Identification and characterization of porcine Rotavirus A in Chilean swine population

Rotavirus A (RVA) is a common cause of diarrhea in newborn pigs, leading to significant economic losses. RVA is considered a major public health concern due to genetic evolution, high prevalence, and pathogenicity in humans and animals. The objective of this study was to identify and characterize RVA in swine farms in Chile. A total of 154 samples (86 oral fluids and 68 fecal samples) were collected, from 22 swine farms. 58 (38%) samples belonging to 14 farms were found positive for RVA by real-time RT-PCR. The samples with low Ct values (21) and the two isolates were selected for whole genome sequencing. Nearly complete genomes were assembled from both isolates and partial genomes were assembled from five clinical samples. BLAST analysis confirmed that these sequences are related to human and swine-origin RVA. The genomic constellation was G5/G3-P[7]-I5-R1-C1-M1-A8-N1-T1-E1-H1. Phylogenetic analysis showed that VP4, VP1, VP2, NSP2, NSP3, NSP4, and NSP5 sequences were grouped in monophyletic clusters, suggesting a single introduction. The phylogenies for VP7, VP6, VP3, and NSP1 indicated two different origins of the Chilean sequences. The phylogenetic trees showed that most of the Chilean RVA sequences are closely related to human and swine-origin RVA detected across the world. The results highlight the potential zoonotic nature of RVA circulating in Chilean swine farms. Therefore, it is important to continue RVA whole genome sequencing globally to fully understand its complex epidemiology and early detection and characterization of zoonotic strains.

The Epidemiological and clinical profiles of acute diarrhea due rotavirus in children aged 0-71 months hospitalized at Kalembe-lembe pediatric hospital in Kinshasa, Democratic Republic of Congo

This research is based on a retrospective analysis of medical records filed in the archives of the emergency departments of Kalembe-lembe Hospital in the provincial city of Kinshasa in the Democratic Republic of Congo. The study involved 324 records of patients aged 0-71 months admitted to the emergency departments and hospitalized for acute diarrhea from January 1 to December 31, 2015. The aim was to inventory the cases of rotavirus diarrhea and/or other germs (individually or in combination) to study their epidemiological and clinical aspects. Thus, the epidemiological and clinical parameters (age, sex, season, symptoms, frequency and physical aspects of stools, dehydration status and duration of hospitalization) of diarrheic children diagnosed as positive for rotavirus were compared with those infected with other germs (individually or in combination with rotavirus or other viruses). The search for the etiological agents of the diarrhea was performed in 56.48% of the cases. The results of this work allowed us to show: (i) a predominance of infections by viruses (69.94%) including rotavirus (48.08%), (ii) high rates of infections by etiological agents of diarrhea including rotavirus in children under 12 months, (iii) a high proportion of vomiting, (iii) a high proportion of vomiting, fever, physical asthenia and restlessness or frequent and liquid stools or moderate dehydration in children infected with rotavirus, (iv) specific clinical pictures according to the etiological agents of diarrhea or their combinations.

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

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

Impact assessment of the incorporation of the rotavirus vaccine in the province of San Luis - Argentina

Rotavirus (RV) is the main cause of acute gastroenteritis (AGE) in young children. The San Luis province of Argentina introduced RV vaccination in May 2013. We estimate vaccine impact (RVI) using real-world data. Data on all-cause AGE cases and AGE-related hospitalisations for San Luis and the adjacent Mendoza province (control group) were obtained and analysed by interrupted time-series methods. Regardless of the model used for counterfactual predictions, we estimated a reduction in the number of all-cause AGE cases of 20-25% and a reduction in AGE-related hospitalisations of 55-60%. The vaccine impact was similar for each age group considered (<1 year, <2 years and <5 years). RV vaccination was estimated to have reduced direct medical costs in the province by about 4.5 million pesos from May 2013 to December 2014. Similar to previous studies, we found a higher impact of RV vaccination in preventing severe all-cause AGE cases requiring hospitalisation than in preventing all-cases AGE cases presenting for medical care. An assessment of the economic value of RV vaccination could take other benefits into account in addition to the avoided medical costs and the costs of vaccination.

Tracking enteric viruses in green vegetables from central Argentina: potential association with viral contamination of irrigation waters

Consumption of green vegetable products is commonly viewed as a potential risk factor for infection with enteric viruses. The link between vegetable crops and fecally contaminated irrigation water establishes an environmental scenario that can result in a risk to human health. The aim of this work was to analyze the enteric viral quality in leafy green vegetables from Córdoba (Argentina) and its potential association with viral contamination of irrigation waters. During July-December 2012, vegetables were collected from peri-urban green farms (n = 19) and its corresponding urban river irrigation waters (n = 12). Also, urban sewage samples (n = 6) were collected to analyze the viral variants circulating in the community. Viruses were eluted and concentrated by polyethylene glycol precipitation and then were subject to Reverse Transcription Polymerase Chain Reaction to assess the genome presence of norovirus, rotavirus and human astrovirus. The concentrates were also inoculated in HEp-2 (Human Epidermoid carcinoma strain #2) cells to monitor the occurrence of infective enterovirus. The frequency of detection of the viral groups in sewage, irrigation water and crops was: norovirus 100%, 67% and 58%, rotavirus 100%, 75% and 5%, astrovirus 83%, 75% and 32% and infective enterovirus 50%, 33% and 79%, respectively. A similar profile in sewage, irrigation water and green vegetables was observed for norovirus genogroups (I and II) distribution as well as for rotavirus and astrovirus G-types. These results provide the first data for Argentina pointing out that green leafy vegetables are contaminated with a broad range of enteric viruses and that the irrigation water would be a source of contamination. The presence of viral genomes and infective particles in food that in general suffer minimal treatment before consumption underlines that green crops can act as potential sources of enteric virus transmission. Public intervention in the use of the river waters as irrigation source is needed.

