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

SARS-CoV-2 humoral immunity in people living with HIV-1

The effect of COVID-19 on the high number of immunocompromised people living with HIV-1 (PLWH), particularly in Africa, remains a critical concern. Here, we identify key areas that still require further investigation, by examining COVID-19 vaccine effectiveness, and understanding antibody responses in SARS-CoV-2 infection and vaccination in comparison with people without HIV-1 (PWOH). We also assess the potential impact of pre-existing immunity against endemic human coronaviruses on SARS-CoV-2 responses in these individuals. Lastly, we discuss the consequences of persistent infection in PLWH (or other immunocompromised individuals), including prolonged shedding, increased viral diversity within the host, and the implications on SARS-CoV-2 evolution in Africa.

Molecular Epidemiology of SARS-CoV-2 within Accra Metropolis Postlockdown

Introduction

Currently, sequencing has been the only tool for the identification of circulating severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants. However, it is known to be an expensive and laborious approach involving high technical expertise. Considering the reduced adherence to preventive measures postlockdown in Accra, this study presents an alternative method that leverages polymerase chain reaction (PCR) to identify circulating SARS-CoV-2 variants in the Accra Metropolis postlockdown.

Methods

This prospective cross-sectional study was conducted between July and December 2022. Nasopharyngeal samples were collected from 268 consenting participants. Samples were subjected to nucleic acid extraction and followed by real-time polymerase chain reaction for the detection and quantification of SARS-CoV-2 RNA. SARS-CoV-2 positive samples were subsequently subjected to variant identification using rapid PCR. Findings. The prevalence of SARS-CoV-2 within the Accra Metropolis was 30.2%. The majority of the SARS-CoV-2 infection was diagnosed in females, participants aged 41-50 years, and symptomatic participants. Participants aged ≤10 years and females recorded the highest viral load while participants aged 41-50 years recorded the highest number of infections. The SARS-CoV-2 variants detected were Alpha (64.2%), Delta (22.2%), and Omicron (13.6%). Predictors of SARS-CoV-2 infection identified were chills, cough, headache, body weakness, sore throat, and dyspnoea in order of decreasing association with SARS-CoV-2 infection. There was a strong association between symptom status, gender, age, and SARS-CoV-2 infection.

Conclusion

There was a high prevalence of SARS-CoV-2 within the Accra Metropolis postlockdown within the sampling period. The Alpha variant of SARS-CoV-2 is the predominant circulating variant, and persons presenting with symptoms are most likely to be diagnosed with COVID-19. Children aged ≤10 years serve as a reservoir for infection transmission.

First Molecular Detection of SARS-CoV-2 in Sewage and Wastewater in Ghana

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is shed in the stool of infected individuals and can be detected in sewage and wastewater contaminated with infected stool. This study is aimed at detecting the virus and its potential survival in sewage and wastewater in Ghana. The cross-sectional study included samples from 16 validated environmental surveillance sites in 7 regions of Ghana. A total of 354 samples composed of wastewater (280) and sewage (74) were collected from November 2020 to November 2022. Overall, 17% of the samples were positive for SARS-CoV-2 by real-time PCR, with 6% in sewage and 11% in wastewater. The highest number of positive samples was collected from the Greater Accra Region (7.3%) with the least recorded in the Bono East Region (0.6%). Further characterization of the positive samples using the next-generation sequencing (NGS) approach yielded two variants: Alpha (B.1.1.7) and Delta (AY.36). Attempts to isolate SARS-CoV-2 in the Vero cell line were not successful probably due to the low viral load concentrations (Ct values > 35) or prolonged exposure to high temperatures rendering the virus noninfectious. Our findings suggest that SARS-CoV-2 RNA in sewage and wastewater may not be infectious, but the prevalence shows that the virus persists in the communities within Ghana.

Genomic evolution of BA.5.2 and BF.7.14 derived lineages causing SARS-CoV-2 outbreak at the end of 2022 in China

Since the end of 2022, when China adjusted its COVID-19 response measures, the SARS-CoV-2 epidemic has rapidly grown in the country. It is very necessary to monitor the evolutionary dynamic of epidemic variants. However, detailed reports presenting viral genome characteristics in China during this period are limited. In this study, we examined the epidemiological, genomic, and evolutionary characteristics of the SARS-CoV-2 genomes from China. We analyzed nearly 20,000 genomes belonging to 17 lineages, predominantly including BF.7.14 (22.3%), DY.2 (17.3%), DY.4 (15.5%), and BA.5.2.48 (11.9%). The Rt value increased rapidly after mid-November 2022, reaching its peak at the end of the month. We identified forty-three core mutations in the S gene and forty-seven core mutations in the ORF1ab gene. The positive selection of all circulating lineages was primarily due to non-synonymous substitutions in the S1 region. These findings provide insights into the genomic characteristics of SARS-CoV-2 genomes in China following the relaxation of the 'dynamic zero-COVID' policy and emphasize the importance of ongoing genomic monitoring.

