Evolutionary changes between pre- and post-vaccine South African group A G2P[4] rotavirus strains, 2003-2017.

The transient upsurge of G2P[4] group A rotavirus (RVA) after Rotarix vaccine introduction in several countries has been a matter of concern. To gain insight into the diversity and evolution of G2P[4] strains in South Africa pre- and post-RVA vaccination introduction, whole-genome sequencing was performed for RVA positive faecal specimens collected between 2003 and 2017 and samples previously sequenced were obtained from GenBank (n=103; 56 pre- and 47 post-vaccine). Pre-vaccine G2 sequences predominantly clustered within sub-lineage IVa-1. In contrast, post-vaccine G2 sequences clustered mainly within sub-lineage IVa-3, whereby a radical amino acid (AA) substitution, S15F, was observed between the two sub-lineages. Pre-vaccine P[4] sequences predominantly segregated within sub-lineage IVa while post-vaccine sequences clustered mostly within sub-lineage IVb, with a radical AA substitution R162G. Both S15F and R162G occurred outside recognised antigenic sites. The AA residue at position 15 is found within the signal sequence domain of Viral Protein 7 (VP7) involved in translocation of VP7 into endoplasmic reticulum during infection process. The 162 AA residue lies within the hemagglutination domain of Viral Protein 4 (VP4) engaged in interaction with sialic acid-containing structure during attachment to the target cell. Free energy change analysis on VP7 indicated accumulation of stable point mutations in both antigenic and non-antigenic regions. The segregation of South African G2P[4] strains into pre- and post-vaccination sub-lineages is likely due to erstwhile hypothesized stepwise lineage/sub-lineage evolution of G2P[4] strains rather than RVA vaccine introduction. Our findings reinforce the need for continuous whole-genome RVA surveillance and investigation of contribution of AA substitutions in understanding the dynamic G2P[4] epidemiology.

Whole Genome In-Silico Analysis of South African G1P[8] Rotavirus Strains Before and After Vaccine Introduction Over A Period of 14 Years.

Rotavirus G1P[8] strains account for more than half of the group A rotavirus (RVA) infections in children under five years of age, globally. A total of 103 stool samples previously characterized as G1P[8] and collected seven years before and seven years after introducing the Rotarix® vaccine in South Africa were processed for whole-genome sequencing. All the strains analyzed had a Wa-like constellation (G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1). South African pre- and post-vaccine G1 strains were clustered in G1 lineage-I and II while the majority (84.2%) of the P[8] strains were grouped in P[8] lineage-III. Several amino acid sites across ten gene segments with the exception of VP7 were under positive selective pressure. Except for the N147D substitution in the antigenic site of eight post-vaccine G1 strains when compared to both Rotarix® and pre-vaccine strains, most of the amino acid substitutions in the antigenic regions of post-vaccine G1P[8] strains were already present during the pre-vaccine period. Therefore, Rotarix® did not appear to have an impact on the amino acid differences in the antigenic regions of South African post-vaccine G1P[8] strains. However, continued whole-genome surveillance of RVA strains to decipher genetic changes in the post-vaccine period remains imperative.

Report of the 1st African Enteric Viruses Genome Initiative (AEVGI) Data and Bioinformatics Workshop on whole-genome analysis of some African rotavirus strains held in Bloemfontein, South Africa.

The University of the Free State - Next Generation Sequencing (NGS) Unit, Bloemfontein, South Africa, hosted a data and bioinformatics workshop from 19 to 22 June 2018. The workshop was coordinated by the African Enteric Viruses Genome Initiative (AEVGI) with support from the Bill & Melinda Gates Foundation. The event introduced technologies in NGS and data analysis with focus on the rotavirus (RV) genome. The workshop fostered interactions and networking between professionals, scientific experts, technicians and students. The courses provided an overview of RV diarrhoea and its burden in Africa, while highlighting the key resources and methodologies in NGS and advanced bioinformatics in deciphering vaccine impact. It was concluded that, despite the reported significant decline in RV associated-diarrhoea mortality and morbidity in Africa due to RV vaccine impact, the need for continuous surveillance and genomic characterization to better understand the ever-changing dynamics of RV strains is imperative.

