Molecular characterization of VP4, VP6 and VP7 genes of a rare G8P[14] rotavirus strain detected in an infant with gastroenteritis in Italy

In this study, the molecular characterization of a rare G8P[14] group A rotavirus (GARV) strain detected in Northern Italy during the 2004-2005 epidemiological rotavirus season is described. Two hundred and seventy three rotavirus-like particle positive stools out of 856 stools from children (31.9%) hospitalized with gastroenteritis were analyzed using polyacrilamide gel electrophoresis and 271 GARVs were genotyped by VP7 and VP4 specific RT-PCRs. One strain (PR/1300/04) with a long electropherotype (e-type) displayed the G8 specificity and was VP4 un-typeable. The P and the subgroup (SG) specificities were determined by sequencing the VP4 and the VP6 gene, respectively. The PR/1300/04 strain exhibited P[14] and SGI specificities. By sequence and phylogenetic analyses of the VP4, VP6 and VP7 amplicons, the PR/1300/04 VP4 and VP6 genes were demonstrated to be of human rotavirus origin, with the VP4 gene closely related to the human Italian PA169 strain (G6P[14]), while the VP7 gene was of animal origin (bovine). These data suggest that the Italian PR/1300/04 strain could be a reassortant between a PA169-like Italian strain with P[14] specificity, long e-type and SGI, and a G8 animal strain. The increasing number of reports of atypical GARVs in humans suggests that interspecies transmission of genes greatly contributes to the GARV genetic evolution.     

Diversity of viruses associated with acute gastroenteritis in children hospitalized with diarrhea in Ho Chi Minh City, Vietnam

A molecular epidemiological study on common diarrheal viruses was conducted in Ho Chi Minh City, Vietnam between October 2002 and September 2003. Fecal samples were collected from 1,010 hospitalized children with acute gastroenteritis. Those samples were screened for groups A, B, and C rotavirus, adenovirus, genogroups I and II norovirus (NoV), sapovirus (SaV), and human astrovirus (HAstV) by RT-multiplex PCR, and the positive specimens were characterized further by ELISA, nested PCR, or sequencing. Among the diarrheal viruses detected, group A rotavirus was the most common, with a proportion of 67.4%, whereas NoV GII, adenovirus, SaV, and HAstV were also found in 5.5, 3.2, 0.8, and 0.6%, respectively. It is noteworthy that the group C rotavirus was first reported in Vietnam, with a proportion of 0.5% in this study. Fifty-six of 1,010 (5.5%) samples were found positive with more than one viral agent, in which 25 samples contained both group A rotavirus and NoV GII. Group A rotavirus could be identified throughout year with the peaks in both the dry and rainy season, whereas other viruses prevailed mainly in the rainy season. G-typing for the group A rotavirus showed that genotype 1 was still the most prevailing (33.0%), but interestingly, serotype 9 was emergent and became the third most common rotavirus G-type in these samples (13.7%). The four most common G-P combinations globally, G1P[8], G2P[4], G3P[8], and G4P[8] were found in 46.8% of rotavirus-positive samples, and it is of interest that one unusual rotavirus G9P[19] strain was first detected in Vietnam. The majority of NoV strains belonged to GII/4, and SaV strains mainly clustered with the Manchester strain (GI/1). Twenty-seven out of 32 adenovirus strains were identified as serotype 41. All HAstVs belonged to genotype 1. The results indicated clearly the impact of viral agents causing gastroenteritis and the importance of vaccination against diarrhea in Vietnam.     

Distribution of human group a rotavirus VP7 and VP4 types circulating in Seoul,Korea between 1998 and 2000

Three hundred forty-eight fecal specimens collected from young children with acute diarrhea in Seoul, Korea between January 1998 and February 2000 were examined for G and P types. Of these, 205 samples (59%) were confirmed as group A rotavirus by ELISA for the detection of VP6 antigen. Confirmed rotavirus isolates were characterized using G serotyping ELISA and RT-PCR methodologies for G and P genotyping of the outer capsid proteins VP7 and VP4, respectively. Serotyping of the outer capsid protein, VP7, revealed G4 as the dominant circulating serotype (41%) followed by G1 (28%) and quite a high incidence of mixed infection (14%). Genotyping of the VP4 protein was carried out on 55 of the rotavirus isolates with the dominant type being P[8] (46%). Of interest were a number of unusual G and P type combinations detected in Korea for the first time, especially the P[4] genotype associated with non-G2 serotypes. There were also a number of P[6] isolates identified including one G2P[6] isolate.     

