High SARS-CoV-2 Seroprevalence among Healthcare Workers in Bamako, Mali

SARS-CoV-2 seroprevalence among Beninese pregnant women in the third year of the pandemic

BACKGROUND

Pregnant women are a vulnerable population to COVID-19 given an increased susceptibility to severe SARS-CoV-2 infection and pregnancy complications. However, few SARS-CoV-2 serological surveys have been performed among this population to assess the extent of the infection in sub-Saharan countries. The objectives of this study were to determine SARS-CoV-2 seroprevalence among Beninese pregnant women, to identify spatial seropositivity clusters and to analyse factors associated with the infection.

METHODS

A cross-sectional study including women in their third trimester of pregnancy attending the antenatal care (ANC) clinics at Allada (south Benin) and Natitingou (north Benin) was conducted. Rapid diagnostic tests (RDT) for detection of IgG/IgM against the SARS-CoV-2 spike protein were performed using capillary blood. Seroprevalence of SARS-CoV-2 antibodies and associations between SARS-CoV-2 serostatus and maternal characteristics were analyzed by multivariate logistic regression. Spatial analyses were performed using the spatial scan statistics to identify spatial clusters of SARS-CoV-2 infection.

RESULTS

A total of 861 pregnant women were enrolled between May 4 and June 29, 2022. 58/861 (6.7%) participants reported having received COVID-19 vaccine. None of the participants had been diagnosed with COVID-19 during their pregnancy. SARS-CoV-2 antibodies were detected in 607/802 (75.7%; 95% CI 72.56%-78.62%) of unvaccinated participants. Several urban and rural spatial clusters of SARS-CoV-2 cases were identified in Allada and one urban spatial cluster was identified in Natitingou. Unvaccinated participants from Allada with at least one previous morbidity were at a three-times higher risk of presenting SARS-CoV-2 antibodies (OR = 2.89; 95%CI 1.19%-7.00%).

CONCLUSION

Three out of four pregnant women had SARS-CoV-2 antibodies, suggesting a high virus circulation among pregnant women in Benin, while COVID-19 vaccination coverage was low. Pregnant women with comorbidities may be at increased risk of SARS-CoV-2 infection. This population should be prioritized for COVID-19 diagnosis and vaccination in order to prevent its deleterious effects.

TRIAL REGISTRATION

NCT06170320 (retrospectively registered on December 21, 2023).

Seroprevalence of SARS-CoV-2 Antibodies and Associated Factors in Bamako, Mali: A Population-Based Cross-Sectional Study in September 2022

BACKGROUND

The sero-epidemiological characteristics of SARS-CoV-2 infections in Mali are not yet well understood. This study assessed SARS-CoV-2 antibody seroprevalence and factors associated with antibody responses in the general population of Bamako, the capital city and epicenter of COVID-19, to assess the magnitude of the pandemic and contribute to control strategy improvements in Mali.

METHODS

A cross-sectional survey was conducted in September 2022 to collect sociodemographic information, clinical characteristics, comorbid factors, and blood samples. ELISA was performed to determine anti-Spike (anti-S) and anti-RBD antibody levels. A total of 3601 participants were enrolled in REDCap. R-Studio was used for the statistical analysis. The chi-squared (χ2) test was used to compare the proportions across different groups. Logistic regression models were used to elucidate factors associated with antibody responses.

RESULT

The sex ratio for female-to-male was 3.6:1. The most representative groups were the 20-29-year-olds (28.9%, n = 1043) and the 30-39-year-olds (26.9%, n = 967). The COVID-19 vaccine coverage among the participants was 35.8%, with vaccines from Covishield AstraZeneca (13.4%), Johnson & Johnson (16.7%), Sinovac (3.9%), and BioNTech Pfizer (1.8%). Overall, S protein and RBD antibody seroprevalences were remarkably high in the study population (98% and 97%, respectively). Factors such as youth (1-9 years old) and male sex were associated with lower SARS-CoV-2 antibody responses, whereas COVID-19 vaccinations were associated with increased antibody responses.

CONCLUSION

This serosurvey demonstrated the high seroprevalence of SARS-CoV-2 antibodies and highlighted the factors influencing antibody responses, while clearly underlining an underestimation of the pandemic in Mali.

