Prevalence and Diversity of Hepatitis Virus Markers among Patients with Acute Febrile Jaundice in Chad

peer reviewedOnly a minority of the patients with acute febrile jaundice evaluated through the Yellow Fever surveillance program were found positive for antibodies against Yellow Fever Virus (YFV). In order to characterize patients with acute febrile jaundice negative for YFV, we collected 255 sera between January to December 2019. We screened for HBV antigens, and antibodies against HCV and HEV. The seroprevalences observed were 10.6% (27/255) for HBV, 2% (5/255) for HCV, 17.3% (44/255) for HEV IgG, 4.3% (11/255) for HEV IgM, and 12.5% (32/255) for both IgG and IgM HEV. Prevalence of HEV was significantly higher in females than males (p < 0.01). HEV IgG prevalence was highest in those 20–29 years old, but the highest incidence rate (IgM positive) was in children 0–9 years old. Exposure to HEV was higher in the Sahelian zone (55.8%, 95%CI: 40.97–70.66) than in the Sudanese zone (30.2%, 95% CI: 24.01–36.37, p = 0.003). The high prevalence rates and hepatitis virus diversity underline the challenge of routine clinical diagnosis in Chad’s Yellow Fever surveillance program

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

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

Prevalence and Diversity of Hepatitis Virus Markers among Patients with Acute Febrile Jaundice in Chad

Only a minority of the patients with acute febrile jaundice evaluated through the Yellow Fever surveillance program were found positive for antibodies against Yellow Fever Virus (YFV). In order to characterize patients with acute febrile jaundice negative for YFV, we collected 255 sera between January to December 2019. We screened for HBV antigens, and antibodies against HCV and HEV. The seroprevalences observed were 10.6% (27/255) for HBV, 2% (5/255) for HCV, 17.3% (44/255) for HEV IgG, 4.3% (11/255) for HEV IgM, and 12.5% (32/255) for both IgG and IgM HEV. Prevalence of HEV was significantly higher in females than males (p &lt; 0.01). HEV IgG prevalence was highest in those 20–29 years old, but the highest incidence rate (IgM positive) was in children 0–9 years old. Exposure to HEV was higher in the Sahelian zone (55.8%, 95% CI: 40.97–70.66) than in the Sudanese zone (30.2%, 95% CI: 24.01–36.37, p = 0.003). The high prevalence rates and hepatitis virus diversity underline the challenge of routine clinical diagnosis in Chad’s Yellow Fever surveillance program.</jats:p

SARS-CoV-2 seroprevalence and associated factors among outpatient attendees at health facilities in different provinces in Chad

International audienceBackground Chad with 7,698 confirmed cases of infection and 194 deaths since the beginning of the COVID-19 pandemic, is one of the African countries with the lowest reported case numbers. However, this figure likely underestimates the true spread of the virus due to the low rate of diagnosis. The high rate of asymptomatic infections reflects the reality of SARS-CoV-2 transmission in Chad. In this study, we estimated the seroprevalence and identified factors associated with SARS-CoV-2 infection.Methods A cross-sectional study was conducted between September 2022 and February 2023. A total of 1,290 plasma samples were collected from outpatient attendees at Health Facilities located in 11 provinces of Chad and tested by ELISA method, for the presence of IgG antibodies to SARS-CoV2 nucleocapsid (N) protein. KoboToolbox was used to gather data from the participants and data were analyzed using STATA 16. ResultsThe overall seroprevalence was 83.0% [95% CI = 81.6%-85.5%], with variations between provinces, ranging from 99.2% [95% CI = 94.0%-100%] in Moundou (Southern Chad) to 46.8% [95% CI = 36.0% -57.1%] in Biltine (Eastern Chad). Factors associated with the seroprevalence included military occupation (OR = 0.37 CI [0.80-1.77] p = 0.025) and age group between 55-64 years (OR = 0.33 CI [0.15-0.72] p = 0.005). While, other factors, such as gender and age were not significantly associated with seroprevalence. ConclusionOur results indicated that, the seroprevalence of COVID-19 in Chad is among the highest in Sub-Saharan Africa. These estimates could guide the response and public health policy decisions, enhancing the management of future outbreaks involving respiratory pathogens.</div

SARS-CoV-2 seroprevalence and associated factors among outpatient attendees at health facilities in different provinces in Chad

Abstract Background Chad with 7,698 confirmed cases of infection and 194 deaths since the beginning of the COVID-19 pandemic, is one of the African countries with the lowest reported case numbers. However, this figure likely underestimates the true spread of the virus due to the low rate of diagnosis. The high rate of asymptomatic infections reflects the reality of SARS-CoV-2 transmission in Chad. In this study, we estimated the seroprevalence and identified factors associated with SARS-CoV-2 infection. Methods A cross-sectional study was conducted between September 2022 and February 2023. A total of 1,290 plasma samples were collected from outpatient attendees at Health Facilities located in 11 provinces of Chad and tested by ELISA method, for the presence of IgG antibodies to SARS-CoV2 nucleocapsid (N) protein. KoboToolbox was used to gather data from the participants and data were analyzed using STATA 16. Results The overall seroprevalence was 83.0% [95% CI = 81.6%—85.5%], with variations between provinces, ranging from 99.2% [95% CI = 94.0%—100%] in Moundou (Southern Chad) to 46.8% [95% CI = 36.0% -57.1%] in Biltine (Eastern Chad). Factors associated with the seroprevalence included military occupation (OR = 0.37 CI [0.80–1.77] p = 0.025) and age group between 55–64 years (OR = 0.33 CI [0.15–0.72] p = 0.005). While, other factors, such as gender and age were not significantly associated with seroprevalence. Conclusion Our results indicated that, the seroprevalence of COVID-19 in Chad is among the highest in Sub-Saharan Africa. These estimates could guide the response and public health policy decisions, enhancing the management of future outbreaks involving respiratory pathogens

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

AbstractInvestment in Africa over the past year with regards to SARS-CoV-2 genotyping has led to a massive increase in the number of sequences, exceeding 100,000 genomes generated to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence within their own borders, coupled with a decrease in sequencing turnaround time. Findings from this genomic surveillance underscores the heterogeneous nature of the pandemic but we observe repeated dissemination of SARS-CoV-2 variants within the continent. Sustained investment for genomic surveillance in Africa is needed as the virus continues to evolve, particularly in the low vaccination landscape. These investments are very crucial for preparedness and response for future pathogen outbreaks.One-Sentence SummaryExpanding Africa SARS-CoV-2 sequencing capacity in a fast evolving pandemic.</jats:sec