Omicron B.1.1.529 variant infections associated with severe disease are uncommon in a COVID-19 under-vaccinated, high SARS-CoV-2 seroprevalence population in Malawi.

BACKGROUND: The B.1.1.529 (Omicron) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in the fourth COVID-19 pandemic wave across the southern African region, including Malawi. The seroprevalence of SARS-CoV-2 antibodies and their association with epidemiological trends of hospitalisations and deaths are needed to aid locally relevant public health policy decisions. METHODS: We conducted a population-based serosurvey from December 27, 2021 to January 17, 2022, in 7 districts across Malawi to determine the seroprevalence of SARS-CoV-2 antibodies. Serum samples were tested for antibodies against SARS-CoV-2 receptor binding domain using WANTAI SARS-CoV-2 Receptor Binding Domain total antibody commercial enzyme-linked immunosorbent assay (ELISA). We also evaluated COVID-19 epidemiologic trends in Malawi, including cases, hospitalisations and deaths from April 1, 2021 through April 30, 2022, collected using the routine national COVID-19 reporting system. A multivariable logistic regression model was developed to investigate the factors associated with SARS-CoV-2 seropositivity. FINDINGS: Serum samples were analysed from 4619 participants (57% female; 60% aged 18-50 years), of whom 878/3794 (23%) of vaccine eligible adults had received a single dose of any COVID-19 vaccine. The overall assay-adjusted seroprevalence was 83.7% (95% confidence interval (CI), 79.3%-93.4%). Seroprevalence was lowest among children <13 years of age (66%) and highest among adults 18-50 years of age (82%). Seroprevalence was higher among vaccinated compared to unvaccinated participants (1 dose, 94% vs. 77%, adjusted odds ratio 4.89 [95% CI, 3.43-7.22]; 2 doses, 97% vs. 77%, aOR 6.62 [95% CI, 4.14-11.3]). Urban residents were more likely to be seropositive than those from rural settings (91% vs. 78%, aOR 2.76 [95% CI, 2.16-3.55]). There was at least a two-fold reduction in the proportion of hospitalisations and deaths among the reported cases in the fourth wave compared to the third wave (hospitalisations, 10.7% (95% CI, 10.2-11.3) vs. 4.86% (95% CI, 4.52-5.23), p < 0.0001; deaths, 3.48% (95% CI, 3.18-3.81) vs. 1.15% (95% CI, 1.00-1.34), p < 0.0001). INTERPRETATION: We report reduction in proportion of hospitalisations and deaths from SARS-CoV-2 infections during the Omicron variant dominated wave in Malawi, in the context of high SARS-CoV-2 seroprevalence and low COVID-19 vaccination coverage. These findings suggest that COVID-19 vaccination policy in high seroprevalence settings may need to be amended from mass campaigns to targeted vaccination of reported at-risk populations. FUNDING: Supported by the Bill and Melinda Gates Foundation (INV-039481)

Prevalence of endemic respiratory viruses during the COVID-19 pandemic in urban and rural Malawi

Background Non-pharmaceutical interventions (NPI) during the COVID-19 pandemic disrupted respiratory virus circulation. Malawi employed multiple NPI but did not impose a “lockdown”. We aimed to investigate endemic respiratory virus circulation patterns in urban and rural Malawi during this period. Methods Within a prospective cohort of randomly selected households in an urban and rural community in Malawi, adult participants provided upper respiratory tract samples at four timepoints, between February 2021 and April 2022. PCR for SARS-CoV-2, influenza and other endemic respiratory viruses was performed. Results 1626 URT samples from 945 participants in 542 households were included. Overall, 7.6% (n = 123) of samples were PCR-positive for 1 respiratory virus; SARS-CoV-2 (4.4%) and rhinovirus (2.0%) were most frequently detected. No influenza A virus was detected. Influenza B and RSV were rare. Significantly higher levels of virus positivity were detected in the rural setting, and at earlier timepoints. Co-infections were infrequent (0.2%; n = 3). Conclusion Endemic respiratory viruses circulated in the community in Malawi during the pandemic, although influenza and RSV were rarely detected. Distinct differences in virus positivity and demographics were observed between urban and rural cohorts. Ongoing surveillance is needed to monitor the impact of continuing co-circulation of SARS-CoV-2 with endemic respiratory viruses

Factors associated with COVID-19 vaccine receipt among mobile phone users in Malawi: Findings from a national mobile-based syndromic surveillance survey, July 2021-April 2022.

