Full genomic characterization and phylogenetic analysis of a zoonotic human G8P[14] rotavirus strain detected in a sample from Guatemala

We report the genomic characterization of a rare human G8P[14] rotavirus strain, identified in a stool sample from Guatemala (GTM) during routine rotavirus surveillance. This strain was designated as RVA/Human-wt/GTM/2009726790/2009/G8P[14], with a genomic constellation of G8-P[14]-I2-R2-C2-M2-A13-N2-T6-E2-H3. The VP4 gene occupied lineage VII within the P[14] genotype. Phylogenetic analysis of each genome segment revealed close relatedness to several zoonotic simian, guanaco and bovine strains. Our findings suggest that strain RVA/Human-wt/GTM/2009726790/2009/G8P[14] is an example of a direct zoonotic transmission event. The results of this study reinforce the potential role of interspecies transmission and reassortment in generating novel and rare rotavirus strains which infect humans.     

Whole genome characterization of feline-like G3P[8] reassortant rotavirus A strains bearing the DS-1-like backbone genes detected in Vietnam, 2016

While conducting rotavirus gastroenteritis surveillance in Vietnam, two G3P[8] rotavirus A specimens possessing an identical short RNA electropherotype were detected. They were RVA/Human-wt/VNM/0232/2016/G3P[8] and RVA/Human-wt/VNM/0248/2016/G3P[8], and recovered from 9 and 23 months old boys, respectively. The patients developed diarrhoea within one-week interval in March 2016 but in places >100 km apart in northern Vietnam. Whole genome sequencing of the two G3P[8] rotavirus A strains revealed that their genomic RNA sequences were identical across the 11 genome segments, suggesting that they derived from a single clone. The backbone gene constellation was I2-R2-C2-M2-A2-N2-T2-E2-H2. The backbone genes and the VP4 gene had a virtually identical nucleotide sequences with identities ranging from 99.2 to 100% to the corresponding genes of RVA/Human-wt/VNM/1149/2014/G8P[8]; the prototype of recently-emerging bovine-like G8P[8] reassortant strains in Vietnam. On the other hand, the VP7 gene was 98.8% identical with that of RVA/Human-wt/CHN/E2451/2011/G3P[9], and they were clustered together in the lineage represented by RVA/Cat-tc/JPN/FRV-1/1986/G3P[9]. The observations led us to hypothesise that one of the bovine-like G8P[8] strains bearing the DS-1-like backbone genes reassorted with a locally circulating FRV-1-like strain to gain the G3 VP7 gene and to emerge as a thus-far undescribed feline-like G3P[8] reassortant strain. The identification of feline-like G3P[8] strains bearing the DS-1-like backbone genes exemplifies the strength and necessity of the whole genome sequencing approach in monitoring, describing and understanding the evolutionary changes that are occurring in emerging strains and their interactions with co-circulating strains.     

Genomic characterization of G3P[6], G4P[6] and G4P[8] human rotaviruses from Wuhan,China: Evidence for interspecies transmission and reassortment events

We report here the whole genomic analyses of two G4P[6] (RVA/Human-wt/CHN/E931/2008/G4P[6], RVA/Human-wt/CHN/R1954/2013/G4P[6]), one G3P[6] (RVA/Human-wt/CHN/R946/2006/G3P[6]) and one G4P[8] (RVA/Human-wt/CHN/E2484/2011/G4P[8]) group A rotavirus (RVA) strains detected in sporadic cases of diarrhea in humans in the city of Wuhan, China. All the four strains displayed a Wa-like genotype constellation. Strains E931 and R1954 shared a G4-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1 constellation, whilst the 11 gene segments of strains R946 and E2484 were assigned to G3-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1 and G4-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 genotypes, respectively. Phylogenetically, the VP7 gene of R946, NSP3 gene of E931, and 10 of 11 gene segments of E2484 (except for VP7 gene) belonged to lineages of human RVAs. On the other hand, based on available data, it was difficult to ascertain porcine or human origin of VP3 genes of strains E931 and R946, and NSP2 genes of strains R946 and R1954. The remaining genes of E2484, E931, R946 and R1954 were close to those of porcine RVAs from China, and/or porcine-like human RVAs. Taken together, our observations suggested that strain R1954 might have been derived from porcine RVAs, whilst strains R946 and E931 might be reassortants possessing human RVA-like gene segments on a porcine RVA genetic backbone. Strain E2484 might be derived from reassortment events involving acquisition of a porcine-like VP7 gene by a Wa-like human RVA strain. The present study provided important insights into zoonotic transmission and complex reassortment events involving human and porcine RVAs, reiterating the significance of whole-genomic analysis of RVA strains.     