Genotype diversity of group A rotavirus strains in children with acute diarrhea in urban Burkina Faso, 2008-2010

In this study, the diversity of G and P genotypes of rotavirus strains in Burkinabe children were examined. Between November 2008 and February 2010, 447 stool samples were collected from children <5 years of age with acute diarrhea visiting hospital in Ouagadougou. Group A rotavirus was previously detected in 151/447 (33.8%) of the samples tested by an immunochromatographic test and these samples were now tested further for rotavirus G and P genotypes by RT-PCR. Of these, the rotavirus type genes were amplified by RT-PCR for 140/151 (92.7%) samples and G and P genotypes were successfully determined for 81 (57.9%) and 130 (92.9%) samples, respectively. The most prevalent G genotypes were G1, 34/140 (24.3%), and G9, 21/140 (15%), while the predominant P genotypes were P[6], 56/140 (40%), and P[8], 54/140 (38.6%). Among the single infections, 63/140 (45%), the predominant G/P combinations were: G1P[8] (33%), G9P[8] (29%), and G2P[6] (14%). The unusual strains G1P[9] (3%), G12P[6] (3%), G10P[6] (2%), and G2P[8] (2%) were also detected. In a high number of strains 61/140 (43.6%), the G genotype could not be determined and mixed infections were determined in 17/140 (12.1%) of strains identified. This study highlights the high diversity and presence of unusual rotavirus strains in children in Burkina Faso.     

Detection and characterization of group A rotaviruses in children hospitalized with acute gastroenteritis in Norway, 2006–2008

To assess the genetic diversity of rotavirus strains in Norway, the distribution of rotavirus genotypes was studied in children admitted to hospital with acute gastroenteritis. The detection of rotavirus in stool samples was compared using an enzyme‐linked immunosorbent assay (ELISA), an immunochromatographic test and RT‐PCR. Children <5 years of age admitted to hospital with diarrhea in three large hospitals were enrolled prospectively from March 2006 to February 2008. Rotavirus was detected in 58% of the children by the immunochromatographic test, in 63% by ELISA and 72% by RT‐PCR. A total of 219 (70%) rotavirus isolates were characterized in order to determine the genotype. The predominant G types included G1 (53%), G9 (16%), and G3 (13%), and the frequency of G3 varied more than G9 between seasons (8–20%). The P[8] genotype was identified in 188 (86%) of samples, and the globally common genotype combinations G1P[8], G2P[4], G3P[8], G4P[8], and G9P[8] accounted together for >80% of infection. No unusual rotavirus strains were detected, and only four samples contained mixed infections. This study demonstrates that ELISA has similar specificity but lower sensitivity compared to RT‐PCR. The immunochromatographic test had the lowest sensitivity and specificity compared to the other assays. Rotaviruses causing severe gastroenteritis leading to hospitalization of children <5 years of age in Norway include the common genotypes, however, a considerable geographical and seasonal variation was observed in the distribution of these genotypes. These data may be important for assessing the need for introducing rotavirus vaccines into immunization programs in Norway. J. Med. Virol. 81:1839–1844, 2009. © 2009 Wiley‐Liss, Inc.     

