infections that have remained undetected presents a challenge to tracking the progress of the pandemic and estimating the extent of population immunity. METHODS: We used residual blood samples from women attending antenatal care services at three hospitals in Kenya between August 2020 and October 2021and a validated IgG ELISA for SARS-Cov-2 spike protein and adjusted the results for assay sensitivity and specificity. We fitted a two-component mixture model as an alternative to the threshold analysis to estimate of the proportion of individuals with past SARS-CoV-2 infection. RESULTS: We estimated seroprevalence in 2,981 women; 706 in Nairobi, 567 in Busia and 1,708 in Kilifi. By October 2021, 13% of participants were vaccinated (at least one dose) in Nairobi, 2% in Busia. Adjusted seroprevalence rose in all sites; from 50% (95%CI 42-58) in August 2020, to 85% (95%CI 78-92) in October 2021 in Nairobi; from 31% (95%CI 25-37) in May 2021 to 71% (95%CI 64-77) in October 2021 in Busia; and from 1% (95% CI 0-3) in September 2020 to 63% (95% CI 56-69) in October 2021 in Kilifi. Mixture modelling, suggests adjusted cross-sectional prevalence estimates are underestimates; seroprevalence in October 2021 could be 74% in Busia and 72% in Kilifi. CONCLUSIONS: There has been substantial, unobserved transmission of SARS-CoV-2 in Nairobi, Busia and Kilifi Counties. Due to the length of time since the beginning of the pandemic, repeated cross-sectional surveys are now difficult to interpret without the use of models to account for antibody waning.

Efficacy and safety of the anti-SARS-CoV-2 BNT162b2 vaccine among SLE patients: the covalus project

PurposeVaccination in patients with autoimmune disease like systemic lupus erythematosus (SLE) raises a special concern because its impact on autoimmunity remains partially unknown. While clinical data from large cohort are reassuring [1], very little has been described on the post vaccination immune system reaction. Besides, long-term efficacy of the vaccine, especially regarding T-cell response has not been evaluated in detail.MethodsWe conducted a prospective observational study that included all the adult SLE patients vaccinated by the BNT162b2 anti-SARS-CoV-2 vaccine in a single tertiary medical center in Paris. We evaluated the efficacy and the safety of the vaccine just before the first dose and then one month (M1), three months (M3) and six months (M6) later. Apart from the standard clinical and biological follow-up, we measured, at each time, the proportion of plasmacytoid dendritic cells (PDCs) producing interferon-α (IFN-α) using intracellular flow cytometry staining. We quantified the activation of autoimmune T cells at each visit by stimulating the peripheral blood mononuclear cells (PBMCs) with nuclear antigens and quantifying the proportion of activated (CD154+ CD69+) among non-naïve (CD45-RA -) CD4 T cells. We also evaluated the anti-SARS-CoV-2 T cell response by an Interferon Gamma Release Assay (IGRA) test.ResultsWe included 57 SLE patients and 11 healthy volunteers (HV) vaccinated by the BNT162b2 vaccine according to the French national recommendations. SLE patients were mostly female (49/57, 86.0%) with a median [IQR] age of 44.0 [38.1–50.8] years and a time since SLE diagnosis of 10.8 [4.2–19-8] years. Their treatment regimen was heterogeneous: 47/57 (82.5%) received hydroxychloroquine;35 (61.4%) steroids, and 10 (17.5%) were on another immunosuppressive drug (mycophenolate mofetil, azathioprine or rituximab). We observed only one clinical SLE flare during the post vaccination follow-up. Except for this patient, we observed no modification in the anti-dsDNA titer among SLE patients. At M3 compared to T0, we observed more PDCs producing INF-α in the SLE group: 1.17% [0.72–1.77] vs 0.68% [0.34–1.18], p=0.002 but not in the HV group. The proportion of non-naïve CD4 T cells activated (CD154+ CD69+) by the nuclear antigens did not change after vaccination. Regarding the T cell response, we observed that 71% of the SLE patients had a positive IGRA test at M3, whereas at M6, only 36% of them had a positive IGRA test. The antiviral T cell response correlated well with the humoral response: there was no patient with negative anti-Spike serology and positive IGRA and 78% of patients with a positive serology had a positive IGRA test.ConclusionWe observed that BNT162b2 vaccine had a mild impact on innate and adaptative immunity on SLE patients. The antiviral T cell response was well correlated to the humoral anti-Spike response and decreased significantly from M3 to M6.