Multispecies reassortant bovine rotavirus strain carries a novel simian G3-like VP7 genotype

Rotavirus-A (RVAs), are the major cause of severe gastroenteritis in the young of mammals and birds. RVA strains possessing G6, G8, and G10 genotypes in combination with P[1] or P[11] have been commonly detected in cattle. During a routine surveillance for enteric viruses in a bovine population on North-Western temperate Himalayan region of India, an uncommon bovine RVA strain, designated as RVA/Cow-wt/IND/M1/09/2009 was detected in a diarrhoeic crossbred calf. The examination of nearly complete genome sequence of this RVA strain revealed an unusual G-P combination (G3P[11]) on a typical bovine RVA genotype backbone (I2-R2-C2-M2-A11-N2-T6-E2-H3). The VP7 gene of M1/09 isolate displayed a maximum nucleotide sequence identity of 73.8% with simian strain (RVA/Simian-tc/USA/RRV/1975/G3P[3]). The VP4 and NSP5 genes clustered with an Indian pig strain, RVA/Pig-wt/IND/AM-P66/2012/G10P[11] (99.6%), and a caprine strain, RVA/Goat-tc/BGD/GO34/1999/G6P[1] (98.9%) from Bangladesh, respectively, whilst the, VP6, NSP1, NSP3 and NSP4 genes were identical or nearly identical to Indian bovine strains (RVA/Cow-wt/IND/B-72/2008/G10P[X], RVA/Cow-wt/IND/B85/2010/GXP[X], and RVA/Cow-wt/IND/C91/2011/G6P[X]). The remaining four genes (VP1, VP2, VP3 and NSP2) were more closely related to RVA/Human-wt/ITA/PAI11/1996/G2P[4] (93.5%), RVA/Sheep-wt/CHN/LLR/1985/G10P[15] (88.8%), RVA/Human-tc/SWE/1076/1983/G2P2A[6] (93.2%) and RVA/Human-wt/AUS/CK20003/2000/G2P[4] (91.2%), respectively. Altogether, these findings are suggestive of multiple independent interspecies transmission and reassortment events between co-circulating bovine, porcine, ovine and human rotaviruses. The complete genome sequence information is necessary to establish the evolutionary relationship, interspecies transmission and ecological features of animal RVAs from different geographical regions.     

Whole genomic analysis reveals the porcine origin of human G9P[19] rotavirus strains Mc323 and Mc345

The group A rotavirus (RVA) P[19] is a rare P-genotype of the RVA VP4 gene, reported so far in humans and pigs. Whole genomic analyses of P[19] strains are essential to study their origin and evolutionary patterns. To date, all the 11 genes of only two P[19] strains, RVA/Human-wt/IND/RMC321/1990/G9P[19] and RVA/Human-wt/IND/mani-97/2006/G9P[19], have been analyzed, providing evidence for their porcine origin. In the present study, the whole genomes of the first reported human P[19] strains, RVA/Human-tc/THA/Mc323/1989/G9P[19] and RVA/Human-tc/THA/Mc345/1989/G9P[19], were analyzed. Strains Mc323 and Mc345 exhibited a G9-P[19]-I5-R1-C1-M1-A8-N1-T1-E1-H1 genotype constellation. With the exception of the NSP5 gene, both the strains were closely related to each other. Most of the genes of Mc323 (VP2-4, VP6-7, NSP1-4 genes) and Mc345 (VP2-4, VP6-7 and NSP1-5 genes) appeared to be of porcine origin, whilst the exact origin of VP1 and NSP5 genes of Mc323 and VP1 gene of Mc345 could not be ascertained. Therefore, strains Mc323 and Mc345 were found to have a porcine RVA genetic backbone, and are likely of porcine origin. Taken together, our observations corroborated the hypothesis that P[19] strains might be derived from porcine RVAs, providing important insights into the origin of P[19] strains, and on interspecies transmission of RVAs.     

