Genomic analysis of SARS-CoV-2 reveals local viral evolution in Ghana

Proof-of-principle of a technology transfer of a dried blood virus neutralisation assay to a Gavi-eligible country

BACKGROUND

Global health clinical research is commonly led by high-income countries (HICs) as low- and middle-income countries (LMICs) face barriers to participate, including lack of financial and human capacity and lack of research environment. Respiratory syncytial virus (RSV) vaccine development is also led by HICs, while LMICs carry the burden of life-threatening disease. Representative trials and research capacity strengthening in LMICs are needed to ensure global vaccine access and equity. This study aims to transfer an RSV neutralisation assay, which uses live cells and virus with inherent high variation, to a country eligible to receive support from the Gavi, the Vaccine Alliance.

METHODS

Using a train-the-trainer approach, a Ghanaian researcher was trained in the Netherlands on the dried blood-based RSV neutralisation assay. Subsequently, a Dutch researcher visited Ghana to support the process of adapting the technique to the Ghanaian setting. In a previously validated RSV neutralisation assay on dried blood, Hep-2 cells were infected with a serial dilution of sample-virus mixture to determine the half-maximal inhibitory concentration. Fifty-one dried blood and serum samples were tested in parallel in both countries to assess concordance.

RESULTS

Training and technology transfer was deemed successful, which was defined as neutralisation measurements by the Ghana team and high concordance (Lin's concordance correlation coefficient (CCC)>0.8). Neutralising capacity measured in identical samples in Ghana and the Netherlands correlated highly (Lin's CCC=0.87; Spearman rho=0.89) but was systematically lower in Ghana than the Netherlands.

CONCLUSION

We show successful transfer of an RSV neutralisation assay, thereby strengthening the laboratory research capacity in a Gavi-eligible country. Reliable measurement of RSV neutralising antibodies in a Gavi-eligible country and the use of dried blood can contribute to inclusion of LMICs in RSV vaccine development and access.

Detection of SARS-CoV-2 Variants Imported Through Land Borders at the Height of the COVID-19 Pandemic in Ghana, 2022

Background The World Health Organization recommends surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at points of entry to systematically collect and analyze data to inform decisions about the effective and appropriate use of resources needed for interventions. This study sought to determine the prevalence of SARS-CoV-2 and its variants imported into Ghana by travelers entering the country via land borders from February to July 2022. Methods A cross-sectional approach was employed, where recruited participants consented to the collection of oropharyngeal and nasopharyngeal samples. Specimens were analyzed for the presence of SARS-CoV-2 ribonucleic acid (RNA) using a commercially available VeriQ nCoV-OM COVID-19 Multiplex Detection kit. Amplicon sequencing protocols (ARTIC network, Oxford Nanopore Technologies (ONT), New England Biolabs, British Columbia Centre for Disease Control (BCCDC), COVID-19 Genomics UK (COG-UK), Canadian COVID-19 Genomics Network (CanCOGen), and ONT MinION) were used for SARS-CoV-2 sequencing. Logistic regression and phylogenetic analyses were conducted on the generated data. Results We detected a SARS-CoV-2 prevalence of 3.6% (170/4,621) among a total of 4,621 travelers screened. The average age of travelers was 32.11 ± 11.77, with the majority being male (68%, 3,132/4,621). After adjusting for educational status, household size, vaccination status, and study site, those with primary and tertiary education levels had 1.74 (95% CI: 1.16-2.62, P = 0.007) and 2.27 (95% CI: 1.27-4.05, P = 0.006) higher odds of testing positive for SARS-CoV-2 compared to those with no education. Vaccinated travelers had 0.65 odds (95% CI: 0.48-0.89, P = 0.007) of testing positive for SARS-CoV-2. The Omicron variant (B.1.1.529) emerged as the predominant lineage, constituting 77% (27/35) of isolates, compared to Alpha, Delta, and Recombinant variants. Phylogenetic analysis corroborated this finding, highlighting Delta and Omicron as the dominant circulating SARS-CoV-2 variants. Notably, Ghanaian strains from this study clustered with global variants, suggesting multiple introductions, likely through land borders. Conclusion A low prevalence of SARS-CoV-2 was recorded in this study, prompting the decision to reopen land borders and ease pandemic-related travel restrictions. Omicron was identified as the dominant variant. These findings emphasize the crucial role of routine surveillance at port health and advocate for a collaborative approach to addressing public health crises, preventing unnecessary travel and trade restrictions through data-based decision-making.