Rotavirus Genotypes and Vaccine Effectiveness from a Sentinel, Hospital-Based, Surveillance Study for Three Consecutive Rotavirus Seasons in Lebanon

Introduction

Globally, rotavirus (RV) is the leading cause of gastroenteritis (GE) in children. Longitudinal data about changes in RV genotype distribution and vaccine effectiveness (VE) are scarce. This study was conducted in Lebanon over 3 consecutive RV seasons to estimate the rate of RVGE hospitalization, identify RV genotypes, determine the seasonal and geographical variations, and calculate RV VE.

Materials and Methods

This prospective, multicenter, hospital-based surveillance study was conducted between 2011 and 2013 and enrolled children (<5 years) admitted for GE. Socio-demographic and clinical data about the current episode of GE at admission were collected. Genotypes were determined from stool samples testing positive for RV by PCR.

Results

Of 1,414 cases included in the final analysis, 83% were <2 years old and 55.6% were boys. Median duration of hospitalization was 4 days and 91.6% of GE cases were severe (Vesikari score ≥11). PCR testing showed that 30.3% of subjects were RV-positive of which 62.1% had fever versus 71.1% of RV-negative subjects (P = 0.001). RV was predominantly detected in the cold season from November till March (69.9%). G and P genotype pairs for all RV-positive stool specimens showed a predominance of G1P[8] in 36% (n = 154) of specimens, G9P[8] in 26.4% (n = 113), and G2P[4] in 17.8% (n = 76). RV-negative subjects were more likely to be RV-vaccinated (21%) compared to the RV-positive subjects (11.3%) (P<0.001), with a vaccine breakthrough rate of 18.8%. The ratio of RV1-vaccinated for each RV5-vaccinated subject was 7.8 and VE against RV disease was 68.4% (95%CI, 49.6%-80.2%).

Conclusion

RV is a major cause of GE requiring hospitalization of children under 5 years of age in Lebanon. A few genotypes predominated over the three RV seasons studied. Mass RV vaccination will likely decrease the burden of hospitalization due to RV. VE is similar to what has been observed for other middle-income countries.

Rotavirus epidemiology and surveillance before vaccine introduction in Argentina, 2012-2014

Group A Rotavirus has been widely described as one of the most important infantile diarrheal pathogens worldwide. In Argentina, it is responsible for over 200,000 acute diarrhea cases and from 30 to 50 deaths annually in children under 5 years. The aim of this study is to analyze frequency, seasonality, age group distribution, and circulating genotypes based on data notified in the 2012-2014 period and in turn to assess the pre-vaccine scenario, considering that rotavirus vaccine was introduced in 2015. Data were taken from the Viral Diarrhea Notification module of the Argentine SNVS-SIVILA surveillance tool. Analyses of circulating genotypes were performed on rotavirus-positive stool specimens by conventional binary characterization of the outermost capsid genes. Overall data showed rotavirus detection in about 25% of samples tested, and higher rates in children under 2 years old were observed. Rotavirus positive cases were distributed according to a typical winter seasonal pattern. A heterogeneous regional pattern of prevalence was also observed, with higher rates detected in the North region. Genotype co-circulation and annual fluctuation were observed. In general, G1P[8], G2P[4], G3P[8], and G12P[8] were the most frequently detected genotypes. This study represents the last survey taken of a population considered to be naïve. J. Med. Virol. 89:423-428, 2017. © 2016 Wiley Periodicals, Inc.

Rotavirus seasonality in urban sewage from Argentina: effect of meteorological variables on the viral load and the genetic diversity

In Argentina, the rotavirus disease exhibits seasonal variations, being most prevalent in the fall and winter months. To deepen the understanding of rotavirus seasonality in our community, the influence of meteorological factors on the rotavirus load and the genetic diversity in urban raw sewage from Córdoba city, Argentina were evaluated. Wastewater samples were collected monthly during a three-year study period and viral particles were concentrated by polyethylene glycol precipitation. RT-nested PCR was applied for rotavirus detection, and VP7/VP4 characterization and real-time PCR for rotavirus quantification. Both molecular techniques showed relatively similar sensitivity rates and revealed rotavirus presence in urban wastewater in cold and warm seasons, indicating its circulation in the local community all year round. However, a slight trend for rotavirus circulation was noted by real-time PCR in the fall and winter seasons, showing a significantly higher peak of rotavirus concentration at mean temperatures lower than 18°C and also higher, although not statistically different during drier weather. VP7 and VP4 gene characterization showed that G1 and P[8] genotypes were dominant, and temporal variations in genotype distribution were not observed. Rotavirus spread is complex and our results point out that weather factors alone cannot explain the seasonal quantitative pattern of the rotavirus disease. Therefore, alternative transmission routes, changes in human behavior and susceptibility, and the stability and survivability of the virus might all together contribute to the seasonality of rotavirus. The results obtained here provide evidence regarding the dynamics of rotavirus circulation and maintenance in Argentina.

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).

Genetic diversity of G3 rotavirus strains circulating in Argentina during 1998-2012 assessed by full genome analyses

Seasonal shifts in the predominant strains and the periodic emergence of new strains are epidemiological features of human rotaviruses. After the sporadic detection in two samples in 1998, G3P[8] strains reemerged as the predominant rotavirus during 2008-2009 in Argentina. Notably, in 2011 6.3% (37/587) of samples presented the G3P[6] genotypes, which coincided with the recent detection of G3P[6] and G2P[6] strains in South America and Europe. Analyses of the 11 gene segments of four G3P[8] and two G3P[6] strains revealed that G3P[8] strains detected a decade apart (1998 and 2009) presented minor differences, while the G3P[6] strains presented a complete different genomic constellation albeit showing a similar VP7 gene. This study provides insights in the dynamics and evolution of one of the genotypes with the wider range of hosts and inter-species transmission potential.