Subregional origins of emerging SARS-CoV-2 variants during the second pandemic wave in Côte d'Ivoire

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with increased transmissibility, virulence and immune escape abilities have heavily altered the COVID-19 pandemic's course. Deciphering local and global transmission patterns of those variants is thus key in building a profound understanding of the virus' spread around the globe. In the present study, we investigate SARS-CoV-2 variant epidemiology in Côte d'Ivoire, Western sub-Saharan Africa. We therefore generated 234 full SARS-CoV-2 genomes stemming from Central and Northern Côte d'Ivoire. Covering the first and second pandemic wave the country had been facing, we identified 20 viral lineages and showed that in Côte d'Ivoire the second pandemic wave in 2021 was driven by the spread of the Alpha (B.1.1.7) and Eta (B.1.525) variant. Our analyses are consistent with a limited number of international introductions of Alpha and Eta into Côte d'Ivoire, and those introduction events mostly stemmed from within the West African subregion. This suggests that subregional travel to Côte d'Ivoire had more impact on local pandemic waves than direct intercontinental travel.

Global prevalence of SARS-CoV-2 3CL protease mutations associated with nirmatrelvir or ensitrelvir resistance

BACKGROUND

Nirmatrelvir-ritonavir (Paxlovid) and ensitrelvir are 3-chymotrypsin-like cysteine protease (3CLpro) inhibitors which have been approved for the treatment of COVID-19 in 2021 and 2022, respectively. Previous studies have identified 3CLpro mutations that are associated with reduced susceptibility to these antivirals. The aim of the current study was to estimate the global prevalence of 3CLpro inhibitor-resistant SARS-CoV-2 strains.

METHODS

We compiled a list of 3CLpro mutations which have been associated with nirmatrelvir or ensitrelvir resistance based on either viral replication or 3CLpro activity assays, and determined their prevalence among 13.4 million sequences deposited in GISAID as of December 14, 2022, about 1 year after the approval of nirmatrelvir-ritonavir. We analyzed the prevalence for different time periods, SARS-CoV-2 lineages and geographical locations.

FINDINGS

Overall, 0.5% (67,095/13,446,588) of the sequences contained at least one mutation that was shown to affect the inhibitory activity of nirmatrelvir or ensitrelvir on viral replication or 3CLpro activity. We did not observe any increasing trend of resistance after the widespread clinical use of nirmatrelvir-ritonavir. G15S (2070 per million) and T21I (1386 per million) were the most prevalent mutations, and these mutations were dominant in some SARS-CoV-2 lineages. E166V and S144E, previously shown to affect the inhibitory activity of nirmatrelvir on viral replication or protease activity by > 100-folds, were found in <1 per million sequences.

INTERPRETATION

Our data suggest that 3CLpro inhibitor resistance is currently rare. However, continuous global genotypic and phenotypic surveillance would be crucial in the early detection of resistant mutants.

FUNDING

Richard and Carol Yu, May Tam Mak Mei Yin, The Shaw Foundation Hong Kong, Michael Tong, Marina Lee, Government Consultancy Service, the Emergency Key Program of Guangzhou Laboratory (See acknowledgements for full list).

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.

The in-hospital tuberculosis diagnostic cascade and early clinical outcomes among people living with HIV before and during the COVID-19 pandemic - a prospective multisite cohort study from Ghana

OBJECTIVES

The COVID-19 pandemic had a disruptive impact on tuberculosis (TB) and HIV services. We assessed the in-hospital TB diagnostic care among people with HIV (PWH) overall and before and during the pandemic.

METHODS

In this prospective study, adult PWH admitted at three hospitals in Ghana were recruited if they had a positive World Health Organization four-symptom screen or one or more World Health Organization danger signs or advanced HIV. We collected data on patient characteristics, TB assessment, and clinical outcomes after 8 weeks and used descriptive statistics and survival analysis.

