Emergence of double- and triple-gene reassortant G1P[8] rotaviruses possessing a DS-1-like backbone after rotavirus vaccine introduction in Malawi

To combat the high burden of rotavirus gastroenteritis, multiple African countries have introduced rotavirus vaccines into their childhood immunization programs. Malawi incorporated a G1P[8] rotavirus vaccine (Rotarix) into its immunization schedule in 2012. Utilizing a surveillance platform of hospitalized rotavirus gastroenteritis cases, we examined the phylodynamics of G1P[8] rotavirus strains that circulated in Malawi before (1998 to 2012) and after (2013 to 2014) vaccine introduction. Analysis of whole genomes obtained through next-generation sequencing revealed that all randomly selected prevaccine G1P[8] strains sequenced (n = 32) possessed a Wa-like genetic constellation, whereas postvaccine G1P[8] strains (n = 18) had a DS-1-like constellation. Phylodynamic analyses indicated that postvaccine G1P[8] strains emerged through reassortment events between human Wa- and DS-1-like rotaviruses that circulated in Malawi from the 1990s and hence were classified as atypical DS-1-like reassortants. The time to the most recent common ancestor for G1P[8] strains was from 1981 to 1994; their evolutionary rates ranged from 9.7 × 10−4 to 4.1 × 10−3 nucleotide substitutions/site/year. Three distinct G1P[8] lineages chronologically replaced each other between 1998 and 2014. Genetic drift was the likely driver for lineage turnover in 2005, whereas replacement in 2013 was due to reassortment. Amino acid substitution within the outer glycoprotein VP7 of G1P[8] strains had no impact on the structural conformation of the antigenic regions, suggesting that it is unlikely that they would affect recognition by vaccine-induced neutralizing antibodies. While the emergence of DS-1-like G1P[8] rotavirus reassortants in Malawi was therefore likely due to natural genotype variation, vaccine effectiveness against such strains needs careful evaluation. IMPORTANCE: The error-prone RNA-dependent RNA polymerase and the segmented RNA genome predispose rotaviruses to genetic mutation and genome reassortment, respectively. These evolutionary mechanisms generate novel strains and have the potential to lead to the emergence of vaccine escape mutants. While multiple African countries have introduced a rotavirus vaccine, there are few data describing the evolution of rotaviruses that circulated before and after vaccine introduction. We report the emergence of atypical DS-1-like G1P[8] strains during the postvaccine era in Malawi. Three distinct G1P[8] lineages circulated chronologically from 1998 to 2014; mutation and reassortment drove lineage turnover in 2005 and 2013, respectively. Amino acid substitutions within the outer capsid VP7 glycoprotein did not affect the structural conformation of mapped antigenic sites, suggesting a limited effect on the recognition of G1-specific vaccine-derived antibodies. The genes that constitute the remaining genetic backbone may play important roles in immune evasion, and vaccine effectiveness against such atypical strains needs careful evaluation

SARS-CoV-2 prevalence and immunity: a hospital-based study from Malawi

Background: COVID-19 transmission and disease dynamics in sub-Saharan Africa are not well understood. Our study aims to provide insight into COVID-19 epidemiology in Malawi by estimating SARS-CoV-2 prevalence and immunity after SARS-CoV-2 infection in a hospital-based setting. Methods: We conducted a hospital-based, convenience sampling, cross-sectional survey for SARS-CoV-2 in Lilongwe, Malawi. Participants answered a questionnaire and were tested for SARS-CoV-2 by enzyme-linked immunosorbent assay and real-time reverse-transcription polymerase chain reaction (RT-PCR). A surrogate virus neutralization test (sVNT) was performed in seropositive samples to estimate immunity. Poisson regression was used to assess SARS-CoV-2 point prevalence association with demographic and behavioral variables. Findings: The study included 930 participants. We found a combined point prevalence of 10.1%. Separately analyzed, RT-PCR positivity was 2.0%, and seropositivity was 9.3%. Of tested seropositive samples, 90.1% were sVNT positive. We found a high rate (45.7%) of asymptomatic SARS-CoV-2 infection. SARS-CoV-2 point prevalence was significantly associated with being a healthcare worker. Interpretation: Our study suggests that official data underestimate COVID-19 transmission. Using sVNTs to estimate immunity in Malawi is feasible and revealed considerable post-infection immunity in our cohort. Subclinical infection and transmission are probably a game-changer in surveillance, mitigation and vaccination strategies.Peer Reviewe