Molecular characterization and genetic variation of the VP7 gene of human rotaviruses isolated in Paraguay

Rotavirus is the main cause of acute diarrhea in infants and young children worldwide. In Paraguay, acute diarrhea ranks fourth among the causes of mortality in children under 4 years of age. Rotavirus was detected in 93 out of 410 patients admitted to three main hospitals in Asunción, Paraguay from August 1998 to August 2000. Samples from 64 patients were analyzed by RT-PCR for G and P typing. G4P[8] (46.9%; 30/64) was the most common strain detected, followed by G9P[8] (17.2%; 11/64) and G1P[8] (10,9%; 7/64). Since G4 was predominant during the epidemiological peaks of 1998 and 1999, four samples were sequenced and all grouped into sublineage Ic. This sublineage was reported for the first time in 1998 in Argentina, southern border of Paraguay, and it was shown to be responsible for the increased prevalence of G4 during the epidemiological season of 1998 in that country. In addition, Paraguayan G1 strains grouped in different lineages (I and II). However, G9 was predominant during the rotavirus epidemiological peak of 2000, and phylogenetic analysis of five samples grouped into a common emergent/reemergent lineage that circulates worldwide. Since vaccination could reduce the severity and the number of cases of rotavirus disease, this study suggests that a vaccine containing recently isolated variants of the most prevalent types (G1-G4) together with the emerging G9 type, might be sufficient to elicit a protective immune response against the rotavirus types circulating currently in Paraguay.     

Mutated G4P[8] rotavirus associated with a nationwide outbreak of gastroenteritis in Nicaragua in 2005

During February and March 2005, one of the largest national recorded outbreaks of severe acute gastroenteritis occurred in Nicaragua, affecting >or=64,000 individuals and causing >or=56 deaths, predominantly in children under 5 years of age. Through a nationwide laboratory-based study, stool samples were collected and investigated for rotavirus. Of 108 stool samples examined, 72 (67%) were positive for rotavirus. While 69% (50/72) of the positive samples were found in children less than 2 years of age, 50% (6/12) of the adult samples were positive. A mutated G4P[8] strain was the most commonly recognized strain (85%), followed by mixed G strains (8%) and G9P[8] (7%) strains. Phylogenetic analysis of the VP7 gene revealed that the G4 strains belonged to the emerging lineage Ic and was distantly related to the ST3 and VA70 G4 strains. Secondary structure predictions of the VP7 G4 protein revealed an insert of an asparagine residue in position 76, which, combined with additional mutations, surprisingly modified two downstream beta-sheets at amino acid positions 80 to 85 and 115 to 119. The 2005 G4P[8] strain compared to a G4P[8] strain from 2002 had a substitution of an asparagine residue for threonine (Asn-->Thr) at position 96 within antigenic region A, thus eliminating a potential glycosylation site. The mutated G4 virus was introduced in Nicaragua after 2002 and probably emerged from Brazil, Argentina, or Uruguay.     

Unexpected substitution of dominant rotavirus G genotypes in French hospitalized children over five consecutive seasons

The study was designed to evaluate the circulation of group A rotaviruses in French hospitalized children, and to detect unusual strains. This prospective study was conducted from 2001 to 2006 in children consulting for acute diarrhea at the pediatric emergency department in three French University Hospitals. The rotaviruses were detected by rapid test and genotyped by RT-PCR on the basis of their outer capsid proteins VP4 (P-type) and VP7 (G-type). The stools from 757 children were analyzed. G1P[8] strains were predominant (44.0%), followed by G9P[8] (17.7%), G3P[8] 13.1%, G4P[8] (9.5%), and G2P[4] (1.8%); mixed rotavirus infections occurred in 2.3%. G9 rotaviruses emerged during the 2004–2005 season (73.4%) and remained the second most prevalent strains. Few unusual strains, G6, G8, G12 and P[6]-types, were detected. The monitoring of rotavirus infections should be maintained to document strain distribution and to assess the emergence of new reassortants that may not respond to current rotavirus vaccines.     

Detection and characterisation of rotaviruses from children less than 5 years hospitalised with acute gastroenteritis in Nagercoil

Group A rotavirus continues to be the major cause of severe gastroenteritis in young children in developing countries. In this study, we report the prevalence and genotype of rotaviruses identified from children <5 years of age hospitalised with acute gastroenteritis from Nagercoil, Tamil Nadu from 2007-2010. From the 139 children included in the study, 71 samples (51%) were positive by ELISA and 65 samples were positive by PCR-based methods. G1P[8] (44.6%) was the most commonly identified genotype. In addition, we report detection of rotavirus in two of three CSF samples from children with seizures.     

