Whole genome characterisation of a porcine-like human reassortant G26P[19] Rotavirus A strain detected in a child hospitalised for diarrhoea in Nepal, 2007

Molecular Characterisation of a Rare Reassortant Porcine-Like G5P[6] Rotavirus Strain Detected in an Unvaccinated Child in Kasama, Zambia

A human-porcine reassortant strain, RVA/Human-wt/ZMB/UFS-NGS-MRC-DPRU4723/2014/G5P[6], was identified in a sample collected in 2014 from an unvaccinated 12 month old male hospitalised for gastroenteritis in Zambia. We sequenced and characterised the complete genome of this strain which presented the constellation: G5-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1. The genotype A8 is often observed in porcine strains. Phylogenetic analyses showed that VP6, VP7, NSP2, NSP4, and NSP5 genes were closely related to cognate gene sequences of porcine strains (e.g., RVA/Pig-wt/CHN/DZ-2/2013/G5P[X] for VP7) from the NCBI database, while VP1, VP3, VP4, and NSP3 were closely related to porcine-like human strains (e.g., RVA/Human-wt/CHN/E931/2008/G4P[6] for VP1, and VP3). On the other hand, the origin of the VP2 was not clear from our analyses, as it was not only close to both porcine (e.g., RVA/Pig-tc/CHN/SWU-1C/2018/G9P[13]) and porcine-like human strains (e.g., RVA/Human-wt/LKA/R1207/2009/G4P[6]) but also to three human strains (e.g., RVA/Human-wt/USA/1476/1974/G1P[8]). The VP7 gene was located in lineage II that comprised only porcine strains, which suggests the occurrence of independent porcine-to-human reassortment events. The study strain may have collectively been derived through interspecies transmission, or through reassortment event(s) involving strains of porcine and porcine-like human origin. The results of this study underline the importance of whole-genome characterisation of rotavirus strains and provide insights into interspecies transmissions from porcine to humans.

G26P[19] rotavirus A strain causing acute gastroenteritis in the American continent

In Brazil, the rotavirus A genotype G26 was first identified in suckling piglets, while the P[19] genotype has not been identified in any animal species so far. This report details the genetic characterisation of a G26P[19] RVA strain detected from an eight year-old child, vaccinated with Rotarix^®, hospitalised with acute diarrhoeal disease in Rio de Janeiro in 2015. Most likely, the genome constellation (I5-R1-C1-M1-A8-N1-T1-E1-H1) observed in the G26P[19] Brazilian strain was a result of interspecies transmission events between humans and pigs. In addition, a rearrangement in the NSP5 gene was observed downstream of the 3’ non-coding region.

Human-porcine reassortant rotavirus generated by multiple reassortment events in a Sri Lankan child with diarrhea

A human-porcine reassortant rotavirus, strain R1207, was identified from 74 group A rotaviruses detected in 197 (37.6%) stool samples collected from patients who attended a tertiary care hospital in Ragama, Sri Lanka. This is the first report of a human-porcine reassortant rotavirus in Sri Lanka. The patient was a 12-month-old boy who had been hospitalized with fever and acute diarrhea with a duration of 6 days. The family had pigs at home before the birth of this boy. However, the neighbors still practice pig farming. The genotype constellation of R1207 was G4-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1. This is based on the assignment of all the eleven gene segments a full genome-based genotyping system. R1207 showed a 4-2-3-2 genomic electrophoretic migration pattern, which is characteristic of group A rotaviruses. Our analyses revealed that five (NSP2, NSP4, VP1, VP2, and VP7) of the 11 genes were closely related to the respective genes of porcine strains. Although the remaining six genes (NSP1, NSP3, NSP5, VP3, VP4, and VP6) were related to human strains, with the exception of the gene sequence of NSP1, all of these human strains were human-porcine reassortants. With a genogroup 1 genetic backbone, this strain was possibly formed via multiple genetic reassortments. We do not know whether this strain is circulating in pigs, as no data are available on porcine rotaviruses in Sri Lanka. Surveillance should be strengthened to determine the epidemiology of this genotype of rotavirus in Sri Lanka and to assess whether the infection was limited or sustained by ongoing human-to-human transmission.

Whole Genome Classification and Phylogenetic Analyses of Rotavirus B strains from the United States

Rotaviruses (RVs) are a major etiological agent of acute viral gastroenteritis in humans and young animals, with rotavirus B (RVB) often detected in suckling and weaned pigs. Group A rotavirus classification is currently based on the two outer capsid proteins, VP7 and VP4, and the middle layer protein, VP6. Using RVB strains generated in this study and reference sequences from GenBank, pairwise identity frequency graphs and phylogenetic trees were constructed for the eleven gene segments of RVB to estimate the nucleotide identity cutoff values for different genotypes and determine the genotype diversity per gene segment. Phylogenetic analysis of VP7, VP4, VP6, VP1–VP3, and NSP1–NSP5 identified 26G, 5P, 13I, 5R, 5C, 5M, 8A, 10N, 6T, 4E, and 7H genotypes, respectively. The analysis supports the previously proposed cutoff values for the VP7, VP6, NSP1, and NSP3 gene segments (80%, 81%, 76% and 78%, respectively) and suggests new cutoff values for the VP4, VP1, VP2, VP3, NSP2, NSP4, and NSP5 (80%, 78%, 79%, 77% 83%, 76%, and 79%, respectively). Reassortment events were detected between the porcine RVB strains from our study. This research describes the genome constellations for the complete genome of Group B rotaviruses in different host species.