Malawi recommended COVID-19 vaccines for adults aged ≥18 years in March 2021. We assessed factors associated with receiving COVID-19 vaccines in Malawi as part of a telephone-based syndromic surveillance survey. We conducted telephone-based syndromic surveillance surveys with questions on COVID-19 vaccine receipt among adults (≥18 years old) upon verbal consent from July 2021 to April 2022. We used random digit dialing to select mobile phone numbers and employed electronic data collection forms on secure tablets. Survey questions included whether the respondent had received at least one dose of a COVID-19 vaccine. We used multivariable analysis to identify factors associated with COVID-19 vaccine receipt. Of the 51,577 participants enrolled; 65.7% were male. Males were less likely to receive the COVID-19 vaccine than females (AOR 0.83, 95% CI 0.80-0.86). Compared to those aged 18-24 years, older age had increased odds of vaccine receipt: 25-34 years (AOR 1.32, 95% CI 1.24-1.40), 35-44 years (AOR 2.00, 95% CI 1.88-2.13), 45-54 years (AOR 3.02, 95% CI 2.82-3.24), 55-64 years (AOR 3.24, 95% CI 2.93-3.57) and 65 years+ (AOR 3.98, 95% CI 3.52-4.49). Respondents without formal education were less likely to receive vaccination compared to those with primary (AOR 1.30, 95% CI 1.14-1.48), secondary (AOR 1.76, 95% CI 1.55-2.01), and tertiary (AOR 3.37, 95% CI 2.95-3.86) education. Respondents who thought COVID-19 vaccines were unsafe were less likely to receive vaccination than those who thought it was very safe (AOR 0.26, 95% CI 0.25-0.28). Residents of the Central and Southern regions had reduced odds of vaccine receipt compared to those in the North (AORs 0.79, (95% CI 0.74-0.84) and 0.55, (95% CI 0.52-0.58) respectively). Radio (72.6%), health facilities (52.1%), and social media (16.0%) were the more common self-reported sources of COVID-19 vaccine information. COVID-19 vaccine receipt is associated with gender, age, education, and residence. It is important to consider these factors when implementing COVID-19 vaccination programs

Prevalence of endemic respiratory viruses during the COVID-19 pandemic in urban and rural Malawi

Background Non-pharmaceutical interventions (NPI) during the COVID-19 pandemic disrupted respiratory virus circulation. Malawi employed multiple NPI but did not impose a “lockdown”. We aimed to investigate endemic respiratory virus circulation patterns in urban and rural Malawi during this period. Methods Within a prospective cohort of randomly selected households in an urban and rural community in Malawi, adult participants provided upper respiratory tract samples at four timepoints, between February 2021 and April 2022. PCR for SARS-CoV-2, influenza and other endemic respiratory viruses was performed. Results 1626 URT samples from 945 participants in 542 households were included. Overall, 7.6% (n = 123) of samples were PCR-positive for 1 respiratory virus; SARS-CoV-2 (4.4%) and rhinovirus (2.0%) were most frequently detected. No influenza A virus was detected. Influenza B and RSV were rare. Significantly higher levels of virus positivity were detected in the rural setting, and at earlier timepoints. Co-infections were infrequent (0.2%; n = 3). Conclusion Endemic respiratory viruses circulated in the community in Malawi during the pandemic, although influenza and RSV were rarely detected. Distinct differences in virus positivity and demographics were observed between urban and rural cohorts. Ongoing surveillance is needed to monitor the impact of continuing co-circulation of SARS-CoV-2 with endemic respiratory viruses

Sociodemographic characteristics of COVID-19 syndromic surveillance study participants, July 2021 to April 2022.

Sociodemographic characteristics of COVID-19 syndromic surveillance study participants, July 2021 to April 2022.</p

Self-reported sources of COVID-19 vaccine information among COVID-19 syndromic surveillance study participants, July 2021 to April 2022.