Uncovering the First Atypical DS-1-like G1P[8] Rotavirus Strains That Circulated during Pre-Rotavirus Vaccine Introduction Era in South Africa.

Emergence of DS-1-like G1P[8] group A rotavirus (RVA) strains during post-rotavirus vaccination period has recently been reported in several countries. This study demonstrates, for the first time, rare atypical DS-1-like G1P[8] RVA strains that circulated in 2008 during pre-vaccine era in South Africa. Rotavirus positive samples were subjected to whole-genome sequencing. Two G1P[8] strains (RVA/Human-wt/ZAF/UFS-NGS-MRC-DPRU1971/2008/G1P[8] and RVA/Human-wt/ZAF/UFS-NGS-MRC-DPRU1973/2008/G1P[8]) possessed a DS-1-like genome constellation background (I2-R2-C2-M2-A2-N2-T2-E2-H2). The outer VP4 and VP7 capsid genes of the two South African G1P[8] strains had the highest nucleotide (amino acid) nt (aa) identities of 99.6-99.9% (99.1-100%) with the VP4 and the VP7 genes of a locally circulating South African strain, RVA/Human-wt/ZAF/MRC-DPRU1039/2008/G1P[8]. All the internal backbone genes (VP1-VP3, VP6, and NSP1-NSP5) had the highest nt (aa) identities with cognate internal genes of another locally circulating South African strain, RVA/Human-wt/ZAF/MRC-DPRU2344/2008/G2P[6]. The two study strains emerged through reassortment mechanism involving locally circulating South African strains, as they were distinctly unrelated to other reported atypical G1P[8] strains. The identification of these G1P[8] double-gene reassortants during the pre-vaccination period strongly supports natural RVA evolutionary mechanisms of the RVA genome. There is a need to maintain long-term whole-genome surveillance to monitor such atypical strains.

Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians.

BACKGROUND: African populations provide a unique opportunity to interrogate host-microbe co-evolution and its impact on adaptive phenotypes due to their genomic, phenotypic, and cultural diversity. We integrate gut microbiome 16S rRNA amplicon and shotgun metagenomic sequence data with quantification of pathogen burden and measures of immune parameters for 575 ethnically diverse Africans from Cameroon. Subjects followed pastoralist, agropastoralist, and hunter-gatherer lifestyles and were compared to an urban US population from Philadelphia. RESULTS: We observe significant differences in gut microbiome composition across populations that correlate with subsistence strategy and country. After these, the variable most strongly associated with gut microbiome structure in Cameroonians is the presence of gut parasites. Hunter-gatherers have high frequencies of parasites relative to agropastoralists and pastoralists. Ascaris lumbricoides, Necator americanus, Trichuris trichiura, and Strongyloides stercoralis soil-transmitted helminths ("ANTS" parasites) significantly co-occur, and increased frequency of gut parasites correlates with increased gut microbial diversity. Gut microbiome composition predicts ANTS positivity with 80% accuracy. Colonization with ANTS, in turn, is associated with elevated levels of TH1, TH2, and proinflammatory cytokines, indicating an association with multiple immune mechanisms. The unprecedented size of this dataset allowed interrogation of additional questions-for example, we find that Fulani pastoralists, who consume high levels of milk, possess an enrichment of gut bacteria that catabolize galactose, an end product of lactose metabolism, and of bacteria that metabolize lipids. CONCLUSIONS: These data document associations of bacterial microbiota and eukaryotic parasites with each other and with host immune responses; each of these is further correlated with subsistence practices.

Pre-vaccine circulating group a rotavirus strains in under 5 years children with acute diarrhea during 1999-2013 in Cameroon.