Asymptomatic Plasmodium falciparum malaria prevalence among adolescents and adults in Malawi, 2015–2016

Malaria remains a significant cause of morbidity and mortality in Malawi, with an estimated 18–19% prevalence of Plasmodium falciparum in children 2–10 years in 2015–2016. While children report the highest rates of clinical disease, adults are thought to be an important reservoir to sustained transmission due to persistent asymptomatic infection. The 2015–2016 Malawi Demographic and Health Survey was a nationally representative household survey which collected dried blood spots from 15,125 asymptomatic individuals ages 15–54 between October 2015 and February 2016. We performed quantitative polymerase chain reaction on 7,393 samples, detecting an overall P. falciparum prevalence of 31.1% (SE = 1.1). Most infections (55.6%) had parasitemias ≤ 10 parasites/µL. While 66.2% of individuals lived in a household that owned a bed net, only 36.6% reported sleeping under a long-lasting insecticide-treated net (LLIN) the previous night. Protective factors included urbanicity, greater wealth, higher education, and lower environmental temperatures. Living in a household with a bed net (prevalence difference 0.02, 95% CI − 0.02 to 0.05) and sleeping under an LLIN (0.01; − 0.02 to 0.04) were not protective against infection. Our findings demonstrate a higher parasite prevalence in adults than published estimates among children. Understanding the prevalence and distribution of asymptomatic infection is essential for targeted interventions

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

Investment in SARS-CoV-2 sequencing in Africa over the past year has led to a major increase in the number of sequences generated, now exceeding 100,000 genomes, used to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence domestically, and highlight that local sequencing enables faster turnaround time 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 shed light on 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 re-emerging 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

Metabolite changes in blood predict the onset of tuberculosis

Data availability: Metabolomic data have been deposited to Metabolomic Workbench48, ID PR000666 and are accessible under http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=PR000666. Data used to generate the figures 2–5 are available as a Source Data file.Electronic supplementary material is available online at: https://www.nature.com/articles/s41467-018-07635-7#Sec23 .Source data are available online at: https://www.nature.com/articles/s41467-018-07635-7#Sec24 .New biomarkers of tuberculosis (TB) risk and disease are critical for the urgently needed control of the ongoing TB pandemic. In a prospective multisite study across Subsaharan Africa, we analyzed metabolic profiles in serum and plasma from HIV-negative, TB-exposed individuals who either progressed to TB 3–24 months post-exposure (progressors) or remained healthy (controls). We generated a trans-African metabolic biosignature for TB, which identifies future progressors both on blinded test samples and in external data sets and shows a performance of 69% sensitivity at 75% specificity in samples within 5 months of diagnosis. These prognostic metabolic signatures are consistent with development of subclinical disease prior to manifestation of active TB. Metabolic changes associated with pre-symptomatic disease are observed as early as 12 months prior to TB diagnosis, thus enabling timely interventions to prevent disease progression and transmission.The Bill & Melinda Gates Foundation Grand Challenges in Global Health Program (BMGF GC6-74, #37772 and GC6-2013, OPP1055806), National Institutes of Health Contract No. HHSN266200700022C/NO1-AI-70022 for the Tuberculosis Research Unit (TBRU)

Neutrophil degranulation, NETosis and platelet degranulation pathway genes are co-induced in whole blood up to six months before tuberculosis diagnosis