Distinct evolutionary origins of G12P[8] and G12P[9] group A rotavirus strains circulating in Brazil

G12 group A rotavirus (RVA) are currently recognized as a globally emerging genotype and have been described in combination with several P-types. In Brazil, G12 RVA strains have been described in the Southern (2003) and Northern (2008–2010) regions, in combination with the P[9] and P[6] genotype, respectively. To date, few complete genomes of G12 RVA strains have been described (none from Brazilian strains), considering G12P[9] genotype just one strain, RVA/Human-tc/THA/T152/1998/G12P[9], has their 11 gene segments characterized. This study aims to determine the genomic constellation of G12P[9] and G12P[8] RVA strains detected in Brazil between 2006 and 2011. Therefore, the eleven gene segments of five Brazilian G12 RVA strains were amplified and sequenced, and the genotype of each gene segment was assigned using phylogenetic analysis. Complete genome analyses of G12 RVA strain circulating between 2006 and 2011 in Brazil revealed a conserved Wa-like genomic constellation for three G12P[8] RVA strains; whereas the two G12P[9] strains possessed distinct reassorted AU-1-like genomic constellations, closely related to the reference strain RVA/Human-tc/THA/T152/1998/G12P[9] in most genes. The results obtained in the current study suggest that G12P[9] (AU-1-like) and G12P[8] (Wa-like) strains detected in different regions of Brazil do not share a common origin. Moreover, while Brazilian G12P[8] RVA strains showed a complete Wa-like human constellation, both G12P[9] strains possessed an NSP1 gene of bovine origin (NSP1), and RVA/Human-wt/BRA/PE18974/2010/G12P[9] also possessed a VP3 gene of canine/feline origin.     

Complex evolutionary patterns of two rare human G3P[9] rotavirus strains possessing a feline/canine-like H6 genotype on an AU-1-like genotype constellation

The group A rotavirus (RVA) G3P[9] is a rare VP7–VP4 genotype combination, detected occasionally in humans and cats. Other than the prototype G3P[9] strain, RVA/Human- tc/JPN/AU-l/1982/G3P3[9], the whole genomes of only two human G3P[9] RVA strains and two feline G3P[9] RVA strains have been analyzed so far, revealing complex evolutionary patterns, distinct from that of AU-1. We report here the whole genomic analyses of two human G3P[9] RVA strains, RVA/Human-tc/CHN/L621/2006/G3P[9] and RVA/Human-wt/CHN/E2451/2011/G3P[9], detected in patients with diarrhea in China. Strains L621 and E2451 possessed a H6 NSP5 genotype on an AU-1-like genotype constellation, not reported previously. However, not all the genes of L621 and E2451 were closely related to those of AU-1, or to each other, revealing different evolutionary patterns among the AU-1-like RVAs. The VP7, VP4, VP6 and NSP4 genes of E2451 and L621 were found to cluster together with human G3P[9] RVA strains believed to be of possible feline/canine origin, and feline or raccoon dog RVA strains. The VP1, VP3, NSP2 and NSP5 genes of E2451 and L621 formed distinct clusters in genotypes typically found in feline/canine RVA strains or RVA strains from other host species which are believed to be of feline/canine RVA origin. The VP2 genes of E2451 and L621, and NSP3 gene of L621 clustered among RVA strains from different host species which are believed to have a complete or partial feline/canine RVA origin. The NSP1 genes of E2451 and L621, and NSP3 gene of E2451 clustered with AU-1 and several other strains possessing a complete or partial feline RVA strain BA222-05-like genotype constellation. Taken together, these observations suggest that nearly all the eleven gene segments of G3P[9] RVA strains L621 and E2451 might have originated from feline/canine RVAs, and that reassortments may have occurred among these feline/canine RVA strains, before being transmitted to humans.     

Sequence analysis of the whole genomes of five African human G9 rotavirus strains