COVID-19 in 16 West African Countries: An Assessment of the Epidemiology and Genetic Diversity of SARS-CoV-2 after Four Epidemic Waves

West Africa faced the COVID-19 pandemic in early March 2020 and, as of March 31, 2022, had more than 900,000 confirmed cases and more than 12,000 deaths. During this period, SARS-CoV-2 genomes evolved genetically, resulting in the emergence of distinct lineages. This review was conducted to provide the epidemiological profile of COVID-19, the mutational profile of SARS-CoV-2, and the dynamics of its lineages in the 16 west African countries by analyzing data from 33 studies and seven situation reports. For a more complete representation of the epidemiology and genetic diversity of SARS-CoV-2, we used reliable public data in addition to eligible studies. As of March 31, 2022, the 16 west African countries experienced four epidemic waves with variable intensities. Higher mortality was noted during the third wave with a case fatality rate (CFR) of 1.9%. After these four epidemic waves, Liberia recorded the highest CFR (4.0%), whereas Benin had the lowest CFR (0.6%). Through mutational analysis, a high genetic heterogeneity of the genomes was observed, with a predominance of mutations in the spike protein. From this high mutational rate, different lineages emerged. Our analysis of the evolutionary diversity allowed us to count 205 lineages circulating in west Africa. This study has provided a good representation of the mutational profile and the prevalence of SARS CoV-2 lineages beyond the knowledge of the global epidemiology of the 16 African countries.

A cross-sectional study on coping strategies of frontline healthcare workers amid the COVID-19 pandemic in a developing country

Objectives

Frontline healthcare workers encountered a heightened susceptibility to negative psychological symptoms and behavioral shifts in light of the coronavirus disease 2019 pandemic. This study determined the coping strategies adopted by frontline healthcare workers in Ghana as well as assessed any differences based on demographics, job title, and ranking in four coronavirus disease 2019-designated centers in the Greater Accra region of Ghana.

Methods

Using a hospital-based, mixed-method approach, the study was conducted between May 2021 and September 2021. A total of 94 frontline healthcare workers were randomly sampled and given a self-administered questionnaire, while 13 healthcare workers took in-depth interviews. Data from the survey were analyzed using both IBM SPSS and IBM AMOS and the interview data were transcribed verbatim and coded using thematic analysis.

Results

The study revealed that coronavirus disease 2019 has affected the psycho-social life of frontline healthcare workers mainly in the form of depression, anxiety, and stress. The three main coping strategies adopted by frontline healthcare workers include personal preventative measures (most dominant), seeking external expert support, and obtaining institutional support. While healthcare workers within the age group 30-39 years were found most compliant with the adoption of personal preventive measures and those below 30 years were found least compliant.

Conclusion

This study concludes that frontline healthcare workers have been affected by a considerable level of anxiety, stress, and depression during the coronavirus disease 2019 pandemic. The study recommends a robust psychological support system at various levels of health care and an Employee Assistance Program with access to a 24-h hotline counseling service for frontline healthcare workers, continuous personal protective equipment provision, regular evidence-based updates on the management of coronavirus disease 2019 patients, and increased commitment from the government in addressing the medical needs of infected frontline healthcare workers.

SARS-CoV-2 Molecular Evolutionary Dynamics in the Greater Accra Region, Ghana

To assess dynamics of SARS-CoV-2 in Greater Accra Region, Ghana, we analyzed SARS-CoV-2 genomic sequences from persons in the community and returning from international travel. The Accra Metropolitan District was a major origin of virus spread to other districts and should be a primary focus for interventions against future infectious disease outbreaks.

Prevalence of SARS-CoV-2 and co-infection with malaria during the first wave of the pandemic (the Burkina Faso case)

Africa accounts for 1.5% of the global coronavirus disease 2019 (COVID-19) cases and 2.7% of deaths, but this low incidence has been partly attributed to the limited testing capacity in most countries. In addition, the population in many African countries is at high risk of infection with endemic infectious diseases such as malaria. Our aim is to determine the prevalence and circulation of SARS-CoV-2 variants, and the frequency of co-infection with the malaria parasite. We conducted serological tests and microscopy examinations on 998 volunteers of different ages and sexes in a random and stratified population sample in Burkina-Faso. In addition, nasopharyngeal samples were taken for RT-qPCR of SARS-CoV-2 and for whole viral genome sequencing. Our results show a 3.2 and a 2.5% of SARS-CoV-2 seroprevalence and PCR positivity; and 22% of malaria incidence, over the sampling period, with marked differences linked to age. Importantly, we found 8 cases of confirmed co-infection and 11 cases of suspected co-infection mostly in children and teenagers. Finally, we report the genome sequences of 13 SARS-CoV-2 isolates circulating in Burkina Faso at the time of analysis, assigned to lineages A.19, A.21, B.1.1.404, B.1.1.118, B.1 and grouped into clades; 19B, 20A, and 20B. This is the first population-based study about SARS-CoV-2 and malaria in Burkina Faso during the first wave of the pandemic, providing a relevant estimation of the real prevalence of SARS-CoV-2 and variants circulating in this Western African country. Besides, it highlights the non-negligible frequency of co-infection with malaria in African communities.

