VP4 genotyping of human rotavirus in the United States

Relationship between asymptomatic rotavirus infection and jaundice in neonates: a retrospective study

Background

Rotavirus (RV) infection in neonates can be mild or even asymptomatic. In RV infection, jaundice is often reported, but the relationship between jaundice and RV infection has not been studied. This study aimed to determine the importance of asymptomatic RV screening in neonates with jaundice.

Methods

Neonates from the neonatal intensive care unit (NICU) of Chonbuk National University Hospital, those transferred from local obstetrics and gynecology hospitals and outpatient clinics were selected from 2014 to 2017. The study included only infants aged between 3 and 28 days. Jaundice was defined according to gestational age and birth age, in accordance with the American Academy of Pediatrics guidelines criteria. RV infection was confirmed by a stool test, and RV screening and laboratory tests were performed at admission.

Results

Among 596 patients, 166 patients had jaundice. RV infection was observed in 70 (42%) jaundice patients. There were 36 (22%) jaundice patients with asymptomatic RV infection. Patients with onset of jaundice 3–7 days after birth had a high incidence of RV infection. When the RV test was positive, the risk of jaundice was significantly high [odds ratio (OR) 1.89; 95% confidence interval (CI), 1.20–2.98; p = 0.006].

Conclusions

Infants with the onset of jaundice > 3 days after birth were likely to have RV infection. Therefore, we suggest that screening tests for RV infection be included as part of the evaluation of jaundiced infants presenting to NICU.

Electronic supplementary material

The online version of this article (10.1186/s12887-018-1352-z) contains supplementary material, which is available to authorized users.

Rotavirus G2P[4] detection in fresh vegetables and oysters in Mexico City

Rotaviruses are the principal cause of dehydration caused by diarrhea in children younger than 2 years of age. Although these viral infections have mainly been associated with ingestion of fecally contaminated food and water, few studies have addressed the presence of the virus in food that is consumed raw or slightly cooked. In this work, 30 oyster samples and 33 vegetable samples were examined for the presence of rotavirus genotypes to evaluate their potential to produce gastrointestinal infections. The rotaviruses were identified by reverse transcriptase PCR amplification of the VP7 gene. G and P genotyping was also performed by reverse transcriptase PCR, with a detection sensitivity of up to 15 PFU/ml. Rotaviruses were found in 17 (26.9%) of 63 samples (10 oysters and 7 vegetables). The G2 genotype was found in 11 (64.7%) of 17 of the rotavirus strains, and 16 (94.1%) of 17 had the P[4] genotype. The combined genotypes found most frequently were G2P[4] (10 [58.82%] of 17), GNTP[4] (6 [35.29%] of 17), and G2P[NT] (1 [5.8%] of 17).

Rotavirus infection: a perspective on epidemiology, genomic diversity and vaccine strategies

For centuries, acute diarrhea has been a major cause of death in young children worldwide, and until 1973, before rotavirus was discovered; no infectious agents could be identified in about 80% of patients admitted to hospital with severe dehydrating diarrhea. Rotaviruses have now been shown to cause 40-50% of severe acute diarrhea in young children worldwide in both developing and developed countries. More than 600,000 young children die and approximately 2.4 million hospitalize annually from rotavirus disease, especially in South-East Asia and sub-Saharan Africa. Two safe and effective vaccines are now licensed in 100 countries but used in 17 countries. Rotarix (GSK) vaccine is derived from single attenuated human rotavirus G1P[8], representative of the most common serotype identified worldwide. RotaTeq (Merck) is a pentavalent mixture of naturally attenuated bovine/human rotavirus reassortants representing G1, G2, G3, G4, and P[8] serotypes. Though these vaccines have already dramatically decreased the morbidity associated with rotavirus in countries where they are widely used, the third generation of vaccines, based on inactivated viruses or recombinant virus like particle are already in pipeline. Continuous surveillance and the genetic and antigenic analysis of the various strains of rotavirus circulating worldwide will aid significantly in assessing the effectiveness of these vaccines and monitor emergence of new strains. Introduction of rotavirus vaccines in national vaccine policy along with other childhood vaccines may result in significant reduction in mortality in children in poor socioeconomic countries.