The G9 rotaviruses are amongst the most common global rotavirus strains causing severe childhood diarrhoea. However, the whole genomes of only a few G9 rotaviruses have been fully sequenced and characterised of which only one G9P[6] and one G9P[8] are from Africa. We determined the consensus sequence of the whole genomes of five African human group A G9 rotavirus strains, four G9P[8] strains and one G9P[6] strain collected in Cameroon (central Africa), Kenya (eastern Africa), South Africa and Zimbabwe (southern Africa) in 1999, 2009 and 2010. Strain RVA/Human-wt/ZWE/MRC-DPRU1723/2009/G9P[8] from Zimbabwe, RVA/Human-wt/ZAF/MRC-DPRU4677/2010/G9P[8] from South Africa, RVA/Human-wt/CMR/1424/2009/G9P[8] from Cameroon and RVA/Human-wt/KEN/MRC-DPRU2427/2010/G9P[8] from Kenya were on a Wa-like genetic backbone and were genotyped as G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1. Strain RVA/Human-wt/ZAF/MRC-DPRU9317/1999/G9P[6] from South Africa was genotyped as G9-P[6]-I2-R2-C2-M2-A2-N1-T2-E2-H2. Rotavirus A strain MRC-DPRU9317 is the second G9 strain to be reported on a DS-1-like genetic backbone, the other being RVA/Human-wt/ZAF/GR10924/1999/G9P[6]. MRC-DPRU9317 was found to be a reassortant between DS-1-like (I2, R2, C2, M2, A2, T2, E2 and H2) and Wa-like (N1) genome segments. All the genome segments of the five strains grouped strictly according to their genotype Wa- or DS-1-like clusters. Within their respective genotypes, the genome segments of the three G9 study strains from southern Africa clustered most closely with rotaviruses from the same geographical origin and with those with the same G and P types. The highest nucleotide identity of genome segments of the study strains from eastern and central Africa regions on a Wa-like backbone was not limited to rotaviruses with G9P[8] genotypes only, they were also closely related to G12P[6], G8P[8], G1P[8] and G11P[25] rotaviruses, indicating a close inter-genotype relationship between the G9 and other rotavirus genotypes. Rotavirus strain MRC-DPRU9317 is the first G9P[6] to be characterised on a DS-1-like genetic backbone with a reassortant segment 8 (NSP2) and fourth G9P[6] to be fully sequenced globally.     

Whole genome characterisation of G11P[25] and G9P[19] rotavirus A strains from adult patients with diarrhoea in Nepal

Rotavirus A (RVA) causes acute diarrhoea in children and less frequently in adults. However, the knowledge about the genotype distribution of RVA strains circulating in adults is limited particularly in developing countries. This study aimed to characterise the RVA strains detected from adult patients with diarrhoea in Nepal. A total of 47 RVA positive stool samples from adult patients with diarrhoea in Kathmandu, Nepal during 2007–2008 were examined for the G and P genotypes by sequencing. Nearly half (49%) of the samples were genotyped as G9P[8] (n = 23), G1P[8], G2P[4] (n = 5 each), G12P[8] (n = 4), G12P[6] (n = 3), G1P[6] (n = 2), G3P[8] and G9P[6] (n = 1 each). Interestingly, two G11P[25] and one G9P[19] strains detected were further subjected to Illumina MiSeq next generation sequencing to determine their whole genome sequences. The genotype constellations of RVA/Human-wt/NPL/TK2615/2008/G11P[25] and RVA/Human-wt/NPL/TK2620/2008/G11P[25] were I12-R1-C1-M1-A1-N1-T1-E1-H1, whereas that of RVA/Human-wt/NPL/TK1797/2007/G9P[19] was I5-R1-C1-M1-A8-N1-T1-E1-H1. The 11 genes of TK2615 and TK2620 were virtually identical, and they were either porcine-like or unique except the VP2 and NSP1 genes which were of human RVA origin. The two G11P[25] strains were also very similar to KTM368, another G11P[25] isolated from a child in Nepal in 2004. On the other hand, no gene of TK1797 was likely to be of human RVA origin. The observation that porcine-like RVAs were detected from adult patients justifies further studies to explore the role of adults in the interspecies transmission of animal RVA to humans.     

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

A rare G26 Rotavirus A strain RVA/Human-wt/NPL/07N1760/2007/G26P[19] was detected in a child hospitalised for acute diarrhoea in Kathmandu, Nepal. The complete genome of 07N1760 was determined in order to explore its evolutionary history as well as examine its relationship to a Vietnamese strain RVA/Human-wt/VNM/30378/2009/G26P[19], the only G26 strain whose complete genotype constellation is known. The genotype constellation of 07N1760 was G26-P[19]-I12-R1-C1-M1-A8-N1-T1-E1-H1, a unique constellation identical to that of the Vietnamese 30378 except the VP6 gene. Phylogenetic analysis revealed that both strains were unrelated at the lineage level despite their similar genotype constellation. The I12 VP6 gene of 07N1760 was highly divergent from the six currently deposited I12 sequences in the GenBank. Except for its NSP2 gene, the remaining genes of 07N1760 shared lineages with porcine and porcine-like human RVA genes. The NSP2 gene belonged to a human RVA N1 lineage which was distinct from typical porcine and porcine-like human lineages. In conclusion, the Nepali G26P[19] strain 07N1760 was a porcine RVA strain which derived an NSP2 gene from a human Wa-like RVA strain by intra-genotype reassortment probably after transmission to the human host.     