Genomic epidemiology of SARS-CoV-2 within households in coastal Kenya: a case ascertained cohort study (preprint)

Background Analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic sequence data from household infections should aid its detailed epidemiological understanding. Using viral genomic sequence data, we investigated household SARS-CoV-2 transmission and evolution in coastal Kenya households. Methods We conducted a case-ascertained cohort study between December 2020 and February 2022 whereby 573 members of 158 households were prospectively monitored for SARS-CoV-2 infection. Households were invited to participate if a member tested SARS-CoV-2 positive or was a contact of a confirmed case. Follow-up visits collected a nasopharyngeal/oropharyngeal (NP/OP) swab on days 1, 4 and 7 for RT-PCR diagnosis. If any of these were positive, further swabs were collected on days 10, 14, 21 and 28. Positive samples with an RT-PCR cycle threshold of <33.0 were subjected to whole genome sequencing followed by phylogenetic analysis. Ancestral state reconstruction was used to determine if multiple viruses had entered households. Results Of 2,091 NP/OP swabs that were collected, 375 (17.9%) tested SARS-CoV-2 positive. Viral genome sequences (>80% coverage) were obtained from 208 (55%) positive samples obtained from 61 study households. These genomes fell within 11 Pango lineages and four variants of concern (Alpha, Beta, Delta and Omicron). We estimated 163 putative transmission events involving members of the sequenced households, 40 (25%) of which were intra-household transmission events while 123 (75%) were infections that likely occurred outside the households. Multiple virus introductions (up-to-5) were observed in 28 (47%) households with the 1-month follow-up period. Conclusions We show that a considerable proportion of SARS-CoV-2 infections in coastal Kenya occurred outside the household setting. Multiple virus introductions frequently occurred into households within the same infection wave in contrast to observations from high income settings, where single introduction appears to be the norm. Our findings suggests that control of SARS-CoV-2 transmission by household member isolation may be impractical in this setting.

The genomic epidemiology of SARS-CoV-2 variants of concern in Kenya (preprint)

The emergence and establishment of SARS CoV 2 variants of concern presented a major global public health crisis across the world. There were six waves of SARS CoV 2 cases in Kenya that corresponded with the introduction and eventual dominance of the major SARS-COV-2 variants of concern, excepting the first 2 waves that were both wildtype virus. We estimate that more than 1000 SARS CoV 2 introductions occurred in the two-year epidemic period (March 2020 to September 2022) and a total of 930 introductions were associated with variants of concern namely Beta (n=78), Alpha(n=108), Delta(n=239) and Omicron (n=505). A total of 29 introductions were associated with A.23.1 variant that circulated in high frequencies in Uganda and Rwanda. The actual number of introductions is likely to be higher than these conservative estimates due to limited genomic sequencing. Our data suggested that cryptic transmission was usually underway prior to the first real-time identification of a new variant, and that multiple introductions were responsible. Following emergence of each VOC and subsequent introduction, transmission patterns were associated with hotspots of transmission in Coast, Nairobi and Western Kenya and follows established land and air transport corridors. Understanding the introduction and dispersal of major circulating variants and identifying the sources of new introductions is important to inform public health control strategies within Kenya and the larger East-African region. Border control and case finding reactive to new variants is unlikely to be a successful control strategy.

Revealing the extent of the first wave of the COVID-19 pandemic in Kenya based on serological and PCR-test data [version 2;peer review: 2 approved, 1 approved with reservations]

Policymakers in Africa need robust estimates of the current and future spread of SARS-CoV-2. We used national surveillance PCR test, serological survey and mobility data to develop and fit a county-specific transmission model for Kenya up to the end of September 2020, which encompasses the first wave of SARS-CoV-2 transmission in the country. We estimate that the first wave of the SARS-CoV-2 pandemic peaked before the end of July 2020 in the major urban counties, with 30-50% of residents infected. Our analysis suggests, first, that the reported low COVID-19 disease burden in Kenya cannot be explained solely by limited spread of the virus, and second, that a 30-50% attack rate was not sufficient to avoid a further wave of transmission.