Molecular epidemiology of group A rotaviruses in water sources and selected raw vegetables in southern Africa

Group A rotaviruses (RVs) are the most important cause of acute viral gastroenteritis in infants and young children. In this study raw and treated drinking water supplies at plants in two geographic areas, as well as selected irrigation water and corresponding raw vegetables in three regions of southern Africa, were screened for the presence of RVs using molecular techniques. Group A RVs were detected in 11.8% of partially treated and 1.7% of finally treated drinking water samples and in 14% of irrigation water samples and 1.7% of corresponding raw vegetable samples. Type-specific reverse transcriptase-PCR and sequence analysis revealed the presence of multiple types (G1, G2, G8, and G9) in irrigation water and single types (G1 or G3) in raw and treated drinking water. Group A RVs detected in all samples consisted of mixed P types (P[4], P[6], P[8], and P[9]), with P[6] predominating. The detection of types G8, G9, and P[6] reflects the emergence of these types in clinical infections. The similarity of environmental types to those in patients with clinical RV infections confirms the value of wastewater screening as a tool for assessing RVs circulating in communities, with the benefit of detecting types that cause both clinical and subclinical infections. The results provide new information on RV types in water and related environments and identify the potential risk of waterborne transmission. In addition, the presence of RVs in drinking water underlines shortcomings in quality specifications. These data provide valuable information regarding the prevalence of RVs in environmental sources, with important implications for vaccine development.

Relationships among porcine and human P[6] rotaviruses: Evidence that the different human P[6] lineages have originated from multiple interspecies transmission events

Porcine rotavirus strains (PoRVs) bearing human-like VP4 P[6] gene alleles were identified. Genetic characterization with either PCR genotyping or sequence analysis allowed to determine the VP7 specificity of the PoRVs as G3, G4, G5 and G9, and the VP6 as genogroup I, that is predictive of a subgroup I specificity. Sequence analysis of the VP8* trypsin-cleavage product of VP4 allowed PoRVs to be characterized further into genetic lineages within the P[6] genotype. Unexpectedly, the strains displayed significantly higher similarity (up to 94.6% and 92.5% at aa and nt level, respectively) to human M37-like P[6] strains (lineage I), serologically classifiable as P2A, or to the atypical Hungarian P[6] human strains (HRVs), designated as lineage V (up to 97.0% aa and 96.1% nt), than to the porcine P[6] strain Gottfried, lineage II (<85.1% aa and 82.2 nt), which is serologically classified as P2B. Interestingly, no P[6] PoRV resembling the original prototype porcine strain, Gottfried, was detected, while Japanase P[6] PoRV clustered with the atypical Japanase G1 human strain AU19. By analysis of the 10th and 11th genome segments, all the strains revealed a NSP4B genogroup (Wa-like) and a NSP5/6 gene of porcine origin. These findings strongly suggest interspecies transmission of rotavirus strains and/or genes, and may indicate the occurrence of at least 3 separate rotavirus transmission events between pigs and humans, providing convincing evidence that evolution of human rotaviruses is tightly intermingled with the evolution of animal rotaviruses.

Characterisation of rotavirus strains among hospitalised and non-hospitalised children in Guinea-Bissau, 2002 A high frequency of mixed infections with serotype G8

BACKGROUND

In a previous community-based cohort study in Guinea-Bissau from 1996 to 1998, characterisation of rotavirus strains showed a high frequency of less common genotypes such as G8 and G9 and a high proportion of mixed infections.

OBJECTIVES AND STUDY DESIGN

In the present study, we examined the prevalence of rotavirus genotypes among 81 hospitalised and 23 non-hospitalised Guinean children with rotavirus associated diarrhoea during the 2002 seasonal rotavirus outbreak. G- and P-types were determined in a two-step procedure using reverse transcription followed by a standard multiplex PCR. The multiplex PCR for G-types was furthermore supplemented with a single locus PCR including the MW8 primer for the G8-genotype.

RESULTS

The dual infection G2/P[4]P[6] (24%) appeared to be the most frequent cause of rotavirus infections followed by G2P[4] (19%), G2P[6] (16%) and G8P[6] (13%). Overall 38% of the infections were mixed and 18% of the samples had the genotype G8. However, by subjecting all samples and not only the strains, which according to the standard multiplex PCR procedure were non-typeable, to a single locus G8-PCR, we found that the genotype G8 appeared in 62% of the infections, either as a single G-strain or in combination with other G-types, especially G2. Including these results, more than 63% of infections emerged as mixed. Neither genotype (including the presence of G8) nor the presence of mixed infections, seem to influence the severity of the rotavirus infection.

CONCLUSION

We found a high frequency of mixed infections especially due to G8-genotypes, which might have implications for development of rotavirus vaccine candidates for use in Africa. Our results do not suggest that a single genotype is associated with severity, but the present study is based on a modest number of samples and results should be interpreted with caution.