Genomic characterization of uncommon human G3P[6] rotavirus strains that have emerged in Kenya after rotavirus vaccine introduction,and pre-vaccine human G8P[4] rotavirus strains

A monovalent rotavirus vaccine (RV1) was introduced to the national immunization program in Kenya in July 2014. There was increased detection of uncommon G3P[6] strains that coincided temporally with the timing of this vaccine introduction. Here, we sequenced and characterized the full genomes of two post-vaccine G3P[6] strains, RVA/Human-wt/KEN/KDH1951/2014/G3P[6] and RVA/Human-wt/KEN/KDH1968/2014/G3P[6], as representatives of these uncommon strains. On full-genomic analysis, both strains exhibited a DS-1-like genotype constellation: G3-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Phylogenetic analysis revealed that all 11 genes of strains KDH1951 and KDH1968 were very closely related to those of human G3P[6] strains isolated in Uganda in 2012–2013, indicating the derivation of these G3P[6] strains from a common ancestor. Because the uncommon G3P[6] strains that emerged in Kenya are fully heterotypic as to the introduced vaccine strain regarding the genotype constellation, vaccine effectiveness against these G3P[6] strains needs to be closely monitored.     

Genetic characterization of a rare bovine-like human VP4 mono-reassortant G6P[8] rotavirus strain detected from an infant in Bangladesh

During an ongoing diarrhea etiology surveillance in Mirzapur, Bangladesh, a rare human G6P[8] RVA strain (RVA/Human-wt/BGD/KH2288/2011/G6P[8]) was detected in a stool sample of a 7-month-old infant with acute diarrhea. Complete genotype analyses revealed that KH2288 possessed the G6-P[8]-I2-R2-C2-M2-A11-N2-T6-E2-H3 genotype constellation. Sequence analysis of the VP7 gene revealed a close phylogenetic relationship with bovine G6 strains from India, whereas, the VP4 gene segment was nearly identical to typical human P[8] strain circulating in Bangladesh and the rest of the world. Phylogenetic analysis of the remaining nine gene segments revealed a close relatedness to either animal or animal derived human RVA strain. We speculated that, strain KH2288 was a monoreassortant between a human RVA strain and a RVA strain typically infecting member of the Artiodactyla, such as cattle, goat or sheep. To our knowledge, this is the first complete genotyping report of a naturally occurring G6P[8] RVA strain, worldwide.     

A decade of G3P[8] and G9P[8] rotaviruses in Brazil: Epidemiology and evolutionary analyses

This study aims to estimate the frequency of group A rotaviruses (RVA) infection with genotypes G3P[8] and G9P[8] in children that suffered from diarrheal disease (DD) between 2001 and 2011 in different Brazilian regions. In addition, the genetic diversity of G3P[8] and G9P[8] RVA strains recovered from vaccinated and non-vaccinated children was assessed. Laboratory-based RVA surveillance included 15,115 cases of DD, and RVA was detected by enzyme immune-assay and/or polyacrylamide gel electrophoresis in 3357 (22%) samples. RVA was genotyped by the semi-nested RT-PCR and among RVA-positive samples, 100 (2.9%) were G3 (63 G3P[8], 32 G3P not typed [NT], and 5 G3P[6]) and 378 (16.2%) were G9 (318 G9P[8], 59 G9P[NT], and 1 G9P[6]). From the G3 and G9 positive samples, 16 and 12, respectively, were obtained from children aged 4–48 months vaccinated with the monovalent vaccine (Rotarix®, RV1). Phylogenetic analyses of the VP7 and VP8¹ encoding genes were performed for 26 G3P[8] and 48 G9P[8] strains. VP8¹ phylogenetic analysis revealed that all strains analyzed belonged to P[8] lineage III, whereas RV1 belongs to P[8]-I lineage. VP7 analysis revealed that all G3 and G9 strains belonged to G3-lineage III and G9-lineage III. The comparison of the VP7 and VP8¹ antigenic epitopes regions of Brazilian strains with RV1 strain revealed several amino acid changes. However, no particular differences among Brazilian strains detected before and after vaccine introduction were observed, or among strains detected from vaccinated and non-vaccinated children. Complete genome characterization of four G3P[8] and seven G9P[8] strains revealed a typical conserved human Wa-like genomic constellation. Changes in the genetic diversity of G3P[8] and G9P[8] RVA detected from 2001 to 2011 in Brazil seemed not be related to RV1 introduction in Brazil.     

