Helen O'Shea

Identification of a G2-like porcine rotavirus bearing a novel VP4 type, P[32]

A porcine group A rotavirus (GARV) strain, 61/07/Ire, was isolated from a 4–5 week asymptomatic piglet, during an epidemiological survey of porcine herds in Southern Ireland, in 2007. The nucleotide (nt) and amino acid (aa) sequence of the full-length VP4 protein of the PoRV strain 61/07/Ire was determined. Based on the entire VP4 open reading frame (nt), strain 61/07/Ire displayed ≤ 76.5% identity to representatives of the established 31 P-types, a value far lower than the percentage identity cutoff value (80%) established by the Rotavirus Classification Working Group (RCWG) to define a novel P genotype. Strain 61/07/Ire revealed low aa identity, ranging from 57.1% to 83.6%, to the cognate sequences of representatives of the various P genotypes. The aa identity was lower in the VP8* trypsin-cleavage fragment of the VP4, which encompasses the VP4 hypervariable region, ranging from 36.9% to 75.3%. Sequence analyses of the VP7, VP6, and NSP4 genes revealed that the GARV strain 61/07/Ire possessed a G2-like VP7, an E9 NSP4 genotype and an I5 VP6 genotype. Altogether, these results indicate that the GARV strain 61/07/Ire should be considered as a prototype of a new VP4 genotype, P[32], and provide further evidence for the vast heterogeneity of group A rotaviruses.

Complete molecular genome analyses of equine rotavirus A strains from different continents reveal several novel genotypes and a largely conserved genotype constellation

In this study, the complete genome sequences of seven equine group A rotavirus (RVA) strains (RVA/Horse-tc/GBR/L338/1991/G13P[18], RVA/Horse-wt/IRL/03V04954/2003/G3P[12] and RVA/Horse-wt/IRL/04V2024/2004/G14P[12] from Europe; RVA/Horse-wt/ARG/E30/1993/G3P[12], RVA/Horse-wt/ARG/E403/2006/G14P[12] and RVA/Horse-wt/ARG/E4040/2008/G14P[12] from Argentina; and RVA/Horse-wt/ZAF/EqRV-SA1/2006/G14P[12] from South Africa) were determined. Multiple novel genotypes were identified and genotype numbers were assigned by the Rotavirus Classification Working Group: R9 (VP1), C9 (VP2), N9 (NSP2), T12 (NSP3), E14 (NSP4), and H7 and H11 (NSP5). The genotype constellation of L338 was unique: G13-P[18]-I6-R9-C9-M6-A6-N9-T12-E14-H11. The six remaining equine RVA strains showed a largely conserved genotype constellation: G3/G14-P[12]-I2/I6-R2-C2-M3-A10-N2-T3-E2/E12-H7, which is highly divergent from other known non-equine RVA genotype constellations. Phylogenetic analyses revealed that the sequences of these equine RVA strains are related distantly to non-equine RVA strains, and that at least three lineages exist within equine RVA strains. A small number of reassortment events were observed. Interestingly, the three RVA strains from Argentina possessed the E12 genotype, whereas the three RVA strains from Ireland and South Africa possessed the E2 genotype. The unusual E12 genotype has until now only been described in Argentina among RVA strains collected from guanaco, cattle and horses, suggesting geographical isolation of this NSP4 genotype. This conserved genetic configuration of equine RVA strains could be useful for future vaccine development or improvement of currently used equine RVA vaccines.

Changing profile of the bovine rotavirus G6 population in the south of Ireland from 2002 to 2009.

Bovine group A rotavirus is one of the main causes of neonatal diarrhoea in calves. This study examined the different G and P genotypes circulating in the bovine population, from 2002-2009, in the south of Ireland. Rotavirus positive bovine faecal samples (n=332) were collected from the Cork Regional Veterinary Laboratory, between 2002 and 2009 and subjected to RNA extraction, PAGE analysis, and G and P genotyping. Genotyping analysis identified G6, G10, P[5], and P[11] to be the predominant G and P genotypes in the present study, with G6 rotavirus responsible for 70-80% of rotavirus infections. The highest combination of G and P types found was G6 P[5], followed by G6 P[5+11] mixed infection. The prevalence of G6 and G10 has shifted over the years, with an increase in the amount of G10 P[11] being detected. Novel combinations (G6+G10P[11], G6+G10P[5+11] and G10P[5+11]) were also detected for the first time. In addition to this, sequence analysis of the VP7 RT-PCR amplicons has revealed that Irish G6 strains are falling within three different lineages, III-V. During this study, two samples, initially genotyped as G8P[11] were identified through sequence analysis as being true G6, lineage III with a high nucleotide identity to Hun4, a G6 human sample from Hungary. The increase in novel G and P type combinations, as well as changes seen in G6 samples could have an impact on rotavirus vaccination programmes, as the current vaccine available may not offer protection against all of these circulating types.

