Without a virus culture system, genetic analysis becomes the principal method to classify norovirus (NoV) strains. Currently, classification of NoV strains beneath the species level has been based on ...sequences from different regions of the viral genome. As a result, the phylogenetic insights of some virus were not appropriately interpreted, and no consensus has been reached to establish a uniform classification scheme. To provide a consistent and reliable scientific basis for classifying NoVs, we analyzed the amino acid sequences for the major capsid protein of 164 NoV strains by first using an alignment based on the predicted 3D structures. A Bayesian tree was generated, and the maximum likelihood pairwise distances of the aligned sequences were used to evaluate the results from the uncorrected pairwise distance method. Analyses of the pairwise distances demonstrated three clearly resolved peaks, suggesting that NoV strains beneath the species level can be classified at three levels: strain (S), cluster (C), and genogroup (G). The uncorrected pairwise distance ranges for S, C, and G were 0–14.1%, 14.3–43.8%, and 44.9–61.4%, respectively. A scheme with 29 genetic clusters 8 in genogroup 1 (G1), 17 in G2, 2 in G3, and 1 each in G4 and G5 was defined on the basis of the tree topology with the standards provided and was supported by the distance analysis. Of these, five clusters in G2 and one in G1 are newly described. This analysis can serve as the basis for a standardized nomenclature to genetically describe NoV strains.
Rotavirus and severe childhood diarrhea Parashar, Umesh D; Gibson, Christopher J; Bresee, Joseph S ...
Emerging infectious diseases,
02/2006, Letnik:
12, Številka:
2
Journal Article
Recenzirano
Odprti dostop
Studies published between 1986 and 1999 indicated that rotavirus causes approximately 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.
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 P2A6) 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.
“Norwalk-like viruses” (NLVs) are the most common cause of outbreaks of nonbacterial gastroenteritis. During molecular surveillance of NLV strains from 152 outbreaks of gastroenteritis that occurred ...in the US between August 1993 and July 1997, we identified an NLV strain that predominated during the 1995–1996 season. The “95/96-US” strain caused 60 outbreaks in geographically distant locations within the US and was identified, by sequence comparisons, in an additional 7 countries on 5 continents during the same period. This is the first demonstration linking a single NLV strain globally and suggests that the circulation of these strains might involve patterns of transmission not previously considered. The diagnostic techniques are now available to establish a global network for surveillance of NLV strains that would highlight the importance of NLVs worldwide and allow molecular identification of common strains having a global distribution so as to consider interventions for their control.
The prospect that rotavirus diarrhea in children may soon be prevented by vaccines has placed a new priority on understanding the diversity of rotavirus strains and the mechanism by which these ...strains evolve over time. We have characterized a total of 465 rotavirus strains collected in North India from 2000 to 2007 for G and P types by reverse transcription-PCR and sequencing. The novel G12 rotavirus strains recently detected in other countries were first detected in India in 2001 and have emerged as the predominant strains in Delhi, India, during 2005 to 2007. While the VP7 sequence was highly homologous among G12 strains isolated in Delhi, suggesting recent emergence from a common ancestor, the strains had a diverse constellation of other gene segments, demonstrating substantial reassortment. For the entire period, the common rotavirus G types G1 (26%), G2 (25%), and G9 (14%) comprised 65% of the strains, and common P types, P4 (19%), P6 (22%), and P8 (35%), comprised 76% of the total P types. Of note, we detected a high percentage of unusual (17%) strains and fecal specimens with mixed (12% G and 15% P) rotavirus infections having a variety of genomic constellations. For the first time, we identified two novel rotavirus strains with unusual G/P combinations, G2P11 and G3P11, in patients with diarrhea. The study highlights the great diversity among rotaviruses isolated from Indian children, the opportunity for genetic reassortment between strains, and the emergence of a novel G12 strain in our country. Due to the demonstrated effect of antigenic diversity on rotavirus vaccines, it will be important to continue careful monitoring of these strains as rotavirus vaccine programs are implemented in India.