Rotavirus Diarrhea among Children in Taiz, Yemen: Prevalence-Risk Factors and Detection of Genotypes

Diarrheal diseases are a great public health problem; they are among the most causes leading to morbidity and mortality of infants and children particularly in developing countries and even in developed countries. Rotavirus is the most common cause of severe gastroenteritis in infants and young children in both developed and developing countries. The purpose of this study was to determine the incidence rate of Rotavirus infection, its genotypes, and risk factors among children with diarrhea in Taiz, Yemen. 795 fecal samples were collected from children (less than 5 years old), suffering from diarrhea and attending the Yemeni-Swedish Hospital (YSH) in Taiz , Yemen, from November 2006 to February 2008. Rotavirus was detected by enzyme linkage immunosorbent assay (ELISA) on stool specimens of children. Genotypes of Rotavirus were characterized by reverse transcriptase-polymerase chain reaction (RT-PCR) and polyacrylamide gel electrophoresis (PAGE). The results showed that 358 (45.2%) were Rotavirus-positive and the most prevalent genotypes were G2P[4] (55%), followed by G1P[8] (15%). In addition, Rotavirus was found through the whole year; however, higher frequency during the summer season (53.4%) and lower frequency during the winter season (37.1%).

Complete genome analysis of a rare group A rotavirus, G11P[25], isolated from a child in Mumbai, India, reveals interspecies transmission and reassortment with human rotavirus strains

Hospital-based rotavirus surveillance was carried out in Mumbai during 2005-2009. An isolate (B08299) with a rare genotype combination (G11P[25]) was detected. The present study was undertaken to characterize the complete genome of the isolate. B08299 exhibited a G11-P[25]-I12-R1-C1-M1-A1-N1-T1-E1-H1 genotype constellation. Phylogenetic analysis of the 11 gene segments of B08299 revealed that the VP2 and NSP5 genes of B08299 had a human origin, while the VP6 gene represented an I12 genotype of obscure origin. The remaining six genes formed a lineage distinct from human and porcine rotaviruses within genotype 1. Analysis of the structural and non-structural genes suggested that B08299 has evolved by gene reassortment. Our findings provide further evidence that interspecies transmission is an important mechanism involved in the evolution and genetic diversity of human rotaviruses in nature.

Rotaviruses: is their surveillance needed?

Rotaviruses, a major cause of gastroenteritis in children worldwide accounts for around 0.5 million deaths annually. Owing to their segmented genome and frequently evolving capability, these display a wide variation in their genotypes. In addition to commonly circulating genotypes (G1, G2, G3, G4, G9, P[4] and P[8]), a number of infrequent genotypes are being continuously reported to infect humans. These viral strains exhibit variation from one geographical setting to another in their distribution. Though the introduction of vaccines (RotaTeq and Rotarix) proved to be very effective in declining rotavirus associated morbidity and mortality, the number of infections remained same. Unusual genotypes significantly contribute to the rotavirus associated diarrhoeal burden, may reduce the efficacy of the vaccines in use and hence vaccinated individuals may not be benefited. Vaccine introduction may bring about a notable impact on the distribution and prevalence of these viruses due to selection pressure. Moreover, there is a sudden emergence of G2 and G3 in Brazil and United States, respectively, during the years 2006-2008 post-vaccination introduction; G9 and G12 became predominant during the years 1986 through 1998 before the vaccine introduction and now are commonly prevalent strains; and disparity in the predominance of strains after introduction of vaccines and their natural fluctuations poses a vital question on the impact of vaccines on rotavirus strain circulation. This interplay between vaccines and rotavirus strains is yet to be explored, but it certainly enforces the need to continuously monitor these changes in strains prevalence in a particular region. Furthermore, these fluctuations should be considered while administration or development of a vaccine, if rotavirus associated mortality is ever to be controlled.

Whole genomic analysis of a porcine-like human G5P[6] rotavirus strain isolated from a child with diarrhoea and encephalopathy in Japan

An unusual rotavirus strain, Ryukyu-1120, with G5P[6] genotypes (RVA/Human-wt/JPN/Ryukyu-1120/2011/G5P[6]) was identified in a stool specimen from a hospitalized child aged 4 years who showed diarrhoea and encephalopathy. In this study, we sequenced and characterized the complete genome of strain Ryukyu-1120. On whole genomic analysis, this strain was found to have a unique genotype constellation: G5-P[6]-I5-R1-C1-M1-A8-N1-T1-E1-H1. The VP6 and NSP1 genotypes I5 and A8 are those commonly found in porcine strains. Furthermore, phylogenetic analysis indicated that each of the 11 genes of strain Ryukyu-1120 appeared to be of porcine origin. Thus, strain Ryukyu-1120 was found to have a porcine rotavirus genetic backbone and is likely to be of porcine origin. To our knowledge, this is the first report of whole-genome-based characterization of the emerging G5P[6] strains in Asian countries. Our observations will provide important insights into the origin of G5P[6] strains and the dynamic interactions between human and porcine rotavirus strains.

Global seasonality of rotavirus disease

BACKGROUND

A substantial number of surveillance studies have documented rotavirus prevalence among children admitted for dehydrating diarrhea. We sought to establish global seasonal patterns of rotavirus disease before the introduction of widespread vaccination.

METHODS

We reviewed studies of rotavirus detection in children with diarrhea published since 1995. We assessed potential relationships between seasonal prevalence and locality by plotting the average monthly proportion of diarrhea cases positive for rotavirus according to geography, country development and latitude. We used linear regression to identify variables that were potentially associated with the seasonal intensity of rotavirus.

RESULTS

Among a total of 99 studies representing all 6 geographic regions of the world, patterns of year-round disease were more evident in low- and low-middle income countries compared with upper-middle and high-income countries where disease was more likely to be seasonal. The level of country development was a stronger predictor of strength of seasonality (P = 0.001) than geographic location or climate. However, the observation of distinctly different seasonal patterns of rotavirus disease in some countries with similar geographic location, climate and level of development indicate that a single unifying explanation for variation in seasonality of rotavirus disease is unlikely.

CONCLUSION

While no unifying explanation emerged for varying rotavirus seasonality globally, the country income level was somewhat more predictive of the likelihood of having seasonal disease than other factors. Future evaluation of the effect of rotavirus vaccination on seasonal patterns of disease in different settings may help understand factors that drive the global seasonality of rotavirus disease.