Serotype diversity and reassortment between human and animal rotavirus strains: implications for rotavirus vaccine programs

The development of rotavirus vaccines that are based on heterotypic or serotype-specific immunity has prompted many countries to establish programs to assess the disease burden associated with rotavirus infection and the distribution of rotavirus strains. Strain surveillance helps to determine whether the most prevalent local strains are likely to be covered by the serotype antigens found in current vaccines. After introduction of a vaccine, this surveillance could detect which strains might not be covered by the vaccine. Almost 2 decades ago, studies demonstrated that 4 globally common rotavirus serotypes (G1-G4) represent >90% of the rotavirus strains in circulation. Subsequently, these 4 serotypes were used in the development of reassortant vaccines predicated on serotype-specific immunity. More recently, the application of reverse-transcription polymerase chain reaction genotyping, nucleotide sequencing, and antigenic characterization methods has confirmed the importance of the 4 globally common types, but a much greater strain diversity has also been identified (we now recognize strains with at least 42 P-G combinations). These studies also identified globally (G9) or regionally (G5, G8, and P2A[6]) common serotype antigens not covered by the reassortant vaccines that have undergone efficacy trials. The enormous diversity and capacity of human rotaviruses for change suggest that rotavirus vaccines must provide good heterotypic protection to be optimally effective.

An efficient virus concentration method and RT-nested PCR for detection of rotaviruses in environmental water samples

Water samples were concentrated by the modified adsorption-elution technique followed by speedVac reconcentration of the filter eluates. Reverse transcriptase-nested polymerase chain reaction (RT-nested PCR) was used to detect rotavirus RNA in concentrates of the water. The detection limit of the rotavirus determined by RT-nested PCR alone was about 1.67 plaque forming units (PFU) per RT-PCR assay and that by RT-nested PCR combined with concentration from 1l seeded tap water sample was 1.46 plaque forming units per assay. Water samples were collected from various sources, concentrated, and determined rotavirus RNA. Of 120 water samples, rotavirus RNA was detected in 20 samples (16.7%); 2/10 (20%) of the river samples, 8/30 (26.7%) of the canal samples, and 10/40 (25%) of the sewage samples but was not found in any tap water samples (0/40). Only three water samples were positive for rotavirus antigen determined using an enzyme-linked immunosorbent assay (ELISA). Alignment analysis of the sequenced PCR product (346-bp fragment) was performed in eight rotavirus-positive samples using the rotavirus sequence deposited in the GenBank. All samples gave the correct VP7 sequence. Results of analysis showed two samples similar to human rotavirus (97-98%), five similar to rotavirus G9 sequence (94-99%), and one sample similar to animal rotavirus (97%). PCR inhibitors were not observed in any concentrated water samples. In all 20 (of 120) samples where rotaviruses were found, fecal coliforms including Escherichia coli were also found, but of the samples testing negative for rotaviruses, 76 were fecal coliforms positive and 69 were E. coli positive. The combination of the virus concentration method and RT-nested PCR described below made it possible to effectively detect rotaviruses in environmental water samples.

Global distribution of rotavirus serotypes/genotypes and its implication for the development and implementation of an effective rotavirus vaccine

A safe and effective rotavirus vaccine is urgently needed, particularly in developing countries. Critical to vaccine development and implementation is a knowledge base concerning the epidemiology of rotavirus G and P serotypes/genotypes throughout the world. The temporal and geographical distribution of human rotavirus G and P types was reviewed by analysing a total of 45571 strains collected globally from 124 studies reported from 52 countries on five continents published between 1989 and 2004. Four common G types (G1, G2, G3 and G4) in conjunction with P[8] or P[4] represented over 88% of the strains analysed worldwide. In addition, serotype G9 viruses associated with P[8] or P[6] were shown to have emerged as the fourth globally important G type with the relative frequency of 4.1%. When the global G and/or P type distributions were divided into five continents/subcontinents, several characteristic features emerged. For example, the P[8]G1 represented over 70% of rotavirus infections in North America, Europe and Australia, but only about 30% of the infections in South America and Asia, and 23% in Africa. In addition, in Africa (i) the relative frequency of G8 was as high as that of the globally common G3 or G4, (ii) P[6] represented almost one-third of all P types identified and (iii) 27% of the infections were associated with rotavirus strains bearing unusual combinations such as P[6]G8 or P[4]G8. Furthermore, in South America, uncommon G5 virus appeared to increase its epidemiological importance among children with diarrhea. Such findings have (i) confirmed the importance of continued active rotavirus strain surveillance in a variety of geographical settings and (ii) provided important considerations for the development and implementation of an effective rotavirus vaccine (e.g. a geographical P-G type adjustment in the formulation of next generation multivalent vaccines).