Characterization of G2P[4] rotavirus strains associated with increased detection in Australian states using the RotaTeq® vaccine during the 2010–2011 surveillance period

The introduction of rotavirus vaccines Rotarix® and RotaTeq® into the Australian National Immunisation Program in July 2007 has resulted in a dramatic decrease in the burden of rotavirus disease. G2P[4] strains became the dominant genotype Australia-wide during the 2010–2011 surveillance period and for the first time since vaccine introduction, a higher proportion were isolated in jurisdictions using RotaTeq® vaccine compared to locations using Rotarix®. Phylogenetic analysis of the VP7 gene of 32 G2P[4] strains identified six genetic clusters, these distinct clusters were also observed in the VP4 gene for a subset of 12 strains. The whole genome was determined for a representative strain of clusters; A (RVA/Human-wt/AUS/SA066/2010/G2P[4]), B (RVA/Human-wt/AUS/WAPC703/2010/G2P[4]), C (RVA/Human-wt/AUS/MON008/2010/G2P[4]) and E (RVA/Human-wt/AUS/RCH041/2010/G2P[4]). All of the strains possessed the archetypal DS-1 like genome constellation G2-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Three of the strains, SA066, MON008 and WAPC703 clustered together and were distinct to RCH041 for all 11 genes. The VP7 genes of 31/32 of the strains characterized in this study possessed five conserved amino acid substitutions when compared to the G2 VP7 gene present in the RotaTeq® vaccine. Three of the substitutions were in the VP7 antigenic regions A and C, the substitutions A87T, D96N and S213D have been reported in the majority of G2P[4] strains circulating globally over the previous decade. These changes may have improved the ability of strains to circulate in settings of high vaccine use.     

Analysis of complete genome sequences of G9P[19] rotavirus strains from human and piglet with diarrhea provides evidence for whole-genome interspecies transmission of nonreassorted porcine rotavirus

Whole genomes of G9P[19] human (RVA/Human-wt/THA/CMH-S070-13/2013/G9P[19]) and porcine (RVA/Pig-wt/THA/CMP-015-12/2012/G9P[19]) rotaviruses concurrently detected in the same geographical area in northern Thailand were sequenced and analyzed for their genetic relationships using bioinformatic tools. The complete genome sequence of human rotavirus RVA/Human-wt/THA/CMH-S070-13/2013/G9P[19] was most closely related to those of porcine rotavirus RVA/Pig-wt/THA/CMP-015-12/2012/G9P[19] and to those of porcine-like human and porcine rotaviruses reference strains than to those of human rotavirus reference strains. The genotype constellation of G9P[19] detected in human and piglet were identical and displayed as the G9-P[19]-I5-R1-C1-M1-A8-N1-T1-E1-H1 genotypes with the nucleotide sequence identities of VP7, VP4, VP6, VP1, VP2, VP3, NSP1, NSP2, NSP3, NSP4, and NSP5 at 99.0%, 99.5%, 93.2%, 97.7%, 97.7%, 85.6%, 89.5%, 93.2%, 92.9%, 94.0%, and 98.1%, respectively. The findings indicate that human rotavirus strain RVA/Human-wt/THA/CMH-S070-13/2013/G9P[19] containing the genome segments of porcine genetic backbone is most likely a human rotavirus of porcine origin. Our data provide an evidence of interspecies transmission and whole-genome transmission of nonreassorted G9P[19] porcine RVA to human occurring in nature in northern Thailand.     

Full genome characterization of a porcine-like human G9P[6] rotavirus strain isolated from an infant in Belgium

Interspecies transmissions of group A rotavirus (RVA) strains among animals and humans are thought to take place frequently. During a RVA surveillance study in Belgium we isolated an unusual G9P[6] RVA strain, RVA/human-wt/BEL/BE2001/2009/G9P[6], from a 1month old boy, which did not cluster with other G9 or P[6] strains isolated in Belgium. In this study we sequenced and characterized the complete genome of this unusual G9P[6] strain BE2001. Phylogenetic analyses of all 11 genes revealed a unique genotype constellation: G9-P[6]-I5-R1-C1-M1-A8-N1-T7-E1-H1. The VP6 and NSP1 genotypes I5 and A8 are genotypes commonly found in porcine RVA strains, while the VP7 and VP4 genes clustered only distantly to human lineages of G9 and P[6], respectively. The VP1, VP2, VP3, NSP2, NSP4 and NSP5 genes all belonged to Wa-like genotypes, but clustered more closely to porcine strains than to human strains. NSP3 belonged to the rare T7 genotype. Thus far, T7 genotypes have only been detected in one porcine-like human strain (RVA/human-tc/CHN/R479/2004/G4P[6]), one bovine-like human strain (RVA/human-xx/IND/mani-265/2007/G10P[6]) and one bovine RVA strain (RVA/cow-tc/GBR/UK/1973/G6P7[5]). Sequence analysis of the BE2001 NSP5 gene segment revealed a 300 nucleotide duplication in the 3' end non-coding region. BE2001 is most likely a direct interspecies transmission between a pig and a human. Inquiry with the patient's physician revealed that the father of the patient had been working on a pig farm in the week the patient became ill, providing a plausible route of transmission.     