Detection of rare reassortant G5P[6] rotavirus, Bulgaria

During the ongoing rotavirus strain surveillance program conducted in Bulgaria, an unusual human rotavirus A (RVA) strain, RVA/Human/BG/BG620/2008/G5P[6], was identified among 2200 genotyped Bulgarian RVAs. This strain showed the following genomic configuration: G5-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1. Phylogenetic analysis of the genes encoding the neutralization proteins and backbone genes identified a probable mixture of RVA genes of human and porcine origin. The VP1, VP6 and NSP2 genes were more closely related to typical human rotavirus strains. The remaining eight genes were either closely related to typical porcine and unusual human-porcine reassortant rotavirus strains or were equally distant from reference human and porcine strains. This study is the first to report an unusual rotavirus isolate with G5P[6] genotype in Europe which has most likely emerged from zoonotic transmission. The absence of porcine rotavirus sequence data from this area did not permit to assess if the suspected ancestral zoonotic porcine strain already had human rotavirus genes in its genome when transmitted from pig to human, or, the transmission was coupled or followed by gene reassortment event(s). Because our strain shared no neutralization antigens with rotavirus vaccines used for routine immunization in children, attention is needed to monitor if this G-P combination will be able to emerge in human populations. A better understanding of the ecology of rotavirus zoonoses requires simultaneous monitoring of rotavirus strains in humans and animals.

Prevalence and molecular genotyping of group a rotaviruses in Iranian children

Rotavirus is the leading cause of acute gastroenteritis in worldwide young children. Effective vaccines to prevent rotavirus infection are currently available, although their clinical use is still limited, and rotavirus still causes many episodes of infantile gastroenteritis, mainly during the winter season. The aim of this study was to evaluate the prevalence of rotavirus infection in children aged <5-years-old who were hospitalised for gastroenteritis. One hundred and sixty-three stool samples from hospitalised children (<5-years-old) complicated with severe diarrhoea, in two hospitals in Jahrom City, Iran were collected from 2009 to 2010. Antigenic prevalence of rotavirus group A was distinguished by enzyme immunoassay. The antigen of group A rotavirus was diagnosed by EIA in 75 of 163 collected samples. The genotype of EIA-positive samples was determined by nested RT-PCR. The frequency of rotavirus genotypes G1, G2, G3, G4 and G9 was 17.33, 13.34, 2.67, 30.66 and 2.67 %, respectively. Also, the frequency of mixed and non-typable genotypes was detected in 2.67 and 30.66 %, respectively. G1/G8 mixed infection was the first of these rotavirus genotypes to be reported in Iran. Detection of high prevalence of group A rotavirus infection in hospitalised children with diarrhoea, and determination of circulating rotavirus genotypes in this region of Iran, provide useful data for formulating effective vaccines; especially for infants less than 5-years-old.

Genetic diversity of group A rotaviruses associated with repeated outbreaks of diarrhea in a farrow-to-finish farm: identification of a porcine rotavirus strain bearing a novel VP7 genotype, G26

Group A rotaviruses (GARs) are one of the most common causes of diarrhea in suckling pigs. Although a number of G and P genotypes have been identified in porcine GARs, few attempts have been made to study the molecular epidemiology of these viruses associated with diarrhea outbreaks within a farm over an extended period of time. Here, we investigated the molecular characteristics of GARs that caused four outbreaks of diarrhea among suckling pigs in a farrow-to-finish farm over the course of a year. G and P genotyping of GARs detected at each outbreak demonstrated genetic diversity in this farm as follows: G9P[23] was detected at the first outbreak, G9P[13]/[22] and G9P[23] at the second, G3P[7] at the third, and G9P[23], G5P[13]/[22], and P[7] combined with an untypeable G genotype at the fourth. Sequence analysis of the detected GARs revealed that such genetic diversity could have resulted not only from the introduction of new GAR strains, but also from gene reassortment between GAR strains within the farm. Further, the GAR strain carrying the untypeable G genotype was shown to be a novel porcine GAR bearing a new G26 genotype, as confirmed by the Rotavirus Classification Working Group.

VP7 Gene of human rotavirus A genotype G5: Phylogenetic analysis reveals the existence of three different lineages worldwide

Group A rotavirus (RV-A) genotype G5, which is common in pigs, was also detected in children with severe diarrhea in Brazil, Argentina, Paraguay, Cameroon, China, Thailand, and Vietnam. To evaluate the evolutionary relationship among RV-A G5 strains, the VP7 and VP4 genes of 28 Brazilian RV-A G5 human strains, sampled between 1986 and 2005, were sequenced and compared with other RV-A G5 strains currently circulating worldwide in animals and humans. The phylogenetic analysis of RV-A G5 VP7 gene strains demonstrates the existence of three main lineages: (a) Lineage I: Brazilian strains grouped with three porcine strains from Thailand; (b) Lineage II: porcine, bovine, and equine strains from different regions; (c) Lineage III: human strains isolated in Asia and Africa, and two porcine strains from Argentina. The VP8* (*non-typable) subunit of VP4 gene sequencing showed that all P[8] strains fell into three major genetic lineages: P[8]-1; P[8]-2; and P[8]-3. These results showed that the RV-A G5 strains circulating in humans are the result of two independent zoonotic transmission events, most likely from pigs.