Frequent reassortments may explain the genetic heterogeneity of rotaviruses: analysis of Finnish rotavirus strains

The predominant rotavirus electropherotypes (e-types) during 17 epidemic seasons (1980 through 1997) in Finland were established, and representative virus isolates were studied by nucleotide sequencing and phylogenetic analysis. The virus isolates were either P[8]G1 or P[8]G4 types. The G1 and G4 strains formed one G1 lineage (VP7-G1-1) and one G4 lineage, respectively. Otherwise, they belonged to two P[8] lineages (VP4-P[8]-1 and -2) unrelated to their G types. Phylogenetic analysis of partial sequences of all 11 RNA segments obtained from the strains also revealed genetic diversity among gene segments other than those defining P and G types. With the exception of segments 1, 3, and 10, the sequences of the other segments could be assigned to 2 to 4 different genetic clusters. The results of this study suggest that, in addition to the RNA segments encoding VP4 and VP7, the other RNA segments may segregate independently as well. In total, the 9 predominant e-types represented 7 different RNA segment combinations when the phylogenetic clusters of their 11 genes were determined. The extensive genetic diversity and number of e-types among rotaviruses are best explained by frequent genetic reassortment.

Detection and characterization of rotavirus G and P types from children participating in a rotavirus vaccine trial in Belém, Brazil

This study sought the characterization of rotaviruses in a trial with a tetravalent rhesus-human rotavirus vaccine in Belém, Brazil in children who received three doses of vaccine or placebo in the 1st, 3rd and 5th months of life. Rotavirus electropherotypes, subgroups, G serotypes, G, [P] and [P], G genotypes were determined in 93.3%, 95.9%, 93.3%, 73.3%, 95.5% and 92.2% of isolates, respectively. Serotypes G1, G2 and G4 were detected in 58.9%, 30% and 4.4% of the cases, respectively. Rotavirus genotype G5 was detected for the first time in Northern region in 4.4% of the infections. Rotavirus genotypes P[8], P[4], P[6] and P[8 + 6] were detected in 54.5%, 26.7%, 12.2%, and 2.2% of the cases, respectively. The predominant genotypes were P[8], G1 and P[4], G2 with 53% and 26.6% of the infections, respectively. Unusual strains accounted for 20.5% including P[4], G1, P[6], G1, P[6], G4, P[6], G5, P[8], G2, P[8], G5. Mixed infections involving P[8 + 6], G2 and P[8 + 6], G1 were also noted. The neonatal P[6] strains associated with diarrhea were detected among children aged 9-24 months. To our knowledge, this study represents the first in Brazil to analyse, on molecular basis, rotavirus genotypes from children participating in a rotavirus vaccine trial. These results are of potential importance regarding future rotavirus vaccination strategies in Brazil.

Genotyping of rotaviruses in environmental water and stool samples in Southern Switzerland by nucleotide sequence analysis of 189 base pairs at the 5' end of the VP7 gene

Stool specimens from children (<4 years old) with diarrhea were collected over a 1-year period in Ticino (southern region of Switzerland). During the same period, environmental samples were collected from surface waters in the proximity of major water treatment plants. From treatment plants, samples were collected from the raw sewage and before the release of the treated water. From rivers, samples were collected before and after receiving the treated waters. A single-step reverse transcription (RT)-PCR amplification of the entire VP7 gene from extracted double-stranded RNA was developed. For the water samples, a further nested PCR was necessary to increase sensitivity. All amplified viral products were sequenced, and the sequence profile was compared to that of the VP7 genes of human and animal rotaviruses from GenBank. Rotavirus strains are characterized by outer capsid proteins G (glycoprotein) and P (protease-cleaved protein). Correct G genotyping of viral sequences from stool and water samples was possible by analyzing only 189 bp at the 5' end of the VP7 gene. In the Ticino region, the most predominant G genotype among clinical and water samples was G1. Genotypes G2 and G4 were found only among clinical samples. We also detected rotavirus G1-type sequences in feces from a healthy adult. This finding corroborates the hypothesis that healthy adults act as potential reservoirs for the spread of rotavirus in the environment. In our experiments, this RT-PCR-based method for rotavirus genotyping has proven to be a useful tool for epidemiological investigations.

VP4 and VP7 genotyping by reverse transcription-PCR of human rotavirus in mexican children with acute diarrhea

Dual typing (VP4 and VP7) of rotavirus obtained from 257 Mexican children during three epidemiological seasons was performed by reverse transcription-PCR. The P1G1 genotype was the most prevalent (40%), followed by P1G3 (19%) and P2G2 (16%). Thirty-one specimens (12%) presented mixed infections, while some genotypes were not found. This is the first dual typing of isolates from diarrhea cases in Mexico.