The aim of this review was to assess all the studies on rotavirus G and P characterization during the pre-vaccine period (1999-2013) in Cameroon to have a better basis for post-vaccine introduction evaluations. A retrospective study was done through a comprehensive review of published (PubMed, Google Scholar) and accessible unpublished data on rotavirus G and P genotypes circulating in five regions of Cameroon. Descriptive data were expressed as frequencies tables and proportions. A total of 1844 rotavirus positive cases were analyzed. In all, 1534 strains were characterized for the P (VP4) specificity. Six different VP4 genotypes were observed, including P [4], P [6], P [8], P [9], P [10] and P [14]. The most predominant P genotypes were P [8] at 42.6%, and P [6] at 37.9%. Mixed infections were observed at 5.3%, whereas 4.1% of the strains were P non-typeable. A total of 1518 rotavirus strains were characterized for the G (VP7) specificity. VP7 genotypes G1, G2, G3, G4, G5, G6, G8, G9, G10 and G12 were observed. G1 (35.3%), G3 (19.5%), G2 (14.9%) and G12 (10.1%) were the predominant G genotypes while G5 and G10 were least prevalent at 0.06% each. Approximately 5.1% of all strains were G non-typeable whereas 5.3% were mixed G genotypes. A total of 1472 strains were characterized for both G and P genes, from which 38 different G-P combinations were observed. Overall, G1P [8] (22%) was identified as the predominant rotavirus strain circulating in Cameroon followed by G3P [6] (15%). In conclusion, we observed that the genotypes identified in Cameroon during 1999-2013 were partially covered by the two WHO recommended rotavirus vaccines. This review provides comprehensive up-to-date information on rotavirus strain surveillance in Cameroon during the pre-vaccination era.

Vitamin A supplements for reducing mother-to-child HIV transmission.

BACKGROUND: Strategies to reduce the risk of mother-to-child transmission of the human immunodeficiency virus (HIV) include lifelong antiretroviral therapy (ART) for HIV-positive women, exclusive breastfeeding from birth for six weeks plus nevirapine or replacement feeding plus nevirapine from birth for four to six weeks, elective Caesarean section delivery, and avoiding giving children chewed food. In some settings, these interventions may not be practical, feasible, or affordable. Simple, inexpensive, and effective interventions (that could potentially be implemented even in the absence of prenatal HIV testing programmes) would be valuable. Vitamin A, which plays a role in immune function, is one low-cost intervention that has been suggested in such settings. OBJECTIVES: To summarize the effects of giving vitamin A supplements to HIV-positive women during pregnancy and after delivery. SEARCH METHODS: We searched the Cochrane Central Register of Controlled Trials (CENTRAL), PubMed, Embase, and the World Health Organization International Clinical Trials Registry Platform (WHO ICTRP) up to 25 August 2017, and checked the reference lists of relevant articles for eligible studies. SELECTION CRITERIA: We included randomized controlled trials conducted in any setting that compared vitamin A supplements to placebo or no intervention among HIV-positive women during pregnancy or after delivery, or both. DATA COLLECTION AND ANALYSIS: At least two review authors independently assessed study eligibility and extracted data. We expressed study results as risk ratios (RR) or mean differences (MD) as appropriate, with their 95% confidence intervals (CI), and conducted random-effects meta-analyses. This is an update of a review last published in 2011. MAIN RESULTS: Five trials met the inclusion criteria. These were conducted in Malawi, South Africa, Tanzania, and Zimbabwe between 1995 and 2005 and none of the participants received ART. Women allocated to intervention arms received vitamin A supplements at a variety of doses (daily during pregnancy; a single dose immediately after delivery, or daily doses during pregnancy plus a single dose after delivery). Women allocated to comparison arms received identical placebo (6601 women, 4 trials) or no intervention (697 women, 1 trial). Four trials (with 6995 women) had low risk of bias and one trial (with 303 women) had high risk of attrition bias.The trials show that giving vitamin A supplements to HIV-positive women during pregnancy, the immediate postpartum period, or both, probably has little or no effect on mother-to-child transmission of HIV (RR 1.07, 95% CI 0.91 to 1.26; 4428 women, 5 trials, moderate certainty evidence) and may have little or no effect on child death by two years of age (RR 1.06, 95% CI 0.92 to 1.22; 3883 women, 3 trials, low certainty evidence). However, giving vitamin A supplements during pregnancy may increase the mean birthweight (MD 34.12 g, 95% CI -12.79 to 81.02; 2181 women, 3 trials, low certainty evidence) and probably reduces the incidence of low birthweight (RR 0.78, 95% CI 0.63 to 0.97; 1819 women, 3 trials, moderate certainty evidence); but we do not know whether vitamin A supplements affect the risk of preterm delivery (1577 women, 2 trials), stillbirth (2335 women, 3 trials), or maternal death (1267 women, 2 trials). AUTHORS' CONCLUSIONS: Antepartum or postpartum vitamin A supplementation, or both, probably has little or no effect on mother-to-child transmission of HIV in women living with HIV infection and not on antiretroviral drugs. The intervention has largely been superseded by ART which is widely available and effective in preventing vertical transmission.

