Mutations in the “a” Determinant Region of Hepatitis B Virus Genotype A among Voluntary Kenyan Blood Donors

Background: Occurrence of mutations within the major antigenic alpha determinant region of hepatitis B surface antigen (HBsAg can alter HBV antigenicity resulting in   failures in diagnosis, vaccine and hepatitis B immunoglobulin therapy. Objective: This study aimed at detection of mutations in the “a” determinant region of HBV surface antigen among voluntary blood donors in Kenya. Design: A cross sectional study involving serology and molecular techniques Settings: This study involved analysis of samples from blood transfusion centers Subjects: A total of 301 blood samples from donor blood were collected for the study. Methods: Sero-status for HBsAg was determined using Enzyme-Linked Immunosorbent Assay (ELISA). A fragment of the S gene including the "a" determinant was amplified by PCR from the HBsAg positive samples and sequenced for mutation analysis. Mutations and phylogenetic analyses were performed using Mega 6 software, Bioedit software and GENETYX® software version 9.1.0. Results: Out of the 301 samples tested 69/301 (22.9%) were Polymerase Chain Reaction (PCR) positive including 2/69(2.9%) were sero-negative for HBsAg. All isolates were genotype A, sub-genotype A1. A total of 29 mutations were observed of which 37.9% were located within the “a” determinant. Mutations T143M and K122R were the most frequent in this study. Escape mutations associated with diagnostic failure, vaccine and immunoglobulin therapy escape were also identified. Conclusions: These findings are important for policies related to vaccine implementation and therapeutic and diagnostic guidelines. Keywords: Escape mutants, genotype, hepatitis B virus, antigenic determinant, surface antigen

Mutations in the “a” Determinant Region of Hepatitis B Virus Genotype A among Voluntary Kenyan Blood Donors

Occurrence of mutations within the major antigenic alpha determinant region of hepatitis B surface antigen (HBsAg can alter HBV antigenicity resulting in   failures in diagnosis, vaccine and hepatitis B immunoglobulin therapy. This study aimed at detection of mutations in the “a” determinant region of HBV surface antigen among voluntary blood donors in Kenya. This was a cross sectional study involving serology and molecular techniques. This study involved analysis of samples from blood transfusion centers. A total of 301 blood samples from donor blood were collected for the study.  Sero-status for HBsAg was determined using Enzyme-Linked Immunosorbent Assay (ELISA). A fragment of the S gene including the "a" determinant was amplified by PCR from the HBsAg positive samples and sequenced for mutation analysis. Mutations and phylogenetic analyses were performed using Mega 6 software, Bioedit software and GENETYX® software version 9.1.0. Out of the 301 samples tested 69/301 (22.9%) were Polymerase Chain Reaction (PCR) positive including 2/69(2.9%) were sero-negative for HBsAg. All isolates were genotype A, sub-genotype A1. A total of 29 mutations were observed of which 37.9% were located within the “a” determinant. Mutations T143M and K122R were the most frequent in this study. Escape mutations associated with diagnostic failure, vaccine and immunoglobulin therapy escape were also identified. These findings are important for policies related to vaccine implementation and therapeutic and diagnostic guidelines. Keywords: Escape mutants, genotype, hepatitis B virus, antigenic determinant, surface antige

Clinical epidemiology of COVID-19 among hospitalized children in rural western Kenya