A phage satellite manipulates the viral DNA packaging motor to inhibit phage and promote satellite spread

ICP1, a lytic bacteriophage of Vibrio cholerae, is parasitized by phage satellites, PLEs, which hijack ICP1 proteins for their own horizontal spread. PLEs' dependence on ICP1's DNA replication machinery, and virion components results in inhibition of ICP1's lifecycle. PLEs' are expected to depend on ICP1 factors for genome packaging, but the mechanism(s) PLEs use to inhibit ICP1 genome packaging is currently unknown. Here, we identify and characterize Gpi, PLE's indiscriminate genome packaging inhibitor. Gpi binds to ICP1's large terminase (TerL), the packaging motor, and blocks genome packaging. To overcome Gpi's negative effect on TerL, a component PLE also requires, PLE uses two genome packaging specifiers, GpsA and GpsB, that specifically allow packaging of PLE genomes. Surprisingly, PLE also uses mimicry of ICP1's pac site as a backup strategy to ensure genome packaging. PLE's pac site mimicry, however, is only sufficient if PLE can inhibit ICP1 at other stages of its lifecycle, suggesting an advantage to maintaining Gpi, GpsA, and GpsB. Collectively, these results provide mechanistic insights into another stage of ICP1's lifecycle that is inhibited by PLE, which is currently the most inhibitory of the documented phage satellites. More broadly, Gpi represents the first satellite-encoded inhibitor of a phage TerL.

Discovery and Characterization of a Pan-betacoronavirus S2-binding antibody

Three coronaviruses have spilled over from animal reservoirs into the human population and caused deadly epidemics or pandemics. The continued emergence of coronaviruses highlights the need for pan-coronavirus interventions for effective pandemic preparedness. Here, using LIBRA-seq, we report a panel of 50 coronavirus antibodies isolated from human B cells. Of these antibodies, 54043-5 was shown to bind the S2 subunit of spike proteins from alpha-, beta-, and deltacoronaviruses. A cryo-EM structure of 54043-5 bound to the pre-fusion S2 subunit of the SARS-CoV-2 spike defined an epitope at the apex of S2 that is highly conserved among betacoronaviruses. Although non-neutralizing, 54043-5 induced Fc-dependent antiviral responses, including ADCC and ADCP. In murine SARS-CoV-2 challenge studies, protection against disease was observed after introduction of Leu234Ala, Leu235Ala, and Pro329Gly (LALA-PG) substitutions in the Fc region of 54043-5. Together, these data provide new insights into the protective mechanisms of non-neutralizing antibodies and define a broadly conserved epitope within the S2 subunit.

Morbidity and mortality burden of COVID-19 in rural Madagascar: results from a longitudinal cohort and nested seroprevalence study

INTRODUCTION

Three years into the pandemic, there remains significant uncertainty about the true infection and mortality burden of COVID-19 in the World Health Organization Africa region. High quality, population-representative studies in Africa are rare and tend to be conducted in national capitals or large cities, leaving a substantial gap in our understanding of the impact of COVID-19 in rural, low-resource settings. Here, we estimated the spatio-temporal morbidity and mortality burden associated with COVID-19 in a rural health district of Madagascar until the first half of 2021.

METHODS

We integrated a nested seroprevalence study within a pre-existing longitudinal cohort conducted in a representative sample of 1600 households in Ifanadiana District, Madagascar. Socio-demographic and health information was collected in combination with dried blood spots for about 6500 individuals of all ages, which were analysed to detect IgG and IgM antibodies against four specific proteins of SARS-CoV-2 in a bead-based multiplex immunoassay. We evaluated spatio-temporal patterns in COVID-19 infection history and its associations with several geographic, socio-economic and demographic factors via logistic regressions.

RESULTS

Eighteen percent of people had been infected by April-June 2021, with seroprevalence increasing with individuals' age. COVID-19 primarily spread along the only paved road and in major towns during the first epidemic wave, subsequently spreading along secondary roads during the second wave to more remote areas. Wealthier individuals and those with occupations such as commerce and formal employment were at higher risk of being infected in the first wave. Adult mortality increased in 2020, particularly for older men for whom it nearly doubled up to nearly 40 deaths per 1000. Less than 10% of mortality in this period would be directly attributed to COVID-19 deaths if known infection fatality ratios are applied to observed seroprevalence in the district.