Public stewardship of private for-profit healthcare providers in low- and middle-income countries.

BACKGROUND: Governments use different approaches to ensure that private for-profit healthcare services meet certain quality standards. Such government guidance, referred to as public stewardship, encompasses government policies, regulatory mechanisms, and implementation strategies for ensuring accountability in the delivery of services. However, the effectiveness of these strategies in low- and middle-income countries (LMICs) have not been the subject of a systematic review. OBJECTIVES: To assess the effects of public sector regulation, training, or co-ordination of the private for-profit health sector in low- and middle-income countries. SEARCH METHODS: For related systematic reviews, we searched the Cochrane Database of Systematic Reviews (CDSR) 2015, Issue 4; Database of Abstracts of Reviews of Effectiveness (DARE) 2015, Issue 1; Health Technology Assessment Database (HTA) 2015, Issue 1; all part of The Cochrane Library, and searched 28 April 2015. For primary studies, we searched MEDLINE, Epub Ahead of Print, In-Process & Other Non-Indexed Citations, MEDLINE Daily and MEDLINE 1946 to Present, OvidSP (searched 16 June 2016); Science Citation Index and Social Sciences Citation Index 1987 to present, and Emerging Sources Citation Index 2015 to present, ISI Web of Science (searched 3 May 2016 for papers citing included studies); Cochrane Central Register of Controlled Trials (CENTRAL), 2015, Issue 3, part of The Cochrane Library (including the Cochrane Effective Practice and Organisation of Care (EPOC) Group Specialised Register) (searched 28 April 2015); Embase 1980 to 2015 Week 17, OvidSP (searched 28 April 2015); Global Health 1973 to 2015 Week 16, OvidSP (searched 30 April 2015); WHOLIS, WHO (searched 30 April 2015); Science Citation Index and Social Sciences Citation Index 1975 to present, ISI Web of Science (searched 30 April 2015); Health Management, ProQuest (searched 22 November 2013). In addition, in April 2016, we searched the reference lists of relevant articles, WHO International Clinical Trials Registry Platform, Clinicaltrials.gov, and various electronic databases of grey literature. SELECTION CRITERIA: Randomised trials, non-randomised trials, interrupted time series studies, or controlled before-after studies. DATA COLLECTION AND ANALYSIS: Two authors independently assessed study eligibility and extracted data, comparing their results and resolving discrepancies by consensus. We expressed study results as risk ratios (RR) or mean differences (MD) with 95% confidence intervals (CI), where appropriate, and assessed the certainty of the evidence using Grades of Recommendation, Assessment, Development and Evaluation (GRADE). We did not conduct meta-analysis because of heterogeneity of interventions and study designs. MAIN RESULTS: We identified 20,177 records, 50 of them potentially eligible. We excluded 39 potentially eligible studies because they did not involve a rigorous evaluation of training, regulation, or co-ordination of private for-profit healthcare providers in LMICs; five studies identified after the review was submitted are awaiting assessment; and six studies met our inclusion criteria. Two included studies assessed training alone; one assessed regulation alone; three assessed a multifaceted intervention involving training and regulation; and none assessed co-ordination. All six included studies targeted private for-profit pharmacy workers in Africa and Asia.Three studies found that training probably increases sale of oral rehydration solution (one trial in Kenya, 106 pharmacies: RR 3.04, 95% CI 1.37 to 6.75; and one trial in Indonesia, 87 pharmacies: RR 1.41, 95% CI 1.03 to 1.93) and dispensing of anti-malarial drugs (one trial in Kenya, 293 pharmacies: RR 8.76, 95% CI 0.94 to 81.81); moderate-certainty evidence.One study conducted in the Lao People's Democratic Republic shows that regulation of the distribution and sale of registered pharmaceutical products may improve composite pharmacy indicators (one trial, 115 pharmacies: improvements in four of six pharmacy indicators; low-certainty evidence).The outcome in three multifaceted intervention studies was the quality of pharmacy practice; including the ability to ask questions, give advice, and provide appropriate treatment. The trials applied regulation, training, and peer influence in sequence; and the study design does not permit separation of the effects of the different interventions. Two trials conducted among 136 pharmacies in Vietnam found that the multifaceted intervention may improve the quality of pharmacy practice; but the third study, involving 146 pharmacies in Vietnam and Thailand, found that the intervention may have little or no effects on the quality of pharmacy practice (low-certainty evidence).Only two studies (both conducted in Vietnam) reported cost data, with no rigorous assessment of the economic implications of implementing the interventions in resource-constrained settings. No study reported data on equity, mortality, morbidity, adverse effects, satisfaction, or attitudes. AUTHORS' CONCLUSIONS: Training probably improves quality of care (i.e. adherence to recommended practice), regulation may improve quality of care, and we are uncertain about the effects of co-ordination on quality of private for-profit healthcare services in LMICs. The likelihood that further research will find the effect of training to be substantially different from the results of this review is moderate; implying that monitoring of the impact is likely to be needed if training is implemented. The low certainty of the evidence for regulation implies that the likelihood of further research finding the effect of regulation to be substantially different from the results of this review is high. Therefore, an impact evaluation is warranted if government regulation of private for-profit providers is implemented in LMICs. Rigorous evaluations of these interventions should also assess other outcomes such as impacts on equity, cost implications, mortality, morbidity, and adverse effects.