Surveillance of rotavirus strains in the United States: identification of unusual strains. The National Rotavirus Strain Surveillance System collaborating laboratories

Rotavirus strains from 964 fecal specimens collected from children at 11 U.S. hospital laboratories from November 1997 to March 1998 and from samples collected at 12 laboratories from November 1998 to March 1999 were typed for G and P proteins. Serotype G1 was the predominant serotype in 1997-1998 (88%), followed by G2 (6.2%), G9 (3.3%), and G3 (1.5%). This pattern was similar to that seen in 1998-1999: G1 (79%), G2 (15%), G9 (3.0%), G4 (1.6%), and G3 (0.3%). Novel P[9] strains were identified in both seasons, and analysis of a 364-nucleotide fragment from gene segment 4 of one of the strains demonstrated 97.3% nucleotide identity with the prototype P3[9],G3 strain, AU1, isolated in Japan. This is the first report of a human AU1-like strain in the United States. These results reinforce our initial findings that serotype G9 persists in the United States but has not become a predominant strain and that the common serotypes G1 to G4 account for almost 90% of strains in circulation. Other uncommon strains exist in the United States but may have been overlooked before because of their low prevalence and the use of inadequate diagnostic tools.

G and P genotyping of rotavirus strains circulating in france over a three-year period: detection of G9 and P[6] strains at low frequencies. The AZAY Group

Rotavirus G and P types from 716 children with acute diarrhea in Dijon from 1995 to 1998 and throughout France during the winter of 1997-1998 were analyzed by reverse transcription-PCR. P[8],G1 predominated, followed by P[8],G4, which emerged during the last winter. G9 and P[6] strains were detected at low frequencies.

VP7 and VP4 genotyping of human group A rotavirus in Buenos Aires, Argentina

Specific and sensitive tests for the detection and typing of group A rotavirus strains are needed for a more comprehensive knowledge of the epidemiology of rotaviral infection. In this study 500 stool specimens taken from 1996 to 1998 from children with acute diarrhea in Buenos Aires were examined. Group A rotavirus was unequivocally demonstrated in 62% of the samples tested by enzyme-linked immunosorbent assay (ELISA) for detection of VP6 antigen, polyacrylamide gel electrophoresis of double-stranded RNA, and reverse transcription-PCR (RT-PCR) for amplification of the VP7:G (1, 062 bp) and VP4:P (876 bp) genes. Only five positive specimens were found by RT-PCR but not by ELISA. G and P typing was carried out by nested amplification of variable sequences of the VP7 and the VP4 genes with six G- and five P-type-specific primers (multiplex PCR). Results obtained by this method showed the prevalence of the following G and P types: G1, 39%; G2, 43%; G4, 4%; P[8], 16%; P[4], 71%. Unexpectedly, the G-P type combination most frequently found was G2P[4] (43%) rather than G1P[8] (12%), which is the most commonly found worldwide. Unusual strains of the type G1P[4] accounted for 14% of the total, while mixed infections with more than one type were found in 10% of the samples. Detection of fecal rotavirus-specific immunoglobulin M (IgM) and IgA antibodies in consecutive samples of two patients taken at daily intervals demonstrated that high levels of IgM and IgA antibodies were detected on day 1 after the onset of disease and that the samples remained positive for about 10 days, after which virus shedding was no longer observed. Multiplex PCR offers a sensitive and specific alternative to determine the prevalence of group A rotavirus G and P types and to identify the emergence of uncommon strains, whereas detection of fecal IgM and IgA antibodies represents a useful supplement to virus detection for the diagnosis of current or recently acquired infections.

VP4 and VP7 genotyping of rotavirus samples recovered from infected children in Ireland over a 3-year period

Between September 1995 and August 1998, the incidence and diversity of the main human rotavirus genotypes (G1, G2, G3, and G4 and P[8], P[4], P[6], and P[9]) among Irish children were determined by using established and adapted reverse transcriptase PCR-based genotyping methods. From a total of 193 rotavirus-positive specimens collected from nine hospitals we successfully identified the P type in 182 (94%) of the samples and the G type in 165 (85.5%) of the samples. Only four samples could not be assigned a G or P type. Two P types existed in Ireland, P[8] (78%) and P[4] (16%), and their relative incidence varied over the 3 years of this study. No P[6] or P[9] types were detected. G1 was the most predominant G type (55%), and the incidences of G2, G3, and G4 isolates were 15.5, 1, and 11%, respectively. Three percent of the samples tested had a mixed G type. A P and G type was assigned to 158 (81.8%) of samples. Of the typeable samples, G1 P[8] was the most prevalent (65%), whereas G2 P[4] (17%), G3 P[8] (1%), G4 P[8] (12%), and mixed types (all G1/ G4 P[8]) (4%) were detected less frequently. In the third year a significant genotypic shift from G1 P[8] to G2 P[4] and G4 P[8] was observed. During the study, we noticed that the inclusion of random primers during cDNA synthesis greatly increased the specificity of the PCR typing assays. No correlation was seen between the contributing hospitals and a specific genotype. In conclusion, the coverage of infection given by the recently licensed tetravalent vaccine would be significantly high in Ireland, although future monitoring of genotypic changes among Irish isolates should be encouraged.