Characterization of human rotaviruses circulating in Iraq in 2008: Atypical G8 and high prevalence of P[6] strains

Fecal samples from 976 children with gastroenteritis were collected and analyzed for group A rotavirus (RVA), in three different cities in Iraq between January 2008 and December 2008. RVA antigen was detected in 394 (40%) of the samples, and 98 samples were available for further genotype analyses using multiplex RT-PCR and sequence analyses for untypeable strains. The G/P-genotype combination was determined for 69 samples, and 19, 2 and 8 samples remained P-untypeable, G-untypeable and G/P-untypeable (UT), respectively. The most prevalent genotype was G2 (40%, 39/98) most often associated with P[6]. G1 was the second most common genotype (16%, 16/98) mainly associated with P[8] and P[UT]. G3, G4 and G9 were detected at a lower prevalence (3%, 11%, 3%, respectively), mainly associated with P[6]. Surprisingly, five G8P[6], and seven G12 RVA strains in combination with P[6] and P[8] were also detected for the first time in Iraq. Overall, a striking high prevalence of 47% of the analyzed samples possessed the P[6] genotype (65% of the P-typed RVA strains). Atypical genotype combinations such as G1P[4], G1P[6], G2P[8] or strains with mixed G-types were detected sporadically. The detection of unusual G8P[6] RVA strains prompted us to further analyze the NSP2, NSP3, NSP4 and NSP5 gene segments of three selected G8P[6] strains, resulting in their designation to the N2, T2, E2 and H2 genotypes, respectively. The VP7, VP4, NSP2, NSP3 and NSP5 gene segments clustered closely with common human RVA strains, whereas the NSP4 gene sequences were found to cluster with animal derived RVA strains, suggesting a potential reassortment event. The high prevalence of RVA strains with the G8, G12 and P[6] genotypes in combination with a DS-1-like genotype constellation in Iraq, needs to be monitored closely as these RVA strains might challenge the effectiveness of current RVA vaccines.     

Multiple reassortment and interspecies transmission events contribute to the diversity of feline, canine and feline/canine-like human group A rotavirus strains

RNA–RNA hybridization assays and complete genome sequence analyses have shown that feline rotavirus (FRV) and canine rotavirus (CRV) strains display at least two distinct genotype constellations (genogroups), represented by the FRV strain RVA/Cat-tc/AUS/Cat97/1984/G3P[3] and the human rotavirus (HRV) strain RVA/Human-tc/JPN/AU-1/1982/G3P3[9], respectively. G3P[3] and G3P[9] strains have been detected sporadically in humans. The complete genomes of two CRV strains (RVA/Dog-tc/ITA/RV198-95/1995/G3P[3] and RVA/Dog-tc/ITA/RV52-96/1996/G3P[3]) and an unusual HRV strain (RVA/Human-tc/ITA/PA260-97/1997/G3P[3]) were determined to further elucidate the complex relationships among FRV, CRV and HRV strains. The CRV strains RV198-95 and RV52-96 were shown to possess a Cat97-like genotype constellation. However, 3 and 5 genes of RV198-95 and RV52-96, respectively, were found in distinct subclusters of the same genotypes, suggesting the occurrence of reassortment events among strains belonging to this FRV/CRV/HRV genogroup. Detailed phylogenetic analyses of the HRV strain PA260-97 showed that (i) 8 genome segments (VP3, VP4, VP6, VP7 and NSP2-5) clustered closely with RV198-95 and/or RV52-96; (ii) 2 genome segments (VP1 and VP2) were more closely related to HRV AU-1; and (iii) 1 genome segment (NSP1) was distantly related to any other established NSP1 genotypes and was ratified as a new NSP1 genotype, A15. These findings suggest that the human strain PA260-97 has a history of zoonotic transmission and is likely a reassortant among FRV/CRV strains from the Cat97 and AU-1-like genogroups. In addition, a potential third BA222-05-like genogroup of FRV and HRV strains should be recognized, consisting of rotavirus strains with a stable genetic genotype constellation of genes also partially related to bovine rotavirus (BRV) and bovine-like rotaviruses. The detailed phylogenetic analysis indicated that three major genotype constellations exist among FRV, CRV and feline/canine-like HRV strains, and that reassortment and interspecies transmission events contribute significantly to their wide genetic diversity.     