Evaluation of BBL™ Sensi-Discs™ and FTA® cards as sampling devices for detection of rotavirus in stool samples.

Rotavirus is the most important cause of severe childhood gastroenteritis worldwide. Rotavirus vaccines are available and rotavirus surveillance is carried out to assess vaccination impact. In surveillance studies, stool samples are stored typically at 4°C or frozen to maintain sample quality. Uninterrupted cold storage is a problem in developing countries because of power interruptions. Cold-chain transportation of samples from collection sites to testing laboratories is costly. In this study, we evaluated the use of BBL™ Sensi-Discs™ and FTA(®) cards for storage and transportation of samples for virus isolation, EIA, and RT-PCR testing. Infectious rotavirus was recovered after 30 days of storage on Sensi-Discs™ at room temperature. We were able to genotype 98-99% of samples stored on Sensi-Discs™ and FTA(®) cards at temperatures ranging from -80°C to 37°C up to 180 days. A field sampling test using samples prepared and shipped from Cameroon, showed that both matrices yielded 100% genotyping success compared with whole stool and Sensi-Discs™ demonstrated 95% concordance with whole stool in EIA testing. The utilization of BBL™ Sensi-Discs™ and FTA(®) cards for stool sample storage and shipment has the potential to have great impact on global public health by facilitating surveillance and epidemiological investigations of rotavirus strains worldwide at a reduced cost.