Predominance of genotype P[9]G3 in rotavirus gastroenteritis in Polish children

Introduction

Rotavirus (RV) infection is the most common cause of gastroenteritis in children. This paper identifies the most common genotypes of rotaviruses isolated from children hospitalized with gastroenteritis and attempts to determine any relationship between infection with a certain rotavirus genotype.

Material and methods

The investigated group consisted of 68 consecutive children with rotavirus gastroenteritis (confirmed by an agglutination test). Rotavirus genotype was determined in stool samples obtained from each child.

Results

The P[9]VP4 genotype was observed in 41/61 positive samples (over 67.2%) that were permanently associated with the G3 VP7 genotype. Moreover, G3 was determined as the most commonly isolated G type (77.94%). As well as the P[9]G3 type, G3 was also found in the P[4] type (5 cases). Twenty-six out of 61 (42.6%) children in whom rotavirus genotype was determined were co-infected with pathogenic bacteria. No statistical correlation was observed between rotavirus P[9]G3 gastroenteritis and digestive tract co-infection with pathogenic bacteria (p > 0.05). Elevated ALT activity was found in 34/59 (57.6%) cases of rotavirus gastroenteritis. Elevated ALT serum level was found to correlate with P[9]G3 rotavirus genotype but concomitant infections did not.

Conclusions

The most common genotype of rotaviruses observed in our group of children, P[9]G3, has rarely been described. Co-infection of the digestive tract with pathogenic bacteria and elevated serum ALT concentrations were found to be the most frequent phenomena. A correlation between P[9]G3 rotavirus genotype and elevated serum ALT level was found, but no significant relationship was identified between concomitant infections and P[9]G3 genotype.     

Rotavirus infection and its genetic characterization in non-hospitalized adults with acute gastroenteritis in Shanghai, China

Rotavirus is a major cause of acute gastroenteritis in infants and young children, while its role as a pathogen in adults has long been underappreciated. In order to describe the epidemiological patterns and genetic characteristics of rotavirus causing sporadic acute gastroenteritis in adults, hospital-based surveillance of rotavirus infections was conducted in Shanghai, China, between June 2010 and May 2011. Stool specimens were collected from outpatients with acute gastroenteritis admitted to three local hospitals. Rotavirus was detected using a colloidal gold test device. G and P genotyping were performed by multiplex PCR assays, and the VP7 gene of G9 strains were sequenced for further genetic characterization. Of 1,479 adult diarrheal stool samples examined during the 1-year surveillance period, 138 (9.3 %) were found to be rotavirus positive. G1 appeared to be the predominant genotype (35.5 %), suggesting a shift from genotype G3 to G1 in the study population in Shanghai. Meanwhile, a high frequency of genotype G9 (27.5 %) was also observed, and G9 was also predominant (38.1 %) in the small number of children (n=123) involved in the present study. Other specificities detected in adults were G2 (12.3 %) and G3 (13.8 %). For P genotyping, only two types, P[8] and P[4], were detected. P[8] was dominant in both children and adults. Sequence and phylogenetic analysis revealed that these strains could be divided into two different groups, with clustering within G9 lineage 3 and the subcluster of Japanese and Chinese G9 strains, respectively. In comparison to the previous data, G9 strains established themselves in a short time span as an important genotype in Shanghai, China.     