Burden and typing of rotavirus group A in Latin America and the Caribbean: systematic review and meta-analysis

The efficacy of licensed rotavirus vaccines has only been shown against certain rotavirus group A (RV-A) types. It is critical to understand the burden of rotavirus gastroenteritis (RVGE) and its prevalent types to assess the potential impact of these vaccines in Latin America and the Caribbean (LA&C). We performed a systematic review and meta-analyses of all the available evidence reported from 1990 to 2009 on the burden of rotavirus disease and strains circulating in LA&C. Eligible studies--185 country-level reports, 174 951 faecal samples--were selected from MEDLINE, Cochrane Library, EMBASE, LILACS, regional Ministries of Health, PAHO, regional proceedings, doctoral theses, reference lists of included studies and consulting experts. Arc-sine transformations and DerSimonian-Laird random-effects model were used for meta-analyses. The proportion of gastroenteritis cases due to rotavirus was 24.3% (95%CI 22.3-26.4) and the incidence of RVGE was 170 per 1000 children-years (95%CI 130-210). We estimated a global annual mortality for 22 countries of 88.2 (95%CI 79.3-97.1) deaths per 100 000 under 5 years (47 000 deaths).The most common G type detected was G1 (34.2%), followed by G9 (14.6%), and G2 (14.4%). The most common P types detected were P[8] (56.2%), P[4] (22.1%) and P[1] 5.4%, and the most prevalent P-G type associations were P[8]G1 17.9%, P[4]G2 9.1% and P[8]G9 8.8%. In the last 10 years, G9 circulation increased remarkably and G5 almost disappeared. More recently, G12 appeared and P[4]G2 re-emerged. To our knowledge, this is the first meta-analysis of rotavirus infection and burden of disease in LA&C.

Water quality issues and infant diarrhoea in a South American province

In the province of Salta, in the Northwest region of Argentina, almost two-thirds of the population live in absolute poverty, and diseases associated with poverty are rampant. Almost 12% of the total population of the province are children below 5 years of age; almost half of these infants are living in situations where the basic necessities are not available. Primitive sanitary conditions, including widespread contamination of available water supplies with pathogens, contribute to a major public health problem. Infant mortality was 17% higher for Salta than for Argentina as a whole in 2001. A major cause of death for these children is infectious disease, especially respiratory and intestinal diseases. In Salta, more than half of the total population of infants is affected by diarrhoea annually. The infectious pathogens are diverse: bacteria (predominantly in spring and summer), viruses (especially in the winter) and parasites (endemic in some situations). This paper evaluates current methods used to test for the presence of pathogens in drinking water; discusses why these methods are less than adequate; documents an episode of contamination in a local water supply source; and suggests appropriate methods that can be used to better address this major public health issue effectively.

Predominance of rotavirus G2P[4] and emergence of G12P[9] strains in Asunción, Paraguay, 2006-2007

Rotavirus is the most common cause of severe diarrhea in children worldwide. Monitoring the diversity of rotavirus strains is of great importance for current and future vaccination programs. To determine the diversity of rotavirus circulating in Asuncion, Paraguay, between 2006 and 2007, we carried out a molecular characterization of rotaviruses detected in children <5 years old and adults (>18 years old). We found that the most common circulating strain was G2P[4] (69/143), followed by G9P[8] (37/143). The temporal distribution of strains showed that, in children, G2P[4] was predominant in 2006, and that G2P[4] and G9P[8] were co-predominant in 2007, whereas in adults, G2P[4] was predominant in both years. Additionally, one G9P[6] and three G12P[9] strains were found in adult samples, making this the first report of these strains circulating in Paraguay. Sequence analysis of the G12P[9] strains suggests across-border migration of this strain within the southern cone of America.

Rotavirus G5P[6] in child with diarrhea, Vietnam

We detected rotavirus G5P[6] with a long RNA pattern in a Vietnamese child with diarrhea. Viral outer capsid protein VP7 and VP4 genes suggest that it likely originated from porcine rotavirus either by genetic reassortment or as whole virions. To our knowledge, this is the first report of human rotavirus G5 in Asia.

Diversity of group A rotavirus strains circulating in Paraguay from 2002 to 2005: Detection of an atypical G1 in South America

BACKGROUND

Group A rotaviruses are the main cause of severe gastroenteritis in children worldwide.

OBJECTIVES

To survey human rotavirus strains circulating in Paraguay.

STUDY DESIGN

One hundred ninety-six rotavirus-positive fecal samples collected from children up to 5 years old, from 2002 to 2005, were characterized.

RESULTS

The most common G genotype detected was G9 (36.2%), followed by G1 (34.2%), G2 (11.7%) and G4 (8.7%). Changes in the G genotype frequency were observed from year to year. The G4 genotype was predominant in 2002; G1 in 2003; and G9 from 2004 to 2005. Sequence and phylogenetic analysis of the VP7 gene from Paraguayan G1 strains suggested that the high frequency of G1 in 2003 could be due to the introduction of an atypical sub-lineage. In addition, there were amino acid changes in the variable/antigenic regions of the VP7 gene from G4 and G9 strains detected in different years.

CONCLUSIONS

This study further indicates that antigenic pressure can drive the evolution of rotaviruses, and also suggests that a vaccine that protects against the most prevalent strains and its variants, will be necessary to elicit a protective immune response against the range of rotavirus types currently circulating in Paraguay.

Detection of human rotavirus G9P[8] strains circulating in Argentina: phylogenetic analysis of VP7 and NSP4 genes

During the surveillance of rotavirus strains that were circulating in Argentinean children from 2000 to 2004, seven rotaviruses were detected bearing the genotype combination G9P[8]. The molecular characterization of the VP7 and NSP4 genes and the RNA migration patterns support the hypothesis that rotaviruses G9 could have been reintroduced into Argentina as a novel G9P[8] strain, rather than represent VP7 gene reassortants from G9P[6] strains that had been circulating previously in this country.

Molecular characterization of calicivirus strains detected in outbreaks of gastroenteritis in Argentina

Eight outbreaks of acute gastroenteritis occurred in Argentina in 2004 were tested for the presence of Calicivirus, Rotavirus and Astrovirus as possible causative agents. Caliciviruses were found in 39 out of the 100 tested samples, followed by six Astrovirus-positive samples and two Rotavirus-positive samples. Thirty-seven out of the 39 Calicivirus-positive samples were typed as Norovirus while the remaining two were typed as Sapovirus. Sequence and phylogenetic analyses of 13 Norovirus-positive samples revealed the presence of strains from the genogroups GI, GII, and GIV. Six Norovirus strains were grouped with the GIV-1 strains, three with the GIIb strains, two with the Farmington Hill-cluster (GII-4) strains, and the remaining two with the GI strains. To our knowledge, this study constitutes the first report of molecular epidemiology of human Caliciviruses associated to gastroenteritis outbreaks in Argentina and the circulation of GIIb and GIV-1 strains in South-America.