RESULTS

We enrolled 248 PWH with a median clusters of differentiation 4 count of 80.5 cells/mm³ (interquartile range 24-193). Of those, 246 (99.2%) patients had a positive World Health Organization four-symptom screen. Overall, 112 (45.2%) patients obtained a sputum Xpert result, 66 (46.5%) in the prepandemic and 46 (43.4%) in the pandemic period; P-value = 0.629. The TB prevalence of 46/246 (18.7%) was similar in the prepandemic 28/140 (20.0%) and pandemic 18/106 (17.0%) population; P-value = 0.548. The 8-week all-cause mortality was 62/246 (25.2%), with no difference in cumulative survival when stratifying for the pandemic period; log-rank P-value = 0.412.

CONCLUSION

The study highlighted a large gap in the access to TB investigation and high early mortality among hospitalized PWH, irrespective of the COVID-19 pandemic.

Whole-genome single molecule real-time sequencing of SARS-CoV-2 Omicron

New variants and genetic mutations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome can only be identified using accurate sequencing methods. Single molecule real-time (SMRT) sequencing has been used to characterize Alpha and Delta variants, but not Omicron variants harboring numerous mutations in the SARS-CoV-2 genome. This study assesses the performance of a target capture SMRT sequencing protocol for whole genome sequencing (WGS) of SARS-CoV-2 Omicron variants and compared it to that of an amplicon SMRT sequencing protocol optimized for Omicron variants. The failure rate of the target capture protocol (6%) was lower than that of the amplicon protocol (34%, p < 0.001) on our data set, and the median genome coverage with the target capture protocol (98.6% [interquartile range (IQR): 86-99.4]) was greater than that with the amplicon protocol (76.6% [IQR: 66-89.6], [p < 0.001]). The percentages of samples with >95% whole genome coverage were 64% with the target capture protocol and 19% with the amplicon protocol (p < 0.05). The clades of 96 samples determined with both protocols were 93% concordant and the lineages of 59 samples were 100% concordant. Thus, target capture SMRT sequencing appears to be an efficient method for WGS, genotyping and detecting mutations of SARS-CoV-2 Omicron variants.

The Global Impact of COVID-19: Historical Development, Molecular Characterization, Drug Discovery and Future Directions

In December 2019, an outbreak of a respiratory disease called the coronavirus disease 2019 (COVID-19) caused by a new coronavirus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began in Wuhan, China. The SARS-CoV-2, an encapsulated positive-stranded RNA virus, spread worldwide with disastrous consequences for people's health, economies, and quality of life. The disease has had far-reaching impacts on society, including economic disruption, school closures, and increased stress and anxiety. It has also highlighted disparities in healthcare access and outcomes, with marginalized communities disproportionately affected by the SARS-CoV-2. The symptoms of COVID-19 range from mild to severe. There is presently no effective cure. Nevertheless, significant progress has been made in developing COVID-19 vaccine for different therapeutic targets. For instance, scientists developed multifold vaccine candidates shortly after the COVID-19 outbreak after Pfizer and AstraZeneca discovered the initial COVID-19 vaccines. These vaccines reduce disease spread, severity, and mortality. The addition of rapid diagnostics to microscopy for COVID-19 diagnosis has proven crucial. Our review provides a thorough overview of the historical development of COVID-19 and molecular and biochemical characterization of the SARS-CoV-2. We highlight the potential contributions from insect and plant sources as anti-SARS-CoV-2 and present directions for future research.

SARS-CoV-2 diagnostic testing rates determine the sensitivity of genomic surveillance programs

The first step in SARS-CoV-2 genomic surveillance is testing to identify people who are infected. However, global testing rates are falling as we emerge from the acute health emergency and remain low in many low- and middle-income countries (mean = 27 tests per 100,000 people per day). We simulated COVID-19 epidemics in a prototypical low- and middle-income country to investigate how testing rates, sampling strategies and sequencing proportions jointly impact surveillance outcomes, and showed that low testing rates and spatiotemporal biases delay time to detection of new variants by weeks to months and can lead to unreliable estimates of variant prevalence, even when the proportion of samples sequenced is increased. Accordingly, investments in wider access to diagnostics to support testing rates of approximately 100 tests per 100,000 people per day could enable more timely detection of new variants and reliable estimates of variant prevalence. The performance of global SARS-CoV-2 genomic surveillance programs is fundamentally limited by access to diagnostic testing.