Selected Viruses Detected on and in our Food

PURPOSE OF REVIEW

The purpose of this review is to provide an update on recent literature and findings concerning selected foodborne viruses. Two groups of viruses were selected: (a) the most important viruses contaminating food, based on numbers of publications in the last 5 years and (b) viruses infecting sources of food that might have an impact on human health.

RECENT FINDINGS

Important foodborne viruses such as norovirus, hepatitis A and rotavirus are usually "only" contaminating food and are detected on the surface of foodstuffs. However, they are threats to human public health and make up for the majority of cases. In contrast, the meaning of viruses born from within the food such as natural animal and plant viruses is still in many cases unknown. An exception is Hepatitis E virus that is endemic in pigs, transmitted via pork meat and is recognised as an emerging zoonosis in industrialised countries.

SUMMARY

Even though the clinical meaning of "new" foodborne viruses, often detected by next generation sequencing, still needs clarification, the method has great potential to enhance surveillance and detection particularly in view of an increasingly globalised food trade.

Epidemiological analysis of porcine rotavirus A genotypes in Germany

Group A porcine rotaviruses are a global threat to animal health in stock breeding. While certain genotypes have shown predominance in other countries, data from Europe's second largest swine population is still scarce. Therefore, porcine rotaviruses taken from different areas of Germany were genotyped to create a basis for comparison with data from neighboring countries. In addition, the potential predominance and regionality based on regions (federal states) have been investigated by examining 101 samples. The study revealed the dominance of the VP7 genotypes G9, G4, G5 as well as VP4 genotypes P[23], P[6], P[32]. The most common genotype combinations were G9P[23], G4P[6], and G9P[32]. Analysis focusing on the regionality aspect revealed that areas with high pig populations promote the emergence of dominant genotype combinations. However, pig populations in Germany cannot be considered individually and therefore results were put into international context, taken from already published genotyping data. In consequence, our data contributes to the fundamental understanding of regional and supraregional rotavirus epidemiology. The detected genotypes provide a basis for prospective porcine rotavirus surveillance, that first of all helps to identify interspecies transmission. Furthermore it may provide supporting data for the selection of particular genotypes, suitable for the production of porcine rotavirus A vaccine candidates.

Role of rotavirus vaccination on an emerging G8P[8] rotavirus strain causing an outbreak in central Japan

BACKGROUND

In this study, we examined the effectiveness of RV1 and RV5 vaccines during an outbreak of G8P[8] rotavirus group A strain (G8P[8]-RVA). These vaccines were originally designed to provide protection against severe diseases caused by common circulating strains, whereas G8P[8]-RVA remains emerging strain and partially heterotypic to the vaccines. It is imperative to investigate vaccine effectiveness (VE) against G8P[8]-RVA because this strain appears to be predominant in recent years, particularly, in post-vaccine era.

METHODS

RVA infection and genotypes were confirmed by polymerase chain reaction (PCR) followed by sequence-based genotyping. VE was determined during an outbreak of G8P[8]-RVA in Shizuoka Prefecture, Japan, in February-July 2017, retrospectively, by comparing vaccination status of children suffering from acute gastroenteritis (AGE) between 'PCR-positive' and 'PCR-negative' cases using conditional logistic regression adjusted for age.

RESULTS

Among 80 AGE children, RVA was detected in 58 (73%), of which 53 (66%) was G8P[8]-RVA. The clinical characteristics of G8P[8]-RVA and other RVA strains were identically severe. Notably, the attack rates of G8P[8]-RVA in vaccinated (61.1%) and unvaccinated (65.5%) children were almost similar. Indeed, no substantial effectiveness were found against G8P[8]-RVA (VE, 14% [95% CI: -140% to 70%]) or other RVA strains (VE, 58% [95% CI: -20% to 90%]) for mild infections. However, these vaccines remained strongly effective against moderate (VE, 75% [95% CI: 1% to 40%]) and severe (VE, 92% [95% CI: 60% to 98%]) RVA infections. The disease severity including Vesikari score, duration and frequency of diarrhea, and body temperature were significantly lower in vaccinated children.

CONCLUSIONS

This study demonstrates the effectiveness of current RV vaccines against moderate and severe, but not against the mild infections during an outbreak caused by unusual G8P[8]-RVA, which was virtually not targeted in the vaccines.