SARS-CoV-2 variants-associated outbreaks of COVID-19 in a tertiary institution, North-Central Nigeria: Implications for epidemic control.

The COVID-19 global pandemic is being driven by evolving SARS-CoV-2 variants with consequential implications on virus transmissibility, host immunity, and disease severity. Continuous molecular and genomic surveillance of the SARS-CoV-2 variants is therefore necessary for public health interventions toward the management of the pandemic. This study is a retrospective analysis of COVID-19 cases reported in a Nigerian tertiary institution from July to December 2021. In total, 705 suspected COVID-19 cases that comprised 547 students and 158 non-students were investigated by real time PCR (RT-PCR); of which 372 (~52.8%) tested positive for COVID-19. Using a set of selection criteria, 74 (~19.9%) COVID-19 positive samples were selected for next generation sequencing. Data showed that there were two outbreaks of COVID-19 within the university community over the study period, during which more females (56.8%) tested positive than males (47.8%) (p<0.05). Clinical data together with phylogenetic analysis suggested community transmission of SARS-CoV-2 through mostly asymptomatic and/or pre-symptomatic individuals. Confirmed COVID-19 cases were mostly mild, however, SARS-CoV-2 delta (77%) and omicron (4.1%) variants were implicated as major drivers of respective waves of infections during the study period. This study highlights the importance of integrated surveillance of communicable disease during outbreaks

Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria.

Identifying the dissemination patterns and impacts of a virus of economic or health importance during a pandemic is crucial, as it informs the public on policies for containment in order to reduce the spread of the virus. In this study, we integrated genomic and travel data to investigate the emergence and spread of the SARS-CoV-2 B.1.1.318 and B.1.525 (Eta) variants of interest in Nigeria and the wider Africa region. By integrating travel data and phylogeographic reconstructions, we find that these two variants that arose during the second wave in Nigeria emerged from within Africa, with the B.1.525 from Nigeria, and then spread to other parts of the world. Data from this study show how regional connectivity of Nigeria drove the spread of these variants of interest to surrounding countries and those connected by air-traffic. Our findings demonstrate the power of genomic analysis when combined with mobility and epidemiological data to identify the drivers of transmission, as bidirectional transmission within and between African nations are grossly underestimated as seen in our import risk index estimates

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Towards a novel polio VLP vaccine: Stabilising the PV-1 capsid by thermal selection.

Poliomyelitis (polio) is a highly infectious and debilitating viral disease caused by poliovirus (PV). The use of an oral (OPV) and an inactivated (IPV) polio vaccine over the years has led to remarkable progress towards the eradication of polio. In order to safeguard against reintroduction of polio, post-eradication, vaccination will continue. However, current OPV and IPV require the propagation of live virus and therefore constitute biological hazards post-eradication. Genome-free empty capsids (ECs) are produced during the PV lifecycle but are conformationally unstable at physiological temperatures, rapidly losing native antigenicity. If stabilised in the native conformation, recombinantly expressed PV ECs could have applications as alternative virus-free vaccines for use post-eradication. In this study, thermally-stable variants were selected through cycles of increasing thermal pressures from 51oC through 53oC to 57oC. Selected viruses were shown to have evolved thermally-stable ECs that retained native antigenicity at elevated temperatures. The capsid-stabilising mutations were identified and stabilising combinations were further investigated. The structural precursor protein (P1) of two mutant virus candidates were co-expressed with the viral protease (3CD) in a plant system which resulted in the production of thermally-stable PV-1 ECs, some of which retained the native antigenicity at temperatures higher than current IPV. The investigated potential for expression of thermally-stable VLPs in yeast is also discussed

Significance of IgG-Avidity in Antenatal Rubella Diagnosis.

Objective: A descriptive study was carried out to determine the significance of IgG-affinity in the serological diagnosis of rubella infections in pregnancy. Materials and methods: A total of 92 pregnant women who had never received antirubella vaccines were recruited by simple random selection and did not exceed 24 weeks of gestation were recruited from the antenatal clinics of the University of Ilorin Teaching Hospital. Rubella virus-specific IgG, IgG-affinity and IgM were tested, using the Indirect ELISA methods. Results:IgG-Affinity tests showed that 2 (2.2%) out of the 92 pregnant women, who were in their first and second trimester pregnancies respectively, had primary Rubella infections, while 1 (1.1%) primigravidae had a re-infection with rubella virus. It was also discovered that out of the 13 multigravid subjects that reported to have lost previous pregnancies, 2 (15.4%) cases may have been due to rubella infections that occurred during organogenesis. Conclusion: Although the isolation of the whole virus or the viral nucleic material is the best basis for diagnosis, IgG-affinity is a proven supplementary serological diagnosis, to distinguish reinfection or viral persistence from primary exposure for prompt and accurate diagnosis. This is necessary for proper counselling of pregnant women especially in low economies where molecular diagnosis may not be affordable