Disease burden and related medical costs of rotavirus infections in Taiwan

Background

The disease burden and associated medical costs of rotavirus infections in inpatient and outpatient sectors in Taiwan were examined in anticipation of the availability of new rotavirus vaccines.

Methods

The yearly national case number and medical costs for all for inpatients and outpatients with acute gastroenteritis (AGE) were extracted from the Bureau of National Health Insurance database in Taiwan according to ICD-9-CM codes. A retrospective study was also performed using records of children with AGE seen at three hospitals in Taiwan in 2001 to identify laboratory confirmed rotavirus infection cases. The annual incidence and related medical costs of AGE due to rotavirus infection were then estimated.

Results

Children <5 years old comprised 83.6% of inpatient and 62.0% of outpatient pediatric AGE cases in Taiwan in 2001. Rotavirus was the most common agent detected among AGE patients in this age group in the three hospitals, and was detected in 32.9% (221/672) of inpatient and 24% (23/96) of outpatient stool specimens tested for microbial etiologies. An estimated 277,400 to 624,892 cases of rotavirus infections sought medical care in Taiwan in 2001, equaling one in 2 to 5 children <5 years old required medical care due to rotavirus infection. The incidence of hospitalization due to rotavirus infections was 1,528–1,997/100,000 for children <5 years old. The total associated medical costs due to rotavirus infection were estimated at US $10–16 millions in Taiwan in 2001. Although the per-capita medical cost of rotavirus infection was lower in Taiwan than in the United States or Hong Kong, the personal economic burden was similar among the three places when normalized for gross national incomes per capita.

Conclusion

Infections caused by rotavirus constitute an important human and economic burden among young children in Taiwan. A safe and effective vaccine is urgently needed.

Molecular epidemiology of group A rotavirus diarrhea among children in Buenos Aires, Argentina, from 1999 to 2003 and emergence of the infrequent genotype G12

To examine the epidemiology of rotaviruses in Buenos Aires, Argentina, we screened 1,212 stool samples from children with diarrhea in the southern district of Buenos Aires from 1999 to 2003. We identified 187 samples (15.4%) that were positive for group A rotavirus by use of antigen enzyme-linked immunosorbent assay. Among these specimens, 112 were available for typing: 93 (83.0%) were single-type infections, 9 (8.0%) were mixed-type infections with more than one G or P type, and 10 (8.9%) were G and/or P nontypeable. In contrast to the findings in our last study, from 1996 to 1998, genotype P[4], G2 strains were almost completely absent and P[8], G1 and P[8], G4 strains were dominant, representing more than 80% of the G and P types found. Genotypes G2 and G9 were detected in few samples, and type G3 was completely absent. We identified several uncommon genotype G12 strains, representing the first detections outside of Asia and the United States, by sequencing. Using a genotype G12-specific reverse transcription-PCR, we identified eight (6.7%) positive samples for the 1999 to 2003 period. The high degree of sequence identity between recent G12 isolates from Argentina, the United States, and Asian countries suggests a relatively recent introduction(s) of these strains into humans from a common progenitor. The Argentinean G12 strains belonged to genotype P[9], similar to most of the recently described Asian G12 strains. The finding of G12 strains in several other regions of the world raises the possibility that G12 may be emerging globally and suggests that surveillance for this strain should be conducted routinely.

Etiology and epidemiology of diarrhea in children in Hanoi, Vietnam

OBJECTIVES

This paper provides a preliminary picture of diarrhea with regards to etiology, clinical symptoms, and some related epidemiologic factors in children less than five years of age living in Hanoi, Vietnam.

METHODS

The study population included 587 children with diarrhea and 249 age-matched healthy controls. The identification of pathogens was carried out by the conventional methods in combination with ELISA, immunoseparation, and PCR. The antibiotic susceptibility was determined by MIC following the NCCLS recommendations.

RESULTS

Of those with diarrhea, 40.9% were less than one year old and 71.0% were less than two years old. A potential pathogen was identified in 67.3% of children with diarrhea. They were group A rotavirus, diarrheagenic Escherichia coli, Shigella spp, and enterotoxigenic Bacteroides fragilis, with prevalences of 46.7%, 22.5%, 4.7%, and 7.3%, respectively. No Salmonella spp or Vibrio cholerae were isolated. Rotavirus and diarrheagenic E. coli were predominant in children less than two years of age, while Shigella spp, and enterotoxigenic B. fragilis were mostly seen in the older children. Diarrheagenic E. coli and Shigella spp showed high prevalence of resistance to ampicillin, chloramphenicol, and to trimethoprim/sulfamethoxazole. Children attending the hospitals had fever (43.6%), vomiting (53.8%), and dehydration (82.6%). Watery stool was predominant with a prevalence of 66.4%, followed by mucous stool (21.0%). The mean episodes of stools per day was seven, ranging from two to 23 episodes. Before attending hospitals, 162/587 (27.6%) children had been given antibiotics. Overall, more children got diarrhea in (i) poor families; (ii) families where piped water and a latrine were lacking; (iii) families where mothers washed their hands less often before feeding the children; (iv) families where mothers had a low level of education; (v) families where information on health and sanitation less often reached their households.

CONCLUSIONS

Group A rotavirus, diarrheagenic Escherichia coli, Shigella spp, and enterotoxigenic Bacteroides fragilis play an important role in causing diarrhea in children in Hanoi, Vietnam. Epidemiological factors such as lack of fresh water supply, unhygienic septic tank, low family income, lack of health information, and low educational level of parents could contribute to the morbidity of diarrhea in children.