Self-reported sources of COVID-19 vaccine information among COVID-19 syndromic surveillance study participants, July 2021 to April 2022.</p

Factors associated with COVID-19 vaccine receipt among COVID-19 syndromic surveillance study participants, logistic regression, adjusted and unadjusted odds ratios, with 95% confidence intervals and p-values.

Factors associated with COVID-19 vaccine receipt among COVID-19 syndromic surveillance study participants, logistic regression, adjusted and unadjusted odds ratios, with 95% confidence intervals and p-values.</p

Characterizing the evolving SARS-CoV-2 seroprevalence in urban and rural Malawi between February 2021 and April 2022 : a population-based cohort study

Objectives: This study aimed to investigate the changing SARS-CoV-2 seroprevalence and associated health and sociodemographic factors in Malawi between February 2021 and April 2022. Methods: In total, four 3-monthly serosurveys were conducted within a longitudinal population-based cohort in rural Karonga District and urban Lilongwe, testing for SARS-CoV-2 S1 immunoglobulin (Ig)G antibodies using an enzyme-linked immunosorbent assay. Population seroprevalence was estimated in all and unvaccinated participants. Bayesian mixed-effects logistic models estimated the odds of seropositivity in the first survey, and of seroconversion between surveys, adjusting for age, sex, occupation, location, and assay sensitivity/specificity. Results: Of the 2005 participants (Karonga, n = 1005; Lilongwe, n = 1000), 55.8% were female and median age was 22.7 years. Between Surveys (SVY) 1 and 4, population-weighted SARS-CoV-2 seroprevalence increased from 26.3% to 89.2% and 46.4% to 93.9% in Karonga and Lilongwe, respectively. At SVY4, seroprevalence did not differ by COVID-19 vaccination status in adults, except for those aged 30+ years in Karonga (unvaccinated: 87.4%, 95% credible interval 79.3-93.0%; two doses: 98.1%, 94.8-99.5%). Location and age were associated with seroconversion risk. Individuals with hybrid immunity had higher SARS-CoV-2 seropositivity and antibody titers, than those infected. Conclusion: High SARS-CoV-2 seroprevalence combined with low morbidity and mortality indicate that universal vaccination is unnecessary at this stage of the pandemic, supporting change in national policy to target at-risk groups

Characterising the evolving SARS-CoV-2 seroprevalence in urban and rural Malawi between February 2021 and April 2022: a population-based cohort study

Objectives: This study aimed to investigate the changing SARS-CoV-2 seroprevalence and associated health and sociodemographic factors in Malawi between February 2021 and April 2022. Methods: In total, four 3-monthly serosurveys were conducted within a longitudinal population-based cohort in rural Karonga District and urban Lilongwe, testing for SARS-CoV-2 S1 immunoglobulin (Ig)G antibodies using an enzyme-linked immunosorbent assay. Population seroprevalence was estimated in all and unvaccinated participants. Bayesian mixed-effects logistic models estimated the odds of seropositivity in the first survey, and of seroconversion between surveys, adjusting for age, sex, occupation, location, and assay sensitivity/specificity. Results: Of the 2005 participants (Karonga, n = 1005; Lilongwe, n = 1000), 55.8% were female and median age was 22.7 years. Between Surveys (SVY) 1 and 4, population-weighted SARS-CoV-2 seroprevalence increased from 26.3% to 89.2% and 46.4% to 93.9% in Karonga and Lilongwe, respectively. At SVY4, seroprevalence did not differ by COVID-19 vaccination status in adults, except for those aged 30+ years in Karonga (unvaccinated: 87.4%, 95% credible interval 79.3-93.0%; two doses: 98.1%, 94.8-99.5%). Location and age were associated with seroconversion risk. Individuals with hybrid immunity had higher SARS-CoV-2 seropositivity and antibody titers, than those infected. Conclusion: High SARS-CoV-2 seroprevalence combined with low morbidity and mortality indicate that universal vaccination is unnecessary at this stage of the pandemic, supporting change in national policy to target at-risk groups

Draft genomes of <i>Aeromonas caviae</i> from patients with cholera-like illness during the 2022-2023 cholera outbreak in Malawi.

Aeromonas caviae is an increasingly recognized etiological agent of acute gastroenteritis. Here, we report five draft genomes of A. caviae isolated from suspected cholera cases during the 2022-2023 cholera outbreak in Malawi