Genetic diversity of SARS-CoV-2 infections in Ghana from 2020-2021

The COVID-19 pandemic is one of the fastest evolving pandemics in recent history. As such, the SARS-CoV-2 viral evolution needs to be continuously tracked. This study sequenced 1123 SARS-CoV-2 genomes from patient isolates (121 from arriving travellers and 1002 from communities) to track the molecular evolution and spatio-temporal dynamics of the SARS-CoV-2 variants in Ghana. The data show that initial local transmission was dominated by B.1.1 lineage, but the second wave was overwhelmingly driven by the Alpha variant. Subsequently, an unheralded variant under monitoring, B.1.1.318, dominated transmission from April to June 2021 before being displaced by Delta variants, which were introduced into community transmission in May 2021. Mutational analysis indicated that variants that took hold in Ghana harboured transmission enhancing and immune escape spike substitutions. The observed rapid viral evolution demonstrates the potential for emergence of novel variants with greater mutational fitness as observed in other parts of the world.

Emergence of the novel SARS-CoV-2 lineage VUI-NP13L and massive spread of P.2 in South Brazil

In this study, we analyzed 340 whole genomes of SARS-CoV-2, which were sampled between April and November 2020 in 33 cities of Rio Grande do Sul, South Brazil. We demonstrated the circulation of two novel emergent lineages, VUI-NP13L and VUI-NP13L-like, and five major lineages that had already been assigned (B.1.1.33, B.1.1.28, P.2, B.1.91, B.1.195). P.2 and VUI-NP13L demonstrated a massive spread in October 2020. Constant and consistent genomic surveillance is crucial to identify newly emerging SARS-CoV-2 lineages in Brazil and to guide decision making in the Brazilian Public Healthcare System.

Predictors of COVID-19 epidemics in countries of the World Health Organization African Region

Countries of the World Health Organization (WHO) African Region have experienced a wide range of coronavirus disease 2019 (COVID-19) epidemics. This study aimed to identify predictors of the timing of the first COVID-19 case and the per capita mortality in WHO African Region countries during the first and second pandemic waves and to test for associations with the preparedness of health systems and government pandemic responses. Using a region-wide, country-based observational study, we found that the first case was detected earlier in countries with more urban populations, higher international connectivity and greater COVID-19 test capacity but later in island nations. Predictors of a high first wave per capita mortality rate included a more urban population, higher pre-pandemic international connectivity and a higher prevalence of HIV. Countries rated as better prepared and having more resilient health systems were worst affected by the disease, the imposition of restrictions or both, making any benefit of more stringent countermeasures difficult to detect. Predictors for the second wave were similar to the first. Second wave per capita mortality could be predicted from that of the first wave. The COVID-19 pandemic highlights unanticipated vulnerabilities to infectious disease in Africa that should be taken into account in future pandemic preparedness planning.

Tracking the introduction and spread of SARS-CoV-2 in coastal Kenya

Genomic surveillance of SARS-CoV-2 is important for understanding both the evolution and the patterns of local and global transmission. Here, we generated 311 SARS-CoV-2 genomes from samples collected in coastal Kenya between 17th March and 31st July 2020. We estimated multiple independent SARS-CoV-2 introductions into the region were primarily of European origin, although introductions could have come through neighbouring countries. Lineage B.1 accounted for 74% of sequenced cases. Lineages A, B and B.4 were detected in screened individuals at the Kenya-Tanzania border or returning travellers. Though multiple lineages were introduced into coastal Kenya following the initial confirmed case, none showed extensive local expansion other than lineage B.1. International points of entry were important conduits of SARS-CoV-2 importations into coastal Kenya and early public health responses prevented established transmission of some lineages. Undetected introductions through points of entry including imports from elsewhere in the country gave rise to the local epidemic at the Kenyan coast.