Characterization of rotavirus P genotypes circulating among paediatric inpatients in northern brazil

Between November 1992 and August 1993, twenty-eight rotavirus-positive stool samples obtained from paediatric inpatients in Belem, Brazil, aged less than four years, were tested by RT-PCR to determine the P genotype specificities. With the exception of 7 non-diarrhoeic children, all patients were either diarrhoeic at admission or developed diarrhoea while in hospital. Rotavirus strains with the gene 4 alleles corresponding to P1B[4] and P1A[8] types (both of which bearing G2 specificity) predominated, accounting for 78.6% of the strains. While only one P2A[6] type strain - with (mixed) G1 and 4 type specificities - was detected, the gene 4 allele could not be identified in 4 (14.3%) of the strains. Most (81%) of the specimens were obtained from children during their first 18 months of life. Rotavirus strains bearing single P1B[4] type-specificity were identified in both diarrhoeic (either nosocomial, 28.6% or community-acquired diarrhoea, 28.6%) and non-diarrhoeic (42.8%) children. P1A[8] gene 4 allele, on the other hand, was detected only among diarrhoeic children, at rates of 57.1% and 42.9% for nosocomial- and- community acquired diarrhoea, respectively. Mixed P1A[8],1B[4] type infection was identified in only one case of community-acquired diarrhoea.

Isolation of a human rotavirus strain with a super-short RNA pattern and a new P2 subtype

Super-short rotavirus strains that have a rearranged gene segment 11 are rarely found in humans, and only five isolates, all from Southeast Asia, have been described in the literature. We report the first isolation in Japan from an infant with severe diarrhea of a rotavirus possessing a super-short RNA pattern. This strain, designated AU19, had a G1 VP7 and is also the first isolate in Japan that possesses a P2[6] VP4. Furthermore, the P2[6] VP4 carried by AU19 was divergent in the hypervariable region of the amino acid sequence from the P2A[6] VP4s carried by asymptomatic neonatal strains or from the P2B[6] VP4 carried by porcine rotavirus strain Gottfried. Thus, AU19 is likely to represent a new VP4 subtype, which we propose to call P2C. Given the recent emergence of the P2[6] VP4s in India, Brazil, and the United States and the role of VP4 in protective immunity, further scrutiny is justified to see whether the emergence of the previously underrepresented P2[6] VP4 serotype is related to this new P2 subtype.

Genetic and antigenic characterization of a serotype P[6]G9 human rotavirus strain isolated in the United States

During an epidemiologic survey of rotavirus infections established to monitor the prevalent G serotypes circulating in the United States, human P[6]G9, subgroup I rotavirus strains causing symptomatic infections were identified as the fourth most common serotype. In this report we describe the molecular and antigenic characterization of one of these P[6]G9 isolates (US1205). Neutralization and sequencing studies have demonstrated that both outer capsid proteins, VP7 and VP4, of US1205 are closely related to but genetically and antigenically distinguishable from those of standard G9 strains (e.g., F45, WI61) and standard P2A[6] strains (e. g., ST3, M37). Thus the complete antigenic type of US1205 is P2A[6]G9, subgroup I. Sequence analysis of the VP6 and NSP4 genes of US1205 indicates that strain US1205 possessed VP6 subgroup I and NSP4A genotype specificities. Finally, Northern hybridization studies suggest that the P[6]G9 strains are closely related to members of the DS-1 genogroup except for their P[6] VP4 gene, which has been commonly identified in strains of both major human genogroups, and their G9 VP7 gene, which may have been derived by reassortment with a Wa genogroup strain. Examination of historic collections and prospective surveillance of strains will be needed to determine whether this strain has been present for some time or if it is emerging to compete with the other common serotypes of rotavirus.

Identification of two lineages (WA-like and F45-like) within the major rotavirus genotype P[8]

The fourth gene of a porcine (S8) and eight human rotavirus isolates possessing the major human VP4 specificity (P1A serotype and/or P[8] genotype) were partially sequenced and compared to other available P[8] sequences from rotaviruses types G1, G3, G5 and G9 specificities which had been originally recovered from children with diarrhea in Japan, Brazil and the USA. Brazilian rotavirus S8 represented the single known porcine rotavirus with this P specificity. Phylogenetic analysis revealed two lineages or subgenotypes within P[8] strains: the F45-like P subgenotype comprised most of the strains, including all the human G5 isolates analyzed, whereas the Wa- or S8-like subgenotype consisted of only a human isolate obtained in the same geographic region as S8 and an American strain with atypical RNA profile besides the prototypes Wa and S8 viruses. A conserved basic amino acid residue at position 131 in VP4 seemed characteristic of the F45-like P[8] subgenotype.