The epidemiology of pediatric COVID-19 in sub-Saharan Africa and the role of fecal-oral transmission in SARS-CoV-2 are poorly understood. Among children and adolescents in Kenya, we identify correlates of COVID-19 infection, document the clinical outcomes of infection, and evaluate the prevalence and viability of SARS-CoV-2 in stool. We recruited a prospective cohort of hospitalized children aged two months to 15 years in western Kenya between March 1 and June 30 2021. Children with SARS-CoV-2 were followed monthly for 180-days after hospital discharge. Bivariable logistic regression analysis was used to identify the clinical and sociodemographics correlates of SARS-CoV-2 infection. We also calculated the prevalence of SARS-CoV-2 detection in stool of confirmed cases. Of 355 systematically tested children, 55 (15.5%) were positive and were included in the cohort. The commonest clinical features among COVID-19 cases were fever (42/55, 76%), cough (19/55, 35%), nausea and vomiting (19/55, 35%), and lethargy (19/55, 35%). There were no statistically significant difference in baseline sociodemographic and clinical characteristics between SARS-CoV-2 positive and negative participants. Among positive participants, 8/55 (14.5%, 95%CI: 5.3%-23.9%) died; seven during the inpatient period. Forty-nine children with COVID-19 had stool samples or rectal swabs available at baseline, 9 (17%) had PCR-positive stool or rectal swabs, but none had SARS-CoV-2 detected by culture. Syndromic identification of COVID-19 is particularly challenging among children as the presenting symptoms and signs mirror other common pediatric diseases. Mortality among children hospitalized with COVID-19 was high in this cohort but was comparable to mortality seen with other common illnesses in this setting. Among this small set of children with COVID-19 we detected SARS-CoV-2 DNA, but were not able to culture viable SARs-CoV-2 virus, in stool. This suggests that fecal transmission may not be a substantial risk in children recently diagnosed and hospitalized with COVID-19 infection

Are slum dwellers at heightened risk of HIV infection than other urban residents? Evidence from population-based HIV prevalence surveys in Kenya

In 2008, the global urban population surpassed the rural population and by 2050 more than 6 billion will be living in urban centres. A growing body of research has reported on poor health outcomes among the urban poor but not much is known about HIV prevalence among this group. A survey of nearly 3000 men and women was conducted in two Nairobi slums in Kenya between 2006 and 2007, where respondents were tested for HIV status. In addition, data from the 2008/2009 Kenya Demographic and Health Survey were used to compare HIV prevalence between slum residents and those living in other urban and rural areas. The results showed strong intra-urban differences. HIV was 12% among slum residents compared with 5% and 6% among non-slum urban and rural residents, respectively. Generally, men had lower HIV prevalence than women although in the slums the gap was narrower. Among women, sexual experience before the age of 15 compared with after 19 years was associated with 62% higher odds of being HIV positive. There was ethnic variation in patterns of HIV infection although the effect depended on the current place of residence

HIV-1 subtype and viral tropism determination for evaluating antiretroviral therapy options: an analysis of archived Kenyan blood samples

<p>Abstract</p> <p>Background</p> <p>Infection with HIV-1 is characterized by genetic diversity such that specific viral subtypes are predominant in specific geographical areas. The genetic variation in HIV-1 <it>pol </it>and <it>env </it>genes is responsible for rapid development of resistance to current drugs. This variation has influenced disease progression among the infected and necessitated the search for alternative drugs with novel targets. Though successfully used in developed countries, these novel drugs are still limited in resource-poor countries. The aim of this study was to determine HIV-1 subtypes, recombination, dual infections and viral tropism of HIV-1 among Kenyan patients prior to widespread use of antiretroviral drugs.</p> <p>Methods</p> <p>Remnant blood samples from consenting sexually transmitted infection (STI) patients in Nairobi were collected between February and May 2001 and stored. Polymerase chain reaction and cloning of portions of HIV-1 <it>gag</it>, <it>pol </it>and <it>env </it>genes was carried out followed by automated DNA sequencing.</p> <p>Results</p> <p>Twenty HIV-1 positive samples (from 11 females and 9 males) were analyzed. The average age of males (32.5 years) and females (26.5 years) was significantly different (p value < 0.0001). Phylogenetic analysis revealed that 90% (18/20) were concordant HIV-1 subtypes: 12 were subtype A1; 2, A2; 3, D and 1, C. Two samples (10%) were discordant showing different subtypes in the three regions. Of 19 samples checked for co-receptor usage, 14 (73.7%) were chemokine co-receptor 5 (CCR5) variants while three (15.8%) were CXCR4 variants. Two had dual/mixed co-receptor use with X4 variants being minor population.</p> <p>Conclusion</p> <p>HIV-1 subtype A accounted for majority of the infections. Though perceived to be a high risk population, the prevalence of recombination in this sample was low with no dual infections detected. Genotypic co-receptor analysis showed that most patients harbored viruses that are predicted to use CCR5.</p

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