The Relevance of Genomic Epidemiology for Control of Tuberculosis in West Africa

Tuberculosis (TB), an airborne infectious disease caused by Mycobacterium tuberculosis complex (MTBC), remains a global health problem. West Africa has a unique epidemiology of TB that is characterized by medium- to high-prevalence. Moreover, the geographical restriction of M. africanum to the sub-region makes West Africa have an extra burden to deal with a two-in-one pathogen. The region is also burdened with low case detection, late reporting, poor treatment adherence leading to development of drug resistance and relapse. Sporadic studies conducted within the subregion report higher burden of drug resistant TB (DRTB) than previously thought. The need for more sensitive and robust tools for routine surveillance as well as to understand the mechanisms of DRTB and transmission dynamics for the design of effective control tools, cannot be overemphasized. The advancement in molecular biology tools including traditional fingerprinting and next generation sequencing (NGS) technologies offer reliable tools for genomic epidemiology. Genomic epidemiology provides in-depth insight of the nature of pathogens, circulating strains and their spread as well as prompt detection of the emergence of new strains. It also offers the opportunity to monitor treatment and evaluate interventions. Furthermore, genomic epidemiology can be used to understand potential emergence and spread of drug resistant strains and resistance mechanisms allowing the design of simple but rapid tools. In this review, we will describe the local epidemiology of MTBC, highlight past and current investigations toward understanding their biology and spread as well as discuss the relevance of genomic epidemiology studies to TB control in West Africa.

Trends of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody prevalence in selected regions across Ghana

Background: We set out to estimate the community-level exposure to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Ghana. Methods: Phased seroprevalence studies of 2729 participants at selected locations across Ghana were conducted. Phase I (August 2020) sampled 1305 individuals at major markets/lorry stations, shopping malls, hospitals and research institutions involved in coronavirus disease 2019 (COVID-19) work. The study utilized a lateral flow rapid diagnostic test (RDT) which detected IgM and IgG antibodies against SARS-CoV-2 nucleocapsid protein. Results: During Phase I, 252/1305 (19%) tested positive for IgM or IgG or both. Exposure was significantly higher at markets/lorry stations (26.9%) compared to malls (9.4%), with 41–60-year group demonstrating highest seropositivity (27.2%). Exposure was higher in participants with no formal education (26.2%) than those with tertiary education (13.1%); and higher in informally employed workers (24.0%) than those in the formal sector (15.0%). Results from phases II and III, in October and December 2020 respectively, implied either reduced transmissions or loss of antibody expression in some participants. The Upper East region showed the lowest seropositivity (2%). Phase IV, in February 2021, showed doubled seropositivity in the upper income bracket (26.2%) since August 2020, reflective of Ghana’s second wave of symptomatic COVID-19 cases. This suggested that high transmission rates had overcome the initial socioeconomic stratification of exposure risk. Reflective of second wave hospitalisation trends, the 21-40 age group demonstrated modal seropositivity (24.9) in Phase IV whilst 40-60 years and 60+ previously demonstrated highest prevalence. Conclusions: Overall, the data indicates higher COVID-19 seroprevalence than officially acknowledged, likely implying a considerably lower-case fatality rate than the current national figure of 0.84%. The data also suggests that COVID-19 is predominantly asymptomatic COVID-19 in Ghana. The observed trends mimic clinical trends of infection and imply that the methodology used was appropriate.

Ghana and the COVID-19 pandemic

A new virus causing predominantly respiratory tract infection was described in China late 2019. The virus was subsequently named the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the disease it causes as COVID-19. Subsequently the virus spread to many parts of the world. This resulted in the World Health Organisation declaring COVID-19 a global pandemic on 11th March 2020.

Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach

The D614G variant of SARS-CoV-2 S-protein emerged in early 2020 and quickly became the dominant circulating strain in Europe and its environs. The variant was characterized by the higher viral load, which is not associated with disease severity, higher incorporation into the virion, and high cell entry via ACE-2 and TMPRSS2. Previous strains of the coronavirus and the current SARS-CoV-2 have demonstrated the selection of mutations as a mechanism of escaping immune responses. In this study, we used molecular dynamics simulation and MM-PBSA binding energy analysis to provide insights into the behaviour of the D614G S-protein at the molecular level and describe the neutralization mechanism of this variant. Our results show that the D614G S-protein adopts distinct conformational dynamics which is skewed towards the open-state conformation more than the closed-state conformation of the wild-type S-protein. Residue-specific variation of amino acid flexibility and domain-specific RMSD suggest that the mutation causes an allosteric conformational change in the RBD. Evaluation of the interaction energies between the S-protein and neutralizing antibodies show that the mutation may enhance, reduce or not affect the neutralizing interactions depending on the neutralizing antibody, especially if it targets the RBD. The results of this study have shed insights into the behaviour of the D614G S-protein at the molecular level and provided a glimpse of the neutralization mechanism of this variant.