Molecular characterization of rare G12P[6] rotavirus isolates closely related to G12 strains from the United States, CAU 195 and CAU 214

Molecular characterization of human group A rotavirus genotypes circulating in Rawalpindi, Islamabad, Pakistan during 2015-2016

Group A rotaviruses (RVA) are one of the major causes of acute gastroenteritis (AGE) in young children worldwide. Owing to lack of proper surveillance programs and health facilities, developing countries of Asia and Africa carry a disproportionately heavy share of the RVA disease burden. The aim of this hospital-based study was to investigate the circulation of RVA genotypes in Rawalpindi and Islamabad, Pakistan in 2015 and 2016, prior to the implementation of RVA vaccine. 639 faecal samples collected from children under 10 years of age hospitalized with AGE were tested for RVA antigen by ELISA. Among 171 ELISA positive samples, 143 were successfully screened for RT-PCR and sequencing. The prevalence of RVA was found to be 26.8% with the highest frequency (34.9%) found among children of age group 6-11 months. The most predominant circulating genotypes were G3P[8] (22.4%) followed by G12P[6] (20.3%), G2P[4] (12.6%), G1P[8] (11.9%), G9P[6] (11.9%), G3P[4] (9.1%), G1P[6] (4.2%), G9P[8] (4.2%), and G3P[6] (0.7%). A single mixed genotype G1G3P[8] was also detected. The findings of this study provide baseline data, that will help to assess if future vaccination campaigns using currently available RVA vaccine will reduce RVA disease burden and instigate evolutionary changes in the overall RVA biology. The high prevalence of RVA infections in Pakistan require to improve and strengthen the surveillance and monitoring system for RVA. This will provide useful information for health authorities in planning public health care strategies to mitigate the disease burden caused by RVA.

Whole-genome analysis of rotavirus G4P[6] strains isolated from Korean neonates: association of Korean neonates and rotavirus P[6] genotypes

Background

Group A rotaviruses are the major causative agents of pediatric gastroenteritis worldwide. Several studies have reported the predominance of G4P[6] rotavirus genotypes in Korean neonates, which is uncommon in other countries. Therefore, the purposes of this study were to determine the genotype constellations of complete genomes of G4P[6] rotavirus strains isolated from Korean neonates using next-generation sequencing, to compare these sequences with other G4P[6] strains in other countries, and to determine the reason for the predominance of G4P[6] genotypes in Korean neonates.

Results

Twenty rotavirus G4P[6] strains, isolated from January 2013 to January 2016, were selected for whole-genome sequencing. Eleven rotavirus genes were amplified using specific primer sets, and sequencing was carried out using an Ion S5 XL next-generation sequencing platform. Genotypes of each gene were determined, and phylogenetic analyses were performed to investigate genetic distances between genes of rotaviruses in this study and those of other rotavirus G4P[6] strains whose whole-genome sequences were previously published. All 20 rotavirus strains in this study had the same genotype: G4-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1, representing the Wa-like genotype constellation. BLAST searches of 20 G4P[6] rotavirus strains revealed that all G4 sequences in this study showed the highest nucleotide identity to G4 sequences of G4P[6] rotavirus strains isolated in Korea in 2008 (GenBank accession number: FJ603447). Additionally, P[6] gene sequences in this study showed the highest nucleotide identity to P[6] sequences of G4P[6] strains detected in Korea in 2002 (AY158093). Phylogenetic and nucleotide sequence analyses showed that G4P[6] strains in this study and previously reported G4P[6] strains in Korea were mostly detected in neonates and had similar G4 and P[6] sequences compared with other G4P[6] strains detected in other countries.

Conclusions

This study showed that the whole-genome constellation of rotavirus G4P[6] strains from Korean neonates resembled a Wa-like genotype constellation. Additionally, rotavirus genotypes detected in Korean neonates had unique P[6] sequences, which may be the cause of Korean neonatal rotavirus infection.

Electronic supplementary material

The online version of this article (10.1186/s13099-019-0318-5) contains supplementary material, which is available to authorized users.

Multiplexed one-step RT-PCR VP7 and VP4 genotyping assays for rotaviruses using updated primers