Prevalence of VP4 and VP7 genotypes of human rotavirus in Ecuadorian children with acute diarrhea

The objective of the present study was to determine rotavirus etiology and prevalence of the different rotavirus serotypes in Ecuadorian children younger than 5 years of age with gastroenteritis. Children (729) less than 5 years of age with acute diarrhea from either public or private primary health care centers in 10 different provinces of Ecuador, between March 2006 and August 2006 were included in the study. Rotavirus infection was diagnosed using a commercial immunoenzymatic test. Rotavirus isolated from stool samples was genotyped. Rotavirus was detected in the feces of 269 of the 729 children (37%) with diarrhea. The most prevalent G genotypes were G9 (46.1%) and G2 (27.2%), while the predominant P genotypes were P[8] (57%) and P[4] (29.5%). Among the single infections, the predominant P/G combinations were: P[8]G9 (56.9%) and P[4]G2 (32.6%). The present countrywide survey is one of the major studies for one single season in Latin America and the first in its class in Ecuador. The value of expanding laboratory capability throughout Latin America in order to monitor rotavirus strains over time, with special attention directed at those strains obtained from children who experience vaccine failure, is critical. Only continuous monitoring of rotavirus disease burden and genotype surveillance will provide this information.     

G[P] type profiles of group A human rotavirus and their distribution in Nizhni Novgorod and Dzerzhinsk in 1997-2005

RT-PCR was used to determine G (VP7) and P (VP4) genotypes of group A rotavirus found in 2454 children with diarrhea in 1997-2005. Eight G[P] combinations, including G1-4 serotypes and P[4, 6, 8, 9] genotypes, were identified. The P[8] genotype was presented by the subtypes P[8]-1 and P[8]-2. In 1997-2005, the spectrum and distribution of G[P] types were as follows: G1P[8]-1 (10%), G1P[8]-2 (67%), G1P[6] (3%), G2P[4] (9%), G3P[8]-2 (5%), G3P[6] (1%), G3P[9] (1%), G4P[8]-2 (3%), G9 (0%), G?P[?] (1%). Five G[P] types of rotavirus were identified in the 2004-2005 season. The G2P[4] type was prevalent (37%), the GI P[8]-2 type was detected in 25% of cases; G3P[8]-2 in 22%; G4P[8]-2 in 12%; G3P in 2%), G[?]P[?] in 2%. The P[8]-1 subgemotype was not found. The spectrum of the G1P[8] types of rotavirus and their distribution should be taken into account while developing a vaccine prophylaxis program against rotavirus gastroenteritis in Russia.     

Rotavirus and norovirus in children with severe diarrhea in Burkina Faso before rotavirus vaccine introduction

Burkina Faso introduced rotavirus vaccine (RotaTeq) to the national immunization program in November 2013. This study describes the detection rates, clinical profiles, and molecular epidemiology of rotavirus and norovirus (NoV) infections among children <5 years hospitalized (n = 154) because of acute diarrhea in Ouagadougou, Burkina Faso, from December 2012 to November 2013, just before the start of vaccination. Overall, 44% and 23% of fecal samples were positive for rotavirus and NoV, respectively, most of them detected during the cold dry season (December‐March). The predominant G/P combinations were G12P[8] (47%) and G6P[6] (30%). G2P[4] (n = 3), G12P[6] (n = 3), and G6P[8] (n = 1) were also detected. Nearly all (94%) successfully genotyped NoV strains belonged to genotype GII.4. The predominance of rotavirus and NoV was noteworthy in the age group ≤6 months, with 67% rotavirus and 22% NoV, respectively. Vomiting was significantly more common among rotavirus‐infected children. To conclude, this study shows high detection rates of both rotavirus and NoV in children with severe diarrhea in Burkina Faso just before the introduction of rotavirus group A vaccination. The results can be used for estimating the impact of rotavirus group A vaccination, which started in the end of 2013. Furthermore, this study shows that the G6P[6] rotavirus strains emerging in Burkina Faso in 2010 is now established as a regionally important genotype.     

Optimization of RT-PCR for the identification of VP4 gene of group A rotaviruses and evaluation of its diagnostic efficiency

A method is suggested for the detection of the human rotavirus VP4 gene by RT-PCR. The method is universal for all [P] types of group A rotavirus in clinical samples. As against RNA electrophoresis and ELISA, it provides for a more accurate detection of rotaviruses by 18.8 and 26.5%, respectively. It was established by RT-PCR in February, 2002, in Nizhny Novgorod, that rotaviruses were responsible for 67% of acute gastroenteritis in hospitalized children.