Knowledge, Attitude and Practices of Pregnant Women Attending University of Ilorin Teaching Hospital with Regard to Rubella

Objective: This study was carried out to clarify the potential health-risk and to determinant the prevalence of antenatal rubella infection in North-Central, Nigeria. Materials and methods: A descriptive cross-sectional survey was carried out among pregnant women to establish the knowledge, attitude and practices with regards to antenatal rubella infection in early pregnancy in Ilorin. A total of 92 subjects were recruited by simple random selection from the antenatal clinics of the University of Ilorin Teaching Hospital, Nigeria. Results: Results showed that congenitally defective eyes or ears were regarded as a greater burden to bear than a congenitally defective heart. Pregnant mothers are more likely to abort a congenitally defective fetus before term. Multigravid pregnant women are more likely to have an abortion (X 2 = 12.48, df = 4, p = 0.014), just as married pregnant women were more likely to abort a congenitally defective fetus before term (X 2 = 23.64, df = 4, p = 0.0). Conclusion: It is a general assumption that Nigeria today is majorly rural, therefore, health educational activities for prompt antenatal reporting in sub-urban Ilorin, and Nigeria as a whole, may be a relevant intervention for pregnant women

Prevalence and Risk Factors of Genital Human Papillomavirus Infections among Women in Lagos, Nigeria

Regional variations exist in HPV prevalence worldwide despite reports of high prevalence rates among African women. Limited data on genital HPV prevalence necessitated this study with the aim of determining the prevalence of genital HPV and associated risk factors among women in Lagos, Nigeria. Exfoliated cervical cells were collected with consent from 165 women using a cervical brush. Viral DNA was extracted and amplified by nested PCR using two sets of consensus primers (MY09/11 and GP5+/6+). An unconditional logistic regression model was used to identify predictors of HPV positivity. The HPV prevalence was 81.82% in all women and 87.59% in women with normal cytology. The risk of HPV infection was significantly increased among women who had a history of STI (odds ratio (OR) 3.94; 95% confidence interval (CI): 1.51–10.25, p = 0.005) while there was a significantly reduced risk of HPV infection among those who used condoms (odds ratio (OR) 3.94; 95% confidence interval (CI): 0.18–0.91, p = 0.03). The HPV prevalence observed shows an increased transmission of the virus in Lagos, Nigeria. Therefore, there is a need for intense public awareness and the implementation of early detection tests, treatment, and vaccination to prevent an increase in cervical cancer cases in Lagos, Nigeria

SARS-CoV-2 variants-associated outbreaks of COVID-19 in a tertiary institution, North-Central Nigeria: Implications for epidemic control. S1 Data

Data for the PLOS ONE paper, "SARS-CoV-2 variants-associated outbreaks of COVID-19 in a tertiary institution, North-Central Nigeria: Implications for epidemic control"

SARS-CoV-2 variants-associated outbreaks of COVID-19 in a tertiary institution, North-Central Nigeria: Implications for epidemic control.

The COVID-19 global pandemic is being driven by evolving SARS-CoV-2 variants with consequential implications on virus transmissibility, host immunity, and disease severity. Continuous molecular and genomic surveillance of the SARS-CoV-2 variants is therefore necessary for public health interventions toward the management of the pandemic. This study is a retrospective analysis of COVID-19 cases reported in a Nigerian tertiary institution from July to December 2021. In total, 705 suspected COVID-19 cases that comprised 547 students and 158 non-students were investigated by real time PCR (RT-PCR); of which 372 (~52.8%) tested positive for COVID-19. Using a set of selection criteria, 74 (~19.9%) COVID-19 positive samples were selected for next generation sequencing. Data showed that there were two outbreaks of COVID-19 within the university community over the study period, during which more females (56.8%) tested positive than males (47.8%) (p<0.05). Clinical data together with phylogenetic analysis suggested community transmission of SARS-CoV-2 through mostly asymptomatic and/or pre-symptomatic individuals. Confirmed COVID-19 cases were mostly mild, however, SARS-CoV-2 delta (77%) and omicron (4.1%) variants were implicated as major drivers of respective waves of infections during the study period. This study highlights the importance of integrated surveillance of communicable disease during outbreaks