CONCLUSION

Our study provides a very granular understanding on COVID-19 transmission and mortality in a rural population of sub-Saharan Africa and suggests that the disease burden in these areas may have been substantially underestimated.

PhyloJunction: a computational framework for simulating, developing, and teaching evolutionary models

We introduce PhyloJunction, a computational framework designed to facilitate the prototyping, testing, and characterization of evolutionary models. PhyloJunction is distributed as an open-source Python library that can be used to implement a variety of models, through its flexible graphical modeling architecture and dedicated model specification language. Model design and use are exposed to users via command-line and graphical interfaces, which integrate the steps of simulating, summarizing, and visualizing data. This paper describes the features of PhyloJunction - which include, but are not limited to, a general implementation of a popular family of phylogenetic diversification models - and, moving forward, how it may be expanded to not only include new models, but to also become a platform for conducting and teaching statistical learning.

Seroprevalence of SARS-CoV-2 IgG among healthcare workers in Lagos, Nigeria

Healthcare workers (HCWs) are disproportionately infected with SARS-CoV-2 when compared to members of the general public; estimating the seroprevalence of SARS-CoV-2 antibody and SARS-CoV-2 infection rate among HCWs is therefore crucial. This study was carried out in four health facilities in Lagos Nigeria to determine the prevalence of IgG antibodies (seroprevalence) and SARS-CoV-2 active infection rate via a positive rtPCR result, the cross-sectional study was conducted between December 2020 and July 2021. Nasopharyngeal and blood samples were collected from HCWs and screened for SARS-CoV-2 infection using the rtPCR technique and antibody using the Abbott anti-SARS-CoV-2 IgG CMIA assay, respectively. Demographic and occupational exposures data were obtained and analysed using descriptive and inferential statistics, variables significant via inferential statistics were subjected to a multivariate analysis. A total of 413 participants were enrolled, with a mean age in years of 38.4±11.0. The seroprevalence was 30.9% (115/372) while 63/395 (15.9%) were actively infected with the virus. HCWs whose job role had direct contact with patients had a higher percentage of SARS-CoV-2 infection when compared with those not in direct contact, also being a health care worker was significantly associated with getting a positive COVID-19 PCR result. In conclusion the SARS-CoV-2 seroprevalence seen in this study was higher than national serosurvey estimates indicating HCWs are at higher risk of COVID-19 infection when compared to the general public. Vaccination and effective implementation of infection control measures are important to protect HCWs.

Molecular architecture and conservation of an immature human endogenous retrovirus

A significant part of the human genome consists of endogenous retroviruses sequences. Human endogenous retrovirus K (HERV-K) is the most recently acquired endogenous retrovirus, is activated and expressed in many cancers and amyotrophic lateral sclerosis and possibly contributes to the aging process. To understand the molecular architecture of endogenous retroviruses, we determined the structure of immature HERV-K from native virus-like particles (VLPs) using cryo-electron tomography and subtomogram averaging (cryoET STA). The HERV-K VLPs show a greater distance between the viral membrane and immature capsid lattice, correlating with the presence of additional peptides, SP1 and p15, between the capsid (CA) and matrix (MA) proteins compared to the other retroviruses. The resulting cryoET STA map of the immature HERV-K capsid at 3.2 Å resolution shows a hexamer unit oligomerized through a 6-helix bundle which is further stabilized by a small molecule in the same way as the IP6 in immature HIV-1 capsid. The HERV-K immature CA hexamer assembles into the immature lattice via highly conserved dimmer and trimer interfaces, whose interactions were further detailed through all-atom molecular dynamics simulations and supported by mutational studies. A large conformational change mediated by the flexible linker between the N-terminal and the C-terminal domains of CA occurs between the immature and the mature HERV-K capsid protein, analogous to HIV-1. Comparison between HERV-K and other retroviral immature capsid structures reveals a highly conserved mechanism for the assembly and maturation of retroviruses across genera and evolutionary time.