The current two-step VP7 and VP4 genotyping RT-PCR assays for rotaviruses have been linked consistently to genotyping failure in an estimated 30% of RVA positive samples worldwide. We have developed a VP7 and VP4 multiplexed one-step genotyping assays using updated primers generated from contemporary VP7 and VP4 sequences. To determine assay specificity and sensitivity, 17 reference virus strains, 6 non-target gastroenteritis viruses and 725 clinical samples carrying the most common VP7 (G1, G2, G3, G4, G9, and G12) and VP4 (P[4], P[6], P[8], P[9] and P[10]) genotypes were tested in this study. All reference RVA strain targets yielded amplicons of the expected sizes and non-target genotypes and gastroenteritis viruses were not detected by either assay. Out of the 725 clinical samples tested, the VP7 and VP4 assays were able to assigned specific genotypes to 711 (98.1%) and 714 (98.5%), respectively. The remaining unassigned samples were re-tested for RVA antigen using EIA and qRT-PCR assays and all were found to be negative. The overall specificity, sensitivity and limit of detection of the VP7 assay were in the ranges of 99.0-100%, 94.0-100% and 8.6×10(1) to 8.6×10(2) copies of RNA/reaction, respectively. For the VP4 assay, the overall specificity, sensitivity and limit of detection assay were in the ranges of 100%, 94.0-100% and ≤1 to 8.6×10(2) copies of RNA/reaction, respectively. Here we report two highly robust, accurate, efficient, affordable and documentable gel-based genotyping systems which are capable of genotyping 97.8% of the six common VP7 and 98.3% of the five common VP4 genotypes of RVA strains which are responsible for approximately 88.2% of all RVA infections worldwide.

Prevalence of rotavirus genotypes in South Korea in 1989-2009: implications for a nationwide rotavirus vaccine program

The epidemiology of human group A rotavirus was analyzed by examining genotypic data acquired from 1989 to 2009 in South Korea. This information was derived from all the available published articles on rotavirus studies in South Korea, retrieved from both the PubMed and KoreaMed databases. Four common G types (G1, G2, G3, and G4) and three common P types (P[8], P[4], and P[6]) accounted for approximately 93% and 99% of the rotavirus reports, respectively. The G9 type was frequently detected after 2000, and because of this prevalence, it is considered to be the fifth most important G type rotavirus after the G1.G4 genotypes. Less common G types of the virus such as G12, G11, and G10 were detected in some geographic settings, and it is important to consider the context of these subtypes and their epidemiological significance. The P[9] virus genotype was observed in the study and has been discussed in many other studies; however, the P[3], P[10] and P[25] genotypes were rarely detected in the epidemiological research. In general, the distributions of the G and P genotypes showed temporal and geographical fluctuations, and a nationwide rotavirus vaccine program that targeted these genotypes demonstrated effectiveness in protecting against the circulating rotavirus strains. However, further analysis is needed to determine the true long-term effectiveness of these vaccines; the analysis should also consider the unexpected effects of vaccinations, such as vaccine-induced diseases, herd immunity, and changes in host susceptibilities.

Phylogenetic analysis of G1P[6] group A rotavirus strains detected in Northeast Brazilian children fully vaccinated with Rotarix™

In 2009 the World Health Organization recommended the use of group A rotavirus (RVA) vaccines in all national immunization programs (NIPs) in order to control severe RVA gastroenteritis disease. In Brazil, Rotarix™ was introduced in the NIP in March 2006, and a significant reduction in mortality rates among children ≤ 5 years old was observed, especially in the Northern and Northeastern Brazil. In the current study the 11 gene segments of six Brazilian G1P[6] RVA strains, isolated in 2009 and 2010 from vaccinated children, were analyzed in order to investigate if the genetic composition of these strains might help to elucidate why they were able to cause acute gastroenteritis in vaccinated children. All six Brazilian RVA strains revealed a complete Wa-like genotype constellation: G1-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1. Phylogenetic analysis showed that all six strains were nearly identical and showed a close genetic relationship with contemporary typical human Wa-like RVA strains. These results suggests that the fact that these strains were able to cause acute gastroenteritis in vaccinated children is likely not due to the genetic background of the strains, but rather to other factors such as host relating factors, co-infecting pathogens or vaccine efficacy. P[6] RVA strains are detected rather occasionally in humans in most regions of the world, except for South Asia and Sub-Saharan Africa. However, recently two studies conducted in Brazil showed the circulation of G12P[6] and G2P[6]. This is the first report on the detection and complete genome analyses of G1P[6] RVA strains in Brazil. Surveillance studies will be crucial to further investigate the prevalence of this genotype in the Brazilian population, and the efficacy of current licensed vaccines, which do not contain the P[6] genotype.

Identification of porcine rotavirus-like genotype P[6] strains in Taiwanese children

The molecular characterization of genotype P[6] rotavirus strains collected from children admitted to hospital with acute dehydrating diarrhoea during a 6-year surveillance period in Taiwan is described in this study. In total, three G4P[6] strains, one G5P[6] and one G12P[6] were characterized by sequencing and phylogenetic analysis of the VP4, VP7, VP6 and NSP4 genes. Whilst all four genes of the single Taiwanese G12P[6] strain clustered with the respective genes of globally common human rotavirus strains, the G4 and G5 strains showed remarkable similarities to porcine rotavirus strains and putative porcine-origin human P[19] strains reported previously from Taiwan. The overall proportion of porcine rotavirus-like strains in Taiwan remains around 1 % among hospitalized children; however, the circulation and sporadic transmission of these heterotypic strains from pigs to humans could pose a public-health concern. Therefore, continuation of strain monitoring is needed in the vaccine era to detect any possible vaccine breakthrough events associated with the introduction of such heterologous rotavirus strains.