Changing profile of rotavirus in Ireland: Predominance of P[8] and emergence of P[6] and P[9] in mixed infections

Six hundred and thirty three fecal specimens were collected from patients under 6 years, suffering from non‐bacterial, putative viral gastroenteritis in the south of Ireland, between 2003 and 2006. Following laboratory identification of rotavirus as the aetiological agent in 558 specimens, reverse transcriptase polymerase chain reaction was employed to amplify the VP7 and VP4 gene segments of 249 and 245 samples, respectively. G and P typing was subsequently carried out on these amplicons. G1 (65.1%), and G3 (16.1%) were found to be the most prevalent circulating G types over the course of the study. Both G2 (1.2%) and G9 (3.6%), were also found to be circulating, however, these types were less frequently detected. Mixed G type infections were found to account for 41 samples (14%). P typing was carried out on 245 samples. P[8] was the most commonly detected P type over the course of the study (93.5%). Both P[6] and P[9], which had not previously been detected in the Irish population, were detected during this investigation. P[6] was detected in both single and mixed P type infections, while P[9] was detected as part of mixed infections only. The key findings of this study were the emergence of P[6] and P[9] as epidemiologically important rotavirus strains in the Irish population. The profile of rotavirus is changing continuously in Ireland, and continued surveillance of the circulating strains is needed to detect the appearance of new strains, or new variants which could escape immune protection induced by an outdated vaccine. J. Med. Virol. 80:524–530, 2008.

Molecular characterization of group A rotaviruses detected in children with gastroenteritis in Ireland in 2006–2009

Community and hospital-acquired cases of human rotavirus are responsible for millions of gastroenteritis cases in children worldwide, chiefly in developing countries, and vaccines are now available. During surveillance activity for human rotavirus infections in Ireland, between 2006 and 2009, a total of 420 rotavirus strains were collected and analysed. Upon either PCR genotyping and sequence analysis, a variety of VP7 (G1-G4 and G9) and VP4 (P[4], P[6], P[8] and P[9]) genotypes were detected. Strains G1P[8] were found to be predominant throughout the period 2006-2008, with slight fluctuations seen in the very limited samples available in 2008-2009. Upon either PCR genotyping and sequence analysis of selected strains, the G1, G3 and G9 viruses were found to contain E1 (Wa-like) NSP4 and I1 VP6 genotypes, while the analysed G2 strains possessed E2 NSP4 and I2 VP6 genotypes, a genetic make-up which is highly conserved in the major human rotavirus genogroups Wa- and Kun-like, respectively. Upon sequence analysis of the most common VP4 genotype, P[8], at least two distinct lineages were identified, both unrelated to P[8] Irish rotaviruses circulating in previous years, and more closely related to recent European humans rotaviruses. Moreover, sequence analysis of the VP7 of G1 rotaviruses revealed the onset of a G1 variant, previously unseen in the Irish population.

Detection and characterization of porcine sapoviruses from asymptomatic animals in Irish farms

Caliciviruses are an important cause of gastroenteritis in humans and animals. Molecular analysis of the polymerase and capsid genes of porcine caliciviruses, sapoviruses (SaVs) and noroviruses (NoVs), has demonstrated a broad range of genetic diversity but information on their epidemiology and pathogenic role in pigs is limited. In this study, 292 faecal samples were obtained from 4-5 to 8-9 week old asymptomatic pigs from four porcine herds in Ireland during 2005-2007 and were screened by RT-PCR using calicivirus-specific primers. Only seven samples from two porcine herds tested positive for porcine calicivirus. By sequence analysis of the partial RNA-dependent RNA polymerase (RdRp) fragment, six samples from one such herd were closely related to each other (>98% nucleotide identity) and were characterised as genogroup (GG) III (Cowden-like) porcine SaVs. These viruses demonstrated an amino acid (aa) identity of 81.3-98.6% to GGIII SaVs. Conversely, one calicivirus strain, 9/07/Ire (identified from a different herd in 2007), was distantly related to GIII SaVs and displayed 94.6-98.6% aa identity to rare K7-like porcine caliciviruses, representatives of a potential novel SaV genogroup (GGVII), described previously in Japan and the USA. Circulation of SaVs in asymptomatic animals might be a mechanism of virus persistence in porcine populations and should be considered with respect to understanding the epidemiology of these viruses in porcine herds.