SARS-CoV-2 seroprevalence at urban and rural sites in Kaduna State, Nigeria, during October/November 2021, immediately prior to detection of the Omicron variant

BACKGROUND

Nigeria is Africa's most populated country. By November 2021 it had experienced three waves of SARS-CoV-2 infection. Peer-reviewed seroprevalence data assessing the proportion of the Nigerian population that have been infected were extremely limited.

METHODS

We conducted a serosurvey in one urban site (n = 400) and one rural site (n = 402) in Kaduna State, Nigeria between 11 October 2021 and 8 November 2021. Z-tests were used to compare seroprevalence across age groups, locations and sexes. T tests were used to determine whether age or household size are associated with seropositivity. Associations between seropositivity and recent history of common Covid-19 symptoms were tested using logistic regression.

RESULTS

SARS-CoV-2 antibodies were detected in 42.5% an 53.5% of participants at the urban and rural sites, respectively The overall age- and sex- stratified seroprevalence was 43.7% (42.2% for unvaccinated individuals). The data indicate an infection rate in Kaduna State ≥359-fold the rate derived from polymerase chain reaction-confirmed cases. In the urban site, seroprevalence among females and participants aged <20 was lower than other groups. Reporting loss of sense of taste and/or smell was strongly associated with seropositive status. Associations with seropositivity were also found for the reporting of dry cough, fever, headache, nausea and sore throat.

CONCLUSIONS

This study provides baseline SARS-CoV-2 seroprevalence in Kaduna State, Nigeria, immediately prior to the spread of the Omicron variant. It indicates that in October/November 2021, approximately 56% of the population did not have detectable antibodies, and population subgroups with particularly low seroprevalence remain. It highlights limitations in using PCR-confirmed cases to estimate infection rates. The data will inform public health strategies in Nigeria and other sub-Saharan African countries with limited SARS-CoV-2 seroprevalence data.

SARS-CoV-2 infection and antibody seroprevalence in routine surveillance patients, healthcare workers and general population in Kita region, Mali: an observational study 2020-2021

OBJECTIVE

To estimate the degree of SARS-CoV-2 transmission among healthcare workers (HCWs) and general population in Kita region of Mali.

DESIGN

Routine surveillance in 12 health facilities, HCWs serosurvey in five health facilities and community serosurvey in 16 villages in or near Kita town, Mali.

SETTING

Kita region, western Mali; local health centres around the central (regional) referral health centre.

PARTICIPANTS

Patients in routine surveillance, HCWs in local health centres and community members of all ages in populations associated with study health centres.

MAIN OUTCOME MEASURES

Seropositivity of ELISA test detecting SARS-CoV-2-specific total antibodies and real-time RT-PCR confirmed SARS-CoV-2 infection.

RESULTS

From 2392 routine surveillance samples, 68 (2.8%, 95% CI: 2.2% to 3.6%) tested positive for SARS-CoV-2 by RT-PCR. The monthly positivity rate was 0% in June-August 2020 and gradually increased to 6% by December 2020 and 6.2% by January 2021, then declined to 5.5%, 3.3%, 3.6% and 0.8% in February, March, April and May 2021, respectively. From 397 serum samples collected from 113 HCWs, 175 (44.1%, 95% CI: 39.1% to 49.1%) were positive for SARS-CoV-2 antibodies. The monthly seroprevalence was around 10% from September to November 2020 and increased to over 40% from December 2020 to May 2021. For community serosurvey in December 2020, overall seroprevalence of SARS-CoV-2 antibodies was 27.7%. The highest age-stratified seroprevalence was observed in participants aged 60-69 years (45.5%, 95% CI: 32.3% to 58.6%). The lowest was in children aged 0-9 years (14.0%, 95% CI: 7.4% to 20.6%).

CONCLUSIONS

SARS-CoV-2 in rural Mali is much more widespread than assumed by national testing data and particularly in the older population and frontline HCWs. The observation is contrary to the widely expressed view, based on limited data, that COVID-19 infection rates were lower in 2020-2021 in West Africa than in other settings.