Genetic characterization of G12P[6] and G12P[8] rotavirus strains collected in six African countries between 2010 and 2014.

BACKGROUND: G12 rotaviruses were first observed in sub-Saharan Africa in 2004 and since then have continued to emerge and spread across the continent and are reported as a significant human rotavirus genotype in several African countries, both prior to and after rotavirus vaccine introduction. This study investigated the genetic variability of 15 G12 rotavirus strains associated with either P[6] or P[8] identified between 2010 and 2014 from Ethiopia, Kenya, Rwanda, Tanzania, Togo and Zambia. METHODS: The investigation was carried out by comparing partial VP7 and partial VP4 sequences of the African G12P[6] and G12P[8] strains with the available GenBank sequences and exploring the recognized neutralization epitopes of these strains. Additionally, Bayesian evolutionary analysis was carried out using Markov Chain Monte Carlo (MCMC) implemented in BEAST to estimate the time to the most recent ancestor and evolutionary rate for these G12 rotavirus strains. RESULTS: The findings suggested that the VP7 and VP4 nucleotide and amino acid sequences of the G12 strains circulating in African countries are closely related, irrespective of country of origin and year of detection, with the exception of the Ethiopian strains that clustered distinctly. Neutralization epitope analysis revealed that rotavirus VP4 P[8] genes associated with G12 had amino acid sequences similar to those reported globally including the vaccine strains in RotaTeq and Rotarix. The estimated evolutionary rate of the G12 strains was 1.016 × 10- 3 substitutions/site/year and was comparable to what has been previously reported. Three sub-clusters formed within the current circulating lineage III shows the diversification of G12 from three independent ancestries within a similar time frame in the late 1990s. CONCLUSIONS: At present it appears to be unlikely that widespread vaccine use has driven the molecular evolution and sustainability of G12 strains in Africa. Continuous monitoring of rotavirus genotypes is recommended to assess the long-term impact of rotavirus vaccination on the dynamic nature of rotavirus evolution on the continent.

Low seroprevalence of hepatitis E virus in pregnant women in an urban area near Pretoria, South Africa.

Objectives: Hepatitis E virus (HEV) infection is a globally neglected health problem with a high burden in resource-poor communities. Pregnant women are at increased risk of complications. This pilot study sought to assess the seroprevalence of HEV infection in pregnant women at Dr George Mukhari Academic Hospital, South Africa. Methods: Stored serum samples from 384 HIV-uninfected pregnant women attending the antenatal clinic were initially screened for HEV total antibody. Positive samples were further evaluated for the presence of IgG and IgM antibody isotypes, using commercial ELISA assays. HEV RNA was assessed in antibody-positive samples utilizing qRT-PCR assay. Results: The sample consisted of women with a median age of 31 years (interquartile range: 28-35 years). Total HEV antibody was detected in 12/384 (3.13%, 95% CI: 1.80-5.38) of these pregnant women. All 12 samples were IgG HEV antibody positive, but none tested positive for IgM antibody or for HEV RNA, demonstrating a lack of current or recent exposure. Conclusions: Our study revealed a low seroprevalence of HEV among pregnant women from an urban area north of Pretoria. This observation warrants further attention to the circulation of HEV in this population, and a greater understanding of the epidemiology of the infection in South Africa.

Impact of vaccine stock-outs on infant vaccination coverage: a hospital-based survey from South Africa.

Introduction: National population-based immunization coverage surveys provide data for validating official administrative coverage figures. However, these costly and logistically challenging surveys are conducted infrequently. This hospital-based records review determined coverage of birth-dose vaccines, fully immunized under 1-y-old coverage (FIC) of 12- to 59-mo-old children; and the reasons for missed vaccinations. Methods: Rotavirus surveillance in South Africa is based on under-5-y-old children being treated for diarrhoea, and includes photocopying the official vaccination document and collecting data on reasons for missed vaccinations. These data were captured from all 508 records collected from 2011 to 2014, and subjected to descriptive statistical analysis. Results: Bacille Calmette Guérin coverage was 99%; oral polio vaccine birth dose (OPV(0)) coverage was 99%. Coverage for 12- to 59-mo-olds ranged from 75% for the pneumococcal conjugate vaccine third dose to 99% for OPV(0). Several instances of subsequent doses being recorded without prior doses being received resulted in a FIC of 55%. In total, 207 vaccinations were missed by 88 children. Vaccine stock-outs were responsible for 62% of missed vaccinations. Conclusions: Efforts to improve vaccine stock management at facility and district levels should be implemented, and should include vaccinator training and supervision to eliminate vaccine stock-outs and missed vaccination opportunities.