Whole genomic analyses of asymptomatic human G1P[6], G2P[6] and G3P[6] rotavirus strains reveal intergenogroup reassortment events and genome segments of artiodactyl origin

Although P[6] group A rotaviruses (RVA) cause diarrhoea in humans, they have been also associated with endemics of predominantly asymptomatic neonatal infections. Interestingly, strains representing the endemic and asymptomatic P[6] RVAs were found to possess one of the four common human VP7 serotypes (G1–G4), and exhibited little antigenic/genetic differences with the VP4 proteins/VP4 encoding genome segments of P[6] RVAs recovered from diarrhoeic children, raising interest on their complete genetic constellations. In the present study, we report the overall genetic makeup and possible origin of three such asymptomatic human P[6] RVA strains, RVA/Human-tc/VEN/M37/1982/G1P2A[6], RVA/Human-tc/SWE/1076/1983/G2P2A[6] and RVA/Human-tc/AUS/McN13/1980/G3P2A[6]. G1P[6] strain M37 exhibited an unusual genotype constellation (G1-P[6]-R1-C1-M1-A1-N1-T2-E1-H1), not reported previously, and was found to originate from possible intergenogroup reassortment events involving acquisition of a DS-1-like NSP3 encoding genome segment by a human Wa-like RVA strain. On the other hand, G2P[6] strain 1076 exhibited a DS-1-like genotype constellation, and was found to possess several genome segments (those encoding VP1, VP3, VP6 and NSP4) of possible artiodactyl (ruminants) origin on a human RVA genetic backbone. The whole genome of G3P[6] strain McN13 was closely related to that of asymptomatic human Wa-like G3P[6] strain RV3, and both strains shared unique amino acid changes, which might have contributed to their attenuation. Taken together, the present study provided insights into the origin and complex genetic diversity of P[6] RVAs possessing the common human VP7 genotypes. This is the first report on the whole genomic analysis of a G1P[6] RVA strain.     

Novel NSP1 genotype characterised in an African camel G8P[11] rotavirus strain

Animal–human interspecies transmission is thought to play a significant role in influencing rotavirus strain diversity in humans. Proving this concept requires a better understanding of the complete genetic constellation of rotaviruses circulating in various animal species. However, very few whole genomes of animal rotaviruses, especially in developing countries, are available. In this study, complete genetic configuration of the first African camel rotavirus strain (RVA/Camel-wt/SDN/MRC-DPRU447/2002/G8P[11]) was assigned a unique G8-P[11]-I2-R2-C2-M2-A18-N2-T6-E2-H3 genotype constellation that has not been reported in other ruminants. It contained a novel NSP1 genotype (genotype A18). The evolutionary dynamics of the genome segments of strain MRC-DPRU447 were rather complex compared to those found in other camelids. Its genome segments 1, 3, 7–10 were closely related (>93% nucleotide identity) to those of human–animal reassortant strains like RVA/Human-tc/ITA/PA169/1988/G6P[14] and RVA/Human-wt/HUN/Hun5/1997/G6P[14], segments 4, 6 and 11 shared common ancestry (>95% nucleotide identity) with bovine rotaviruses like strains RVA/Cow-wt/CHN/DQ-75/2008/G10P[11] and RVA/Cow-wt/KOR/KJ19-2/XXXX/G6P[7], whereas segment 2 was closely related (94% nucleotide identity) to guanaco rotavirus strain RVA/Guanaco-wt/ARG/Rio_Negro/1998/G8P[1]. Its genetic backbone consisted of DS-1-like, AU-1-like, artiodactyl-like and a novel A18 genotype. This suggests that strain MRC-DPRU447 potentially emerged through multiple reassortment events between several mammalian rotaviruses of at least two genogroups or simply strain MRC-DPRU447 display a unique progenitor genotypes. Close relationship between some of the genome segments of strain MRC-DPRU447 to human rotaviruses suggests previous occurrence of reassortment processes combined with interspecies transmission between humans and camels. The whole genome data for strain MRC-DPRU447 adds to the much needed animal rotavirus data from Africa which is limited at the moment.