Data Availability: The full datasets can be obtained from the Gene Expression Omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo/) as GSE94438 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE94438) and GSE89403 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE89403). These details are also provided in the Methods. Additional data on PET-CT scores accompany the revised document as S1 Table (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0278295#pone.0278295.s001).The authors acknowledge the Centre for High Performance Computing (CHPC), South Africa, for providing computational resources to this research project.Mycobacterium tuberculosis (M.tb) causes tuberculosis (TB) and remains one of the leading causes of mortality due to an infectious pathogen. Host immune responses have been implicated in driving the progression from infection to severe lung disease. We analyzed longitudinal RNA sequencing (RNAseq) data from the whole blood of 74 TB progressors whose samples were grouped into four six-month intervals preceding diagnosis (the GC6-74 study). We additionally analyzed RNAseq data from an independent cohort of 90 TB patients with positron emission tomography-computed tomography (PET-CT) scan results which were used to categorize them into groups with high and low levels of lung damage (the Catalysis TB Biomarker study). These groups were compared to non-TB controls to obtain a complete whole blood transcriptional profile for individuals spanning from early stages of M.tb infection to TB diagnosis. The results revealed a steady increase in the number of genes that were differentially expressed in progressors at time points closer to diagnosis with 278 genes at 13–18 months, 742 at 7–12 months and 5,131 detected 1–6 months before diagnosis and 9,205 detected in TB patients. A total of 2,144 differentially expressed genes were detected when comparing TB patients with high and low levels of lung damage. There was a large overlap in the genes upregulated in progressors 1–6 months before diagnosis (86%) with those in TB patients. A comprehensive pathway analysis revealed a potent activation of neutrophil and platelet mediated defenses including neutrophil and platelet degranulation, and NET formation at both time points. These pathways were also enriched in TB patients with high levels of lung damage compared to those with low. These findings suggest that neutrophils and platelets play a critical role in TB pathogenesis, and provide details of the timing of specific effector mechanisms that may contribute to TB lung pathology.SM, EM, GT and GW were supported by the South African Tuberculosis Bioinformatics Initiative (SATBBI), a Strategic Health Innovation Partnership grant from the South African Medical Research Council (https://www.samrc.ac.za/) and South African Department of Science and Innovation (https://www.dst.gov.za/); no grant number. STM received funding from the EDCTP2 program (Grant Number CDF1576) supported by the European Union (http://www.edctp.org/projects-2/#). GW received funding from the South African National Research Foundation (SARChI TB Biomarkers #86535) and the South African Medical Research Council (https://www.samrc.ac.za/). SHEK, TJS and GW received funding from the Bill and Melinda Gates Foundation (Grant Numbers OPP37772 & OPP1055806), (https://www.gatesfoundation.org/) GW received funding from the Bill and Melinda Gates Foundation (Grant Number OPP51919) (https://www.gatesfoundation.org/) through the Catalysis Foundation for Health (https://catalysisfoundation.org/) AGL is supported by the NRF-CSUR (Grant Number CSUR60502163639) and by the Centre for Tuberculosis Research from the South African Medical Research Council (https://www.samrc.ac.za/). JAS is supported by a Clinician Scientist Fellowship (Grant Number MR/R007942/1) jointly funded by the UK Medical Research Council (MRC; https://www.ukri.org/about-us/mrc/) and the UK Department for International Development [DFID; replaced by Foreign, Commonwealth & Development Office (FCDO); https://www.gov.uk/government/organisations/foreign-commonwealth-development-office] under the MRC/DFID Concordat agreement

Immunometabolic signatures predict risk of progression to active tuberculosis and disease outcome

Data Availability: All datasets generated for this study are included in the manuscript with the exception of the rhesus macaque metabolics data which is included as Table S6 [https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2019.00527/full#SM14].Supplementary Material is available online at: https://www.frontiersin.org/articles/10.3389/fimmu.2019.00527/full#supplementary-material .There remains a pressing need for biomarkers that can predict who will progress to active tuberculosis (TB) after exposure to Mycobacterium tuberculosis (MTB) bacterium. By analyzing cohorts of household contacts of TB index cases (HHCs) and a stringent non-human primate (NHP) challenge model, we evaluated whether integration of blood transcriptional profiling with serum metabolomic profiling can provide new understanding of disease processes and enable improved prediction of TB progression. Compared to either alone, the combined application of pre-existing transcriptome- and metabolome-based signatures more accurately predicted TB progression in the HHC cohorts and more accurately predicted disease severity in the NHPs. Pathway and data-driven correlation analyses of the integrated transcriptional and metabolomic datasets further identified novel immunometabolomic signatures significantly associated with TB progression in HHCs and NHPs, implicating cortisol, tryptophan, glutathione, and tRNA acylation networks. These results demonstrate the power of multi-omics analysis to provide new insights into complex disease processes.This work was supported by the Bill & Melinda Gates Foundation (BMGF) Grand Challenges in Global Health (GC6-74 grant 37772, OPP1055806 and OPP1087783 in conjunction with AERAS). This work was also supported by a Strategic Health Innovation Partnership grant from the South African Medical Research Council and Department of Science and Technology/South African Tuberculosis Bioinformatics Initiative. Additional support was provided by the European Union FP7 (ADITEC, 280873 and TBVAC2020, 643381) and the National Institutes of Health [U19 AI106761 and U19 AI135976]. FD was supported by the NCDIR (National Institutes of Health [P41 GM109824]). DT and GT were supported by South African Medical Research Council SHIP funding for the South African Tuberculosis Bioinformatics Initiative to GW