Molecular characterisation of a bovine-like rotavirus detected from a giraffe

BackgroundRotavirus (RV), is a member of the Reoviridae family and an important etiological agent of acute viral gastroenteritis in the young. Rotaviruses have a wide host range infecting a broad range of animal species, however little is known about rotavirus infection in exotic animals. In this paper we report the first characterisation of a RV strain from a giraffe calf.ResultsThis report describes the identification and detailed molecular characterisation of a rotavirus strain detected from a 14-day-old Giraffe (Giraffa camelopardalis), presenting with acute diarrhea. The RV strain detected from the giraffe was characterized molecularly as G10P[11]. Detailed sequence analysis of VP4 and VP7 revealed significant identity at the amino acid sequence level to Bovine RV (BoRV).ConclusionThis study demonstrates the need for continuous surveillance of RV strains in various animal populations, which will facilitate the identification of rotavirus hosts not previously reported. Furthermore, extending typical epidemiology studies to a broader host range will contribute to the timely identification of new emerging strain types.

Molecular characterization of group A rotavirus found in elderly patients in Ireland; Predominance of G1P[8], continued presence of G9P[8], and emergence of G2P[4]†

Rotavirus is a major cause of gastroenteritis in young children worldwide. There have been several recent reports concerning rotavirus isolation from adults, particularly in the elderly, presenting with gastroenteritis. In this study, the authors report on rotavirus outbreaks in five separate elderly care facilities between April, and June 2011 in Ireland. The following genotypes were detected; G1P[8] (n = 5/11), G2P[4] (n = 2/11), and G9P[8] (n = 2/11). Thus, similarities to previous reports were found in that G1P[8] predominated, G9P[8] was still detected but G2P[4] was detected for the first time in a geriatric population in Ireland. Here also described is the detection of Group 2 lineage IIC rotavirus in Ireland for the first time. J. Med. Virol. 84:2008–2017, 2012.

Changing patterns of rotavirus strains circulating in Ireland: Re‐emergence of G2P[4] and identification of novel genotypes in Ireland

Worldwide, Group A Rotavirus (RVA) is recognized as the most common aetiological agent of acute diarrheal disease in children. One hundred and ninety seven positive faecal samples were obtained from patients between 2006 and 2008. Reverse transcriptase polymerase chain reaction (RT‐PCR) was used to amplify the VP7 and VP4 gene segments of these samples, and G and P typing was carried out subsequently. The most common strain type was G1P[8], and the emergent global G9‐type was identified in both years. RVA strain type G2P[4], previously reported in Ireland in 1999, was also detected. Genotypes G2 and G3 in combination with P[4] were detected in 2006–2007 only. There was also an emergence of strain types including G3P[4], G9P[4], G2P[4 + 8] and G2G4P[8] in this study. Molecular analysis of the VP7 genes revealed G1 strains circulating within lineage Ic as previously reported in Ireland. In addition, new sublineage within lineage I of G1 strains was also identified. Analysis of G4 strain NRVL‐Hum‐49 revealed similarity with other human G4 viruses in lineage Ib. G9 strain NRVL‐Hum‐74 clustered with a unique G9 strain, CIT‐254, in lineage IIIc. This data supports the observations made that the profile of RVA strains in Ireland appears to be dynamic. This study demonstrates that the circulation of human rotavirus is changing continuously in Ireland, and continued surveillance of the circulating strains is needed to detect the appearance of new strains, or new variants which may lead to vaccine breakthrough. J. Med. Virol. 87:764–773, 2015.

Complete genomic sequence analyses of the first group A giraffe rotavirus reveals close evolutionary relationship with rotaviruses infecting other members of the Artiodactyla

Group A Rotaviruses (RVA) have been established as significant contributory agents of acute gastroenteritis in young children and many animal species. In 2008, we described the first RVA strain detected in a giraffe calf (RVA/Giraffe-wt/IRL/GirRV/2008/G10P[11]), presenting with acute diarrhoea. Molecular characterisation of the VP7 and VP4 genes revealed the bovine-like genotypes G10 and P[11], respectively. To further investigate the origin of this giraffe RVA strain, the 9 remaining gene segments were sequenced and analysed, revealing the following genotype constellation: G10-P[11]-I2-R2-C2-M2-A3-N2-T6-E2-H3. This genotype constellation is very similar to RVA strains isolated from cattle or other members of the artiodactyls. Phylogenetic analyses confirmed the close relationship between GirRV and RVA strains with a bovine-like genotype constellation detected from several host species, including humans. These results suggest that RVA strain GirRV was the result of an interspecies transmission from a bovine host to the giraffe calf. However, we cannot rule out completely that this bovine-like RVA genotype constellation may be enzootic in giraffes. Future RVA surveillance in giraffes may answer this intriguing question.