Full genomic analysis of human rotavirus strain B4106 and lapine rotavirus strain 30/96 provides evidence for interspecies transmission

The Belgian rotavirus strain B4106, isolated from a child with gastroenteritis, was previously found to have VP7 (G3), VP4 (P[14]), and NSP4 (A genotype) genes closely related to those of lapine rotaviruses, suggesting a possible lapine origin or natural reassortment of strain B4106. To investigate the origin of this unusual strain, the gene sequences encoding VP1, VP2, VP3, VP6, NSP1, NSP2, NSP3, and NSP5/6 were also determined. To allow comparison to a lapine strain, the 11 double-stranded RNA segments of a European G3P[14] rabbit rotavirus strain 30/96 were also determined. The complete genome similarity between strains B4106 and 30/96 was 93.4% at the nucleotide level and 96.9% at the amino acid level. All 11 genome segments of strain B4106 were closely related to those of lapine rotaviruses and clustered with the lapine strains in phylogenetic analyses. In addition, sequence analyses of the NSP5 gene of strain B4106 revealed that the altered electrophoretic mobility of NSP5, resulting in a super-short pattern, was due to a gene rearrangement (head-to-tail partial duplication, combined with two short insertions and a deletion). Altogether, these findings confirm that a rotavirus strain with an entirely lapine genome complement was able to infect and cause severe disease in a human child.

Rotavirus and severe childhood diarrhea

Studies published between 1986 and 1999 indicated that rotavirus causes ≈22% (range 17%–28%) of childhood diarrhea hospitalizations. From 2000 to 2004, this proportion increased to 39% (range 29%–45%). Application of this proportion to the recent World Health Organization estimates of diarrhea-related childhood deaths gave an estimated 611,000 (range 454,000–705,000) rotavirus-related deaths.

Rotavirus types in Europe and their significance for vaccination

The degree of diversity of cocirculating human rotavirus wild-type strains is high. This article reviews the occurrence and frequency of rotavirus types in European children younger than 5 years of age during the past 10-15 years. To enable greater understanding of the overall epidemiologic situation, rotavirus types found in animals in Europe are described. In addition, rotavirus types occurring in children outside Europe are considered. Taken together, these data provide an essential background to the development of rotavirus vaccines. The different concepts of immunization with the 2 main rotavirus candidate vaccines are briefly discussed, and their potential impact on the epidemiology of cocirculating rotavirus wild-type viruses is considered. A case is made for comprehensive surveillance of cocirculating human rotavirus types in Europe after the implementation of rotavirus vaccination.

Detection of group a human rotavirus G9 genotype circulating in Córdoba, Argentina, as early as 1980

The incidence of human rotavirus G types was determined over a 25-year period (1979-2003) by using reverse transcription-PCR (RT-PCR) to examine 519 stool specimens found to be positive for rotavirus by enzyme linked immunosorbent assay (ELISA) or polyacrylamide gel electrophoresis (PAGE). These stool samples were obtained from children under 3 years old who had been treated for acute diarrhea at public hospitals in Córdoba, Argentina. The present study describes the continued circulation of the common human G types G1 (53.8%), G2 (10.2%), G3 (4.4%), and G4 (27%), and also the detection of the unusual types G8 (0.5%) and G9 (4.2%). Genotype G9 was detected during the 1980-1988 and 1997-2003 periods at relatively low rates. Rotavirus G types distribution was independent of age (1-18 months), gender or out-patient or in-patient status. Unexpectedly, 44.6% of mixed infections were detected, involving common and unusual genotypes. Overall, 95.4% of the typed strains belonged to the most prevalent human serotypes (G1-G4) but the detection of G9 infection throughout this study period highlights the importance of this serotype as a human pathogen.

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.

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).

Diarrhea caused by rotavirus in children less than 5 years of age in Hanoi, Vietnam

Group A rotaviruses are the major cause of diarrhea in young children worldwide. From March 2001 to April 2002, 836 children less than 5 years of age were investigated in Hanoi, Vietnam. This included 587 children with diarrhea and 249 age-matched controls. Group A rotavirus was identified in 46.7% of the children with diarrhea and 3.6% of the controls, which was a significant difference. Within the diarrhea group, the highest prevalence was seen in children from 13 to 24 months of age, and the prevalence was higher in males than in females. The symptoms of acute diarrhea caused by rotavirus were watery diarrhea, vomiting, fever, and dehydration. A higher prevalence of rotavirus detection was obtained for children who had all of these symptoms, followed by those who had diarrhea with vomiting-dehydration, fever-dehydration, and dehydration. The high rates occurred from September to December, although the infection was encountered all year round. In 58 patients (21.2% of the rotavirus-infected children), rotavirus infection was detected in association with either diarrheagenic Escherichia coli or Shigella spp. The most frequent combinations were rotavirus-enteroaggregative E. coli and rotavirus-enteropathogenic E. coli. At least one enteropathogen was identified from about 64% percent of the samples. The bacterial infection may not have given rise to clinical symptoms of such severity. The present study demonstrates the burden of rotavirus diarrhea in Hanoi, Vietnam. Continuous surveillance of diarrhea caused by rotavirus in young children would play an important role in diagnosis, treatment, and prophylaxis in order to improve the health of children in Vietnam.

Rotavirus surveillance in the city of Rio de Janeiro-Brazil during 2000-2004: Detection of unusual strains with G8P[4] or G10P[9] specificities

Rotavirus diarrhea is a potentially life-threatening disease that affects millions of children annually around the world. Because protection against rotavirus disease is thought to be type specific, continuous rotavirus surveillance before and after implementation of a vaccine is still of essential importance. Rotavirus surveillance has been conducted in the city of Rio de Janeiro, Brazil since 1982. In the present study, we report rotavirus surveillance data in Rio de Janeiro city from 2000 to 2004. One hundred twenty nine of 1,568 (8.2%) stool samples, collected from children with acute diarrhea between January 2000 and July 2004 were rotavirus-positive. One hundred twenty eight of the 129 (99.2%) rotavirus-positive samples were genotyped for G and/or P specificity. G1 was the predominant strain (49.6%, 64/129) followed by G9 (30.2%, 39/129), and G4 (17.8%, 23/129); G2 and G3 viruses were not detected. One sample (0.8%) was non-typeable. P genotypes were determined for 124 of the 129 (96%) samples, and P[8] was the predominant genotype (90.6%, 117/129). Genotypes P[4] and P[9] were detected in two (1.6%) samples each; one (0.8%) sample presented P[6] genotype; and five (3.8%) samples were non-typeable. Two samples (1.6%) presented mixed P genotypes (P[6] + P[8]). Two unusual strains were isolated: a G8P[4] strain isolated from a non-hospitalized child with diarrhea and a G10P[9] strain isolated from a hospitalized child with diarrhea.