Population-based sero-epidemiological investigation of the dynamics of SARS-CoV-2 infections in the Greater Accra Region of Ghana

The coronavirus disease 2019 (COVID-19) pandemic devastated countries worldwide, and resulted in a global shutdown. Not all infections are symptomatic and hence the extent of SARS-CoV-2 infection in the community is unknown. The paper presents the dynamics of the SARS-CoV-2 epidemic in the Greater Accra Metropolis, describing the evolution of seroprevalence through time and by age group. Three repeated independent population-based surveys at 6-week intervals were conducted in from November 2020 to July 2021. The global and by age-groups weighted seroprevalences were estimated and the risk factors for SARS-CoV-2 antibody seropositivity were assessed using logistic regression. The overall age-standardized SARS-CoV-2 antibody seroprevalence for both spike and nucleocapsid increased from 13.8% (95% CI 11.9, 16.1) in November 2020 to 39.6% (95% CI 34.8, 44.6) in July 2021. After controlling for gender, marital status, education level, and occupation, the older age group over 40 years had a higher odds of seropositivity than the younger age group (OR 3.0 [95% CI 1.1-8.5]) in the final survey. Pupils or students had 3.3-fold increased odds of seropositivity (OR 3.2 [95% CI 1.1-8.5]) compared to the unemployed. This study reinforces that, SARS-CoV-2 infections have been significantly higher than reported.

SARS-COV-2 antibody responses to AZD1222 vaccination in West Africa

Real-world data on vaccine-elicited neutralising antibody responses for two-dose AZD1222 in African populations are limited. We assessed baseline SARS-CoV-2 seroprevalence and levels of protective neutralizing antibodies prior to vaccination rollout using binding antibodies analysis coupled with pseudotyped virus neutralisation assays in two cohorts from West Africa: Nigerian healthcare workers (n = 140) and a Ghanaian community cohort (n = 527) pre and post vaccination. We found 44 and 28% of pre-vaccination participants showed IgG anti-N positivity, increasing to 59 and 39% respectively with anti-receptor binding domain (RBD) IgG-specific antibodies. Previous IgG anti-N positivity significantly increased post two-dose neutralizing antibody titres in both populations. Serological evidence of breakthrough infection was observed in 8/49 (16%). Neutralising antibodies were observed to wane in both populations, especially in anti-N negative participants with an observed waning rate of 20% highlighting the need for a combination of additional markers to characterise previous infection. We conclude that AZD1222 is immunogenic in two independent West African cohorts with high background seroprevalence and incidence of breakthrough infection in 2021. Waning titres post second dose indicates the need for booster dosing after AZD1222 in the African setting despite hybrid immunity from previous infection.

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

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

Multiple introduced lineages and the single native lineage co-driving the four waves of the COVID-19 pandemic in West Africa

Coronavirus disease 2019 (COVID-19) has become a vast burden on public health and socioeconomics in West Africa, but the epidemic situation is unclear. Therefore, we conducted a retrospective analysis of the positive rate, death rate, and diversity of SARS-CoV-2. As of March 31, 2022, a total of 894,813 cases of COVID-19 have been recorded, with 12,028 deaths, both of which were distributed in all 16 countries. There were four waves of COVID-19 during this period. Most cases were recorded in the second wave, accounting for 34.50% of total cases. These data suggest that although West Africa seems to have experienced a low and relatively slow spread of COVID-19, the epidemic was ongoing, evolving with each COVID-19 global pandemic wave. Most cases and most deaths were both recorded in Nigeria. In contrast, the fewest cases and fewest deaths were reported, respectively, in Liberia and Sierra Leone. However, high death rates were found in countries with low incidence rates. These data suggest that the pandemic in West Africa has so far been heterogeneous, which is closely related to the infrastructure of public health and socioeconomic development (e.g., extreme poverty, GDP per capita, and human development index). At least eight SARS-CoV-2 variants were found, namely, Delta, Omicron, Eta, Alpha, Beta, Kappa, Iota, and Gamma, which showed high diversity, implicating that multiple-lineages from different origins were introduced. Moreover, the Eta variant was initially identified in Nigeria and distributed widely. These data reveal that the COVID-19 pandemic in the continent was co-driven by both multiple introduced lineages and a single native lineage. We suggest enhancing the quarantine measures upon entry at the borders and implementing a genome surveillance strategy to better understand the transmission dynamics of the COVID-19 pandemic in West Africa.