Comparison of enzyme immunoassay, PCR, and type-specific cDNA probe techniques for identification of group A rotavirus gene 4 types (P types)

This study was designed to evaluate three techniques most commonly used to identify the VP4 (P) types of human group A fecal rotaviruses. The techniques included PCR with nested primers and hybridization with PCR-generated probes (to determine the P genotypes). The results obtained by these genetic techniques were evaluated against those obtained by an enzyme immunoassay (EIA) incorporating neutralizing monoclonal antibodies (N-MAbs) reacting with three major human P serotypes (serotypes P1A, P1B, and P2A). The P types of the rotaviruses present in 102 fecal specimens were determined under code by each of the three assays. The specificity of each assay was evaluated against a "gold standard" putative P type (P serotype and genotype) deduced from knowledge of the VP7 (G) type and the origin of the fecal specimen. Overall comparison of the results showed respective sensitivities and specificities of 92 and 92% for reverse transcription-PCR, 80 and 99% for hybridization, and 73 and 91% for EIA with N-MAbs. The hybridization assay retained high sensitivity with specimens stored for > or = 10 years. Hybridization assays with nonradioactive probes are relatively inexpensive and are suited for use in developing countries. In summary, both genetic assays showed high sensitivities and specificities in assigning a P type to human fecal rotavirus strains. Further evaluation of the EIA with N-MAbs is required, together with incorporation of new N-MAbs for the detection of the additional P types detected in developing countries.

Use of non-radioactive probes for VP4 typing of human rotaviruses

The rotavirus outer capsid proteins VP4 and VP7 determine the P- and G-serotypes, respectively, of the virus. Three types of VP4 protein are commonly found in human rotaviruses (P4, P6 and P8) which are encoded by distinct VP4 gene alleles. We developed a non-radioactive Northern hybridization method for the P-genotyping of rotavirus field isolates. Double-stranded RNA was isolated from faecal specimens of rotavirus positive patients. Digoxigenin (DIG)-labelled cDNA probes derived from the VP4 gene of the standard strains RV5 (P4), ST3 (P6) and RV4 (P8) were used to discriminate between the different alleles. Although the P4 probe exhibited cross-reactivity with some P8 samples, the P6 and P8 probes were found to be type-specific. In addition, the probes did not react with standard strains representative of other defined human and animal rotavirus P-types. Use of these probes on viral RNA of faecal origin allowed approximately 70% of samples to be assigned a P-type. This method complements PCR- and EIA-based P-typing methods, is relatively inexpensive and is readily applicable to large numbers of samples, thus proving useful for epidemiological studies.

Survey of equine rotaviruses shows conservation of one P genotype in background of two G genotypes

DIG-labelled ssRNA probes were prepared from variable regions of VP4 and VP7 cognate genes, and used in hybridization assays for P and G genotyping of group A cell culture-adapted equine rotaviruses and fecal samples collected from foals with and without diarrhea. The probes confirmed known P and G serotypes of sixteen cell culture-adapted strains. From one-hundred and twenty-one rotavirus-positive samples, 83 reacted when tested for their P and G genotype specific probes. From these, 71 were found to contain G3 P12 genotypes, and 11 G14 P12 genotypes. No sample reacted with H1 or L338 P and G genotype probes. This suggests that the equine rotavirus population is conservative, containing predominantly one P genotype and two G genotypes. One isolate (26/94) whose dsRNA was visualized in an agarose gel did not react with any of the equine probes, and was found to belong to G8 and P1 genotypes. This is the fourth example of a single unique equine isolate (after H1, L338, and R-22). The remaining thirty-eight untypable field isolates had no detectable dsRNA after storage for 1 to 3 years.

Unusual diversity of human rotavirus G and P genotypes in India

Between April and December 1993, we determined P and G genotypes of group A rotavirus strains obtained from children admitted to diarrhea treatment centers in five Indian cities. From a total of 63 rotavirus-positive specimens, we identified 10 different strains with five different G genotypes and four distinct P types by using reverse transcription-PCR. The common worldwide strains G1P8, G2P4, G3P8, and G4P8 were underrepresented among Indian children (33%), whereas strains of P type 6 (G1P6, G2P6, G3P6, G4P6, and G9P6), which primarily infect asymptomatic newborns but are rare in children with diarrhea were common in India (43%). Of these, G9P6, a strain not previously reported to be found in children with diarrhea, was the most prevalent (22%). Eleven percent of the strains were nontypeable, and another 11% of the specimens had mixed infections. Using digoxigenin-labeled, genotype-specific hybridization probes, we confirmed all G9 strains and mixed infections tested and identified three nontypeable strains (one G9 and two P8). The epidemiological significance of G9 rotavirus strains, if confirmed in other settings, may have important implications for vaccine development.