To estimate the global illness and deaths caused by rotavirus disease, we reviewed studies published from 1986 to 2000 on deaths caused by diarrhea and on rotavirus infections in children. We ...assessed rotavirus-associated illness in three clinical settings (mild cases requiring home care alone, moderate cases requiring a clinic visit, and severe cases requiring hospitalization) and death rates in countries in different World Bank income groups. Each year, rotavirus causes approximately 111 million episodes of gastroenteritis requiring only home care, 25 million clinic visits, 2 million hospitalizations, and 352,000-592,000 deaths (median, 440,000 deaths) in children <5 years of age. By age 5, nearly every child will have an episode of rotavirus gastroenteritis, 1 in 5 will visit a clinic, 1 in 65 will be hospitalized, and approximately 1 in 293 will die. Children in the poorest countries account for 82% of rotavirus deaths. The tremendous incidence of rotavirus disease underscores the urgent need for interventions, such as vaccines, particularly to prevent childhood deaths in developing nations.
An innovative strategy to reduce dengue transmission uses the bacterium Wolbachia. We analysed the effects of Wolbachia on dengue transmission dynamics in the presence of two serotypes of dengue ...using a mathematical model, allowing for differences in the epidemiological characteristics of the serotypes. We found that Wolbachia has a greater effect on secondary infections than on primary infections across a range of epidemiological characteristics. If one serotype is more transmissible than the other, it will dominate primary infections and Wolbachia will be less effective at reducing secondary infections of either serotype. Differences in the antibody-dependent enhancement of the two serotypes have considerably less effect on the benefits of Wolbachia than differences in transmission probability. Even if the antibody-dependent enhancement rate is high, Wolbachia is still effective in reducing dengue. Our findings suggest that Wolbachia will be effective in the presence of more than one serotype of dengue; however, a better understanding of serotype-specific differences in transmission probability may be needed to optimize delivery of a Wolbachia intervention.
Between July 2000 and June 2004, fecal specimens from 270 outbreaks of acute gastroenteritis were sent to the Centers for Disease Control and Prevention by local or state health departments for ...calicivirus testing. Of the 226 outbreaks that met the criteria for inclusion in the present study, caliciviruses were detected in 184 (81%) by reverse-transcription polymerase chain reaction and nucleotide sequencing. Nursing homes, retirement centers, and hospitals were the most frequently reported settings, and person-to-person contact was the most common mode of transmission, followed by foodborne spread. Overall, genogroup II norovirus (NoV) strains were the most abundant (79%), followed by genogroup I NoV strains (19%) and sapovirus (2%). Nucleotide-sequence analysis indicated a great diversity of NoV strains and implicated the emergence of one particular sequence variant in outbreaks occurring between July 2002 and June 2003. The public health impact of caliciviruses will not be fully appreciated, nor will interventions be completely evaluated, until methods to detect these viruses are more routinely used
Background. Noroviruses are believed to be the most common etiologic agent of foodborne outbreaks of gastroenteritis, yet diagnostic tests for these agents are not readily available in the United ...States. In the absence of assays to detect norovirus, several clinical and epidemiologic profiles—the criteria of Kaplan et al. (vomiting in >50% of patients, mean incubation period of 24–48 h, mean duration of illness of 12–60 h, and no bacterial pathogen) and the ratios of fever to vomiting and diarrhea to vomiting—have been used to distinguish foodborne outbreaks of gastroenteritis caused by noroviruses from those caused by bacteria. Methods. To examine how well clinical and epidemiological profiles discriminate between foodborne outbreaks of gastroenteritis due to noroviruses and those due to bacteria and to estimate the proportion of reported outbreaks that might be attributable to noroviruses, we reviewed subsets of the 4050 outbreaks reported from 1998 to 2000. Results. The set of criteria of Kaplan et al. is highly specific (99%) and moderately sensitive (68%) in discriminating confirmed outbreaks due to bacteria from those due to norovirus and was the most useful diagnostic aid evaluated. Each individual component of the criteria, the fever-to-vomiting ratio, and the diarrhea-to-vomiting ratio were more sensitive, yet less specific, and therefore less useful, than the criteria of Kaplan et al. We estimated that, at a minimum, 28% of all the foodborne outbreaks reported to the Centers for Disease Control and Prevention may be attributed to norovirus on the basis of these criteria. Conclusion. Until norovirus diagnostic tests become widely available, the criteria of Kaplan et al. remain the most useful and discriminating diagnostic aid to identify foodborne outbreaks of gastroenteritis due to noroviruses.
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 P4, G2 strains were almost completely absent and P8, G1 and P8, 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 P9, 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.
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