Molecular characterization and genetic variation of theVP7 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.

Rotavirus strain surveillance in Latin America: a review of the last nine years

BACKGROUND

Latin America will likely be the first area in the developing world where rotavirus vaccine will be introduced into the routine childhood immunization schedule. In anticipation of that goal, we reviewed the distribution of group A rotavirus genotypes in Latin America to understand the diversity of strains to be targeted by vaccines and to identify novel strains that may pose challenges for vaccines.

METHODS

We reviewed studies characterizing rotavirus strains in Latin America (published in English since 1995) that used molecular methods to type genes encoding the G and P outer capsid proteins, VP7 and VP4, and that reported data on >50 specimens.

RESULTS

Fifteen studies from 5 countries met our criteria. In total, 1989 samples were characterized; 12% (233) were mixed rotavirus infections with more than 1 strain, and 20% (402) were not fully typable. Of the remaining 1354 samples that were fully typed, 83% represented the 4 common strains: P[8],G1 (40%); P[4],G2 (30%); P[8],G3 (6%); P[8],G4 (7%). The unusual strains provide interesting insights into virus evolution: some strains (G5) were regionally common; the emerging G9 strains were widely distributed; many animal-human reassortants were present; and some common serotypes (G3 and G4) were of animal origin. Also an unusual G12 serotype was recently detected in Argentina.

CONCLUSIONS

The common rotavirus serotypes should remain the prime targets for vaccine development. However, the changing profile of rare strains, animal-human reassortants and nontypable strains suggest that rotavirus is constantly evolving. Laboratory surveillance is needed to monitor rotavirus strains now in circulation and to detect those that might escape the immunity induced by vaccines or represent vaccine strains entering the environment.

Evidence of rotavirus intragenic recombination between two sublineages of the same genotype

Rotavirus G4 prevalence increased during the past decade, with one of the highest prevalences reported during rotavirus surveillance in Argentina. Intragenotype diversity analysis has led to its subdivision into lineages (I and II) and sublineages (Ia-Id). On analysis of Argentine and G4 VP7 sequences from other locations, one Argentine strain (ArgRes1723) appeared to be an intermediate between G4 sublineages Ib and Ic. Similarity and bootscanning analyses and Sawyer's test were carried out to demonstrate the recombinant nature of this strain. It was concluded that intragenic recombination occurred between sequences of sublineages Ib and Ic, with a crossover point between nucleotide positions 336 and 387. This study constitutes the first report of a mechanism of evolution in rotaviruses that is currently considered unusual - a recombination event between two strains of the same rotavirus genotype. These results will help increase current knowledge about rotavirus evolution and divergence, improving our understanding of the adaptation mechanisms used by these viruses.

Detection of an unusual human rotavirus strain with G5P[8] specificity in a Cameroonian child with diarrhea

Rotavirus strains detected as part of ongoing strain surveillance in Cameroon, and whose first-round reverse transcription-PCR product could not be genotyped by using conventional genotyping primers, were subjected to sequence analysis for strain characterization. We detected for the first time in Africa a human rotavirus with G5 specificity. The Cameroonian G5 strain had a short electrophoretic pattern and was of VP6 subgroup I specificity and a VP4 P[8] type. The VP7 gene shared a higher nucleic acid and amino acid homology with the porcine G5 strain CC117 (90 and 96%, respectively) than with human G5 strain IAL-28 (86 and 92%, respectively). Phylogenetic analysis showed Cameroonian strain MRC3105 clustered together in the same lineage as two other reported porcine G5 strains. The Cameroonian G5 strain, the first to be reported in humans outside of Latin America, may be a natural reassortant between animal and human rotavirus strains.

Group A rotavirus in sewage samples from Barcelona and Cairo: emergence of unusual genotypes

The presence of rotavirus strains in sewage samples from Cairo, Egypt (November 1998 to October 1999), and Barcelona, Spain (November 1998 to December 2002), was investigated by using a generic molecular detection method based on amplification of a VP6 gene fragment. Overall, 85.7 and 66.9% of the sewage samples from Cairo and Barcelona, respectively, were positive. Positive samples were characterized further, and VP7 and VP4 genotypes were determined. Although 30% of the positive samples from Cairo were G untypeable, the distribution of G types in the positive samples was 69.6% G1, 13% G3, 8.7% G4, and 8.7% G9. The percentage of untypeable samples was much higher for the Barcelona samples (56.5%), and the distribution in the positive samples was 56.4% G1, 31.5% G3, 6% G9, 4% G2, and 2% G5. When the P types were examined, 26.7% of the positive samples from Cairo were untypeable, and the distribution of types in the positive samples was 53.3% P[8], 30% P[6], and 16.6% P[4]. In Barcelona, 27.2% of the samples were P untypeable, and the frequencies of the types detected were 49.7% P[8], 37.2% P[4], 8.8% P[6], and 4.2% P[9]. The distribution for strains from Cairo was 38.5% P[8]G1, 27% P[6]G1, 11.5% P[4]G1, 11.5% P[8]G3, 7.7% P[6]G4, and 3.8% P[8]G9. Strikingly, equivalent frequencies of common and uncommon strains were observed for Barcelona samples, and the distribution was 38.8% P[8]G1, 30.6% P[4]G1, 11.6% P[8]G3, 6.6% P[4]G3, 5.8% P[6]G1, 1.6% P[6]G3, 1.6% P[9]G1, 0.8% P[4]G2, 0.8% P[6]G9, 0.8% P[8]G9, and 0.8% P[8]G5. Additionally, two P[-]G5 strains were isolated in Barcelona, and the porcine or human origin of these strains was unclear. Rotavirus variability exhibited not only a geographic pattern but also a temporal pattern.