Relative frequency of human rotavirus VP4 (P) genotypes recovered over a ten-year period from South African children with diarrhea

The relative frequency and distribution of the VP4 (P) genotypes of 227 human rotavirus field strains were investigated in South Africa. The stool samples were collected between 1984-1993 from infants and young children with diarrhea at Ga-Rankuwa Hospital, Pretoria, South Africa. The RNA was extracted from stools, heat denatured, and dot blotted onto nylon membranes. The blots were hybridized to PCR-generated, 32P radio-labelled VP4-specific probes (corresponding to the hyperdivergent region of the VP4 gene) of the following human rotavirus VP4 genotypes: P4, P6, P8, P9, P10, and P12. Of the 157 rotavirus strains typed by the probes, the P8 genotype was identified most frequently in 63.7% (n = 100) of the samples. The P4 and P6 genotypes were detected less frequently in 22.3% (n = 35) and 8.3% (n = 13) of the samples, respectively. Five cases of dual infection between P8 and P4 genotypes occurred, indicating the potential for reassortment between members of different rotavirus genogroups. The P9 genotype could not be confirmed in 3 cases (1.9%), while the P10 genotype was not observed at all, indicating the scarcity or absence of these VP4 genotypes in this region. Interestingly, we identified the newly-described P12 VP4 genotype in 6 cases (3.8%), suggesting a wide geographical distribution. Furthermore, several samples with sufficient RNA by gel electrophoresis remained untyped by the probes used in this study, and may represent putative "new" human VP4 genotype(s).

Heterogeneity of VP4 neutralization epitopes among serotype P1A human rotavirus strains

We have used serotype-specific VP4 and VP7 neutralizing monoclonal antibodies (Nt-MAbs), as well as subgroup (SG)-specific MAbs, to characterize by enzyme immunoassay rotavirus strains isolated from diarrheic infants in the city of Monterrey, Mexico, from July 1993 to March 1994. Of a total of 465 children studied, 140 were rotavirus positive, including 3 patients infected with non-group A rotaviruses. The SG and VP7 (G) serotype specificities could be determined for 118 (84%) of the 140 rotavirus-positive stool specimens; 4 rotavirus strains were serotype G1 and SGII; 1 strain was serotype G2 and SGI+II; 112 strains were serotype G3 and SGII; 1 strain was serotype G3 and SGI; and none of the strains was serotype G4. Fifty-eight specimens, representing the 13 different group A rotavirus electropherotypes detected, were chosen for VP4 (P) serotyping. Of these, 48 (83%) strains reacted with the P1A serotype-specific Nt-MAb 1A10. None of the strains reacted with the serotype P2-specific Nt-MAbs tested. Not all viruses that reacted with Nt-MAb 1A10 were recognized by Nt-MAbs 2A3 and 2G1, which also recognize P1A strains, indicating heterogeneity of neutralization epitopes among serotype P1A human rotaviruses. This heterogeneity could be relevant for the specificity of the VP4-mediated neutralizing antibody immune response and indicates the need for antigenic characterization, in addition to genomic typing, of the VP4 proteins of circulating human rotavirus field strains.

Distribution of both rotavirus VP4 genotypes and VP7 serotypes among hospitalized and nonhospitalized Israeli children

Human rotaviruses belonging to genotype P9, of probable feline origin, which included both G3 and G1 serotypes, were detected in 3.8% of children shedding rotaviruses who attended sick fund clinics throughout Israel. None were detected in children admitted to hospitals because of severe diarrhea. In contrast, the relative prevalences of genotypes P8 and P4 were similar between the two groups.

Survey of rotavirus G and P types associated with human gastroenteritis in São Paulo, Brazil, from 1986 to 1992

Rotavirus strains causing gastroenteritis in Brazilian children were characterized by PCR-based typing assays. In addition to strains bearing the major human G and P types, large numbers of strains bearing P3 (M37-like), P6 (HCR3-like), untypeable P and G types, and complex mixtures of P and G types not previously recognized were present in the community.

VP4 typing of bovine and porcine group A rotaviruses by PCR

A PCR typing assay was developed to identify rotavirus P types (VP4 specificity) of bovine NCDV, UK, and B223 strains and porcine OSU and Gottfried strains. Thirty-nine human and animal strains representing all known, and some undefined, rotavirus P types were used to develop and evaluate the specificity of the method. No cross-amplification was observed. The PCR results agreed with previous characterizations by monoclonal antibodies, sequence analysis, and hybridization assays, except for the Gottfried strain, which showed a P type distinct from the human asymptomatic strains. Analysis of a small number of field specimens suggested a high level of VP4 polymorphism among porcine strains. The assay should be of value in typing field isolates and tracing interspecies infections.