Complete genome analyses of the first porcine rotavirus group H identified from a South African pig does not provide evidence for recent interspecies transmission events.

Rotaviruses (RVs) are classified into eight species/groups (RVA-RVH) according to the migration patterns of their 11 genome segments, as well as by serological and molecular properties of Viral Protein 6 (VP6). In 1997 a new unclassified RV was reported infecting adults in Bangladesh and China. This virus was initially named novel adult diarrhoea rotavirus (ADRV-N), but later renamed as RVH. Since then, RVH has been detected in humans only very sporadically. However, RVH is increasingly being detected in pig populations in the USA, Brazil and Japan, but not yet in Africa. Unfortunately, whole genome sequence data of porcine RVH strains in GenBank is currently restricted to a single strain (SKA-1) from Japan. Porcine diarrhoeic samples were collected in South Africa and analysed for rotavirus using an RVA ELISA and electropherotyping by PAGE. One sample displayed a 4:2:1:1:1:1:1 migration pattern, typical for RVH. In order to further investigate this strain, sequence-independent amplification followed by random sequencing using the 454/Roche GS FLX Sequencer was performed, resulting in the second complete porcine RVH strain (MRC-DPRU1575) available in databases. Phylogenetically, all segments of MRC-DPRU1575 clustered closely with the SKA-1 strain and in some segments with known porcine RVH strains from Brazil and the USA. In contrast, the porcine RVH strains were only distantly related to human RVH strains from Asia and a partial RVH-like strain recently detected in bats from Cameroon. Overall, strain MRC-DPRU1575 is the first complete genome of a porcine RVH from Africa and allows for the development of improved RVH screening methods. Our analyses indicate that RVH strains cluster according to their host species, not suggesting any evidence of recent interspecies transmission events. However, more RVH genomes from a wider host range are needed to better understand their evolutionary pathways and zoonotic potential.

Epidemiology of rotavirus diarrhea and diversity of rotavirus strains among children less than 5 years of age with acute gastroenteritis in Mauritius: June 2008 to December 2010.

BACKGROUND: Rotavirus is an important etiologic agent of diarrhea worldwide and ongoing surveillance is essential to monitor strain diversity. To describe the epidemiology of rotavirus disease and circulating rotavirus strains in Mauritius, surveillance for rotavirus diarrhea was conducted at 2 regional hospitals from June 2008 through December 2010. METHODS: A total of 787 fecal samples from children <5 years of age admitted to the pediatric ward with acute gastroenteritis was collected within 48 hours of hospitalization and analyzed for group A rotavirus. A subset of rotavirus-positive samples was subjected to polyacrylamide gel electrophoresis and VP4 and VP7 genotyping. RESULTS: Rotavirus was detected in 327 (41.6%) stools. Highest prevalence of rotavirus infection occurred in children <2 years of age, predominately between 12 and 23 months. Three seasonal peaks were observed during the study period: July to October 2008, October to December 2009 and July to October 2010. Polyacrylamide gel electrophoresis analysis of 116 positive samples yielded only long electropherotypes. The predominant circulating strain was G3P[8] (89%) from June through December 2008, G4P[8] (76%) from January through December 2009 and G1P[8] (90%) from January through December 2010. CONCLUSIONS: The diversity of rotavirus strains detected in this study highlights the need for continuous surveillance and data generated can be used to advocate for rotavirus vaccine introduction.

Rotavirus vaccination within the South African Expanded Programme on Immunisation.

Diarrhoeal diseases are ranked the third major cause of childhood mortality in South African children less than 5 years, where the majority of deaths are among black children. Acute severe dehydrating rotavirus diarrhoea remains an important contributor towards childhood mortality and morbidity and has been well documented in South Africa. As the preventive strategy to control rotavirus diarrhoea, South Africa became the first country in the WHO African Region to adopt the rotavirus vaccine in the national childhood immunisation programme in August 2009. The rotavirus vaccine in use, Rotarix, GSK Biologicals, is given at 6 and 14 weeks of age, along with other vaccines as part of Expanded Programme on Immunisation (EPI). Studies which facilitated the introduction of rotavirus vaccine in South Africa included the burden of rotavirus disease and strain surveillance, economic burden of rotavirus infection and clinical trials to assess the safety and efficacy of vaccine candidates. This paper reviews the epidemiology of rotavirus in South Africa, outlines some of the steps followed to introduce rotavirus vaccine in the EPI, and highlights the early positive impact of vaccination in reducing the rotavirus burden of disease based on the post-marketing surveillance studies at Dr George Mukhari hospital, a sentinel site at University of Limpopo teaching hospital in Pretoria, South Africa, which has conducted rotavirus surveillance for >20 years.