Evaluation of nine sets of PCR primers in the RNA dependent RNA polymerase region for detection and differentiation of members of the family Caliciviridae, Norwalk virus and Sapporo virus

Enhancing the sensitivity of Dengue virus serotype detection by RT-PCR among infected children in India

Dengue surveillance relies on reverse transcription-polymerase chain reaction (RT-PCR), for confirmation of dengue virus (DENV) serotypes. We compared efficacies of published and modified primer sets targeting envelope (Env) and capsid-premembrane (C-prM) genes for detection of circulating DENV serotypes in southern India. Acute samples from children with clinically-diagnosed dengue were used for RT-PCR testing. All samples were also subjected to dengue serology (NS1 antigen and anti-dengue-IgM/IgG rapid immunochromatographic assay). Nested RT-PCR was performed on viral RNA using three methods targeting 654bp C-prM, 511bp C-prM and 641bp Env regions, respectively. RT-PCR-positive samples were validated by population sequencing. Among 171 children with suspected dengue, 121 were dengue serology-positive and 50 were dengue serology-negative. Among 121 serology-positives, RT-PCR detected 91 (75.2%) by CprM654, 72 (59.5%) by CprM511, and 74 (61.1%) by Env641. Among 50 serology-negatives, 10 (20.0%) were detected by CprM654, 12 (24.0%) by CprM511, and 11 (22.0%) by Env641. Overall detection rate using three methods sequentially was 82.6% (100/121) among serology-positive and 40.0% (20/50) among serology-negative samples; 6.6% (8/120) had co-infection with multiple DENV serotypes. We conclude that detection of acute dengue was enhanced by a modified RT-PCR method targeting the 654bp C-prM region, and further improved by using all three methods sequentially.

Frequency of Enteropathogen Detection in Suckling and Weaned Pigs with Diarrhea in Japan

Fecal samples from suckling ( n = 153) and weaned ( n = 116) piglets with diarrhea in Japan were examined for shedding of viral, bacterial, and parasitic pathogens using culture, microscopic, and polymerase chain reaction methods. In suckling piglets, diarrhea was attributed to infection with a single etiologic agent in 60.8% of cases and with combinations of agents in 22.2%. In weaned piglets, diarrhea was attributed to a single etiologic agent in 43.1% and to combinations of agents in 47.4% of cases. Rotavirus was the most prevalent agent in suckling (67.3%) and weaned (65.5%) piglets. The detection of other pathogens was associated with age of the animals examined. Coccidia were predominantly isolated from suckling piglets, whereas Escherichia coli was found predominantly in weaned piglets. Although a relationship was not observed between detection rate of rotavirus and age of piglets, a single group of rotavirus was detected in 87.5% of suckling piglets whereas multiple groups were detected in 51.6% of weaned piglets. The results of this study confirm that diarrhea in piglets can, to a variable degree, be causally associated with multiple agents. Additionally, these results suggest reasons why this syndrome can be difficult to control.

Comprehensive review of human sapoviruses

Sapoviruses cause acute gastroenteritis in humans and animals. They belong to the genus Sapovirus within the family Caliciviridae. They infect and cause disease in humans of all ages, in both sporadic cases and outbreaks. The clinical symptoms of sapovirus gastroenteritis are indistinguishable from those caused by noroviruses, so laboratory diagnosis is essential to identify the pathogen. Sapoviruses are highly diverse genetically and antigenically. Currently, reverse transcription-PCR (RT-PCR) assays are widely used for sapovirus detection from clinical specimens due to their high sensitivity and broad reactivity as well as the lack of sensitive assays for antigen detection or cell culture systems for the detection of infectious viruses. Sapoviruses were first discovered in 1976 by electron microscopy in diarrheic samples of humans. To date, sapoviruses have also been detected from several animals: pigs, mink, dogs, sea lions, and bats. In this review, we focus on genomic and antigenic features, molecular typing/classification, detection methods, and clinical and epidemiological profiles of human sapoviruses.

Comparison of primers for the detection of genogroup II noroviruses in India

PURPOSE

Noroviruses (NoV) are increasingly recognized as an important cause for acute gastroenteritis, worldwide. Reverse transcription polymerase chain reaction (RT-PCR) and sequencing are the methods of choice for the detection of NoVs, but there is currently no consensus about the primers to be used in these assays.

MATERIALS AND METHODS

In this study, five published primer sets were evaluated for the detection of genogroup II (GII) NoVs in India. The primers target different regions of the NoV genome. Three primer sets detect an NoV in a single round RT-PCR platform, while the remaining two primer sets are based on a nested RT-PCR platform.

RESULT

A panel of 100 samples from previous studies on norovirus diarrhoea in children were tested by all five primer sets. Of them, 74 samples were identified as positive for NoV, by at least one primer set. Subsets of positive amplicons were sequenced to check for specificity.

CONCLUSION

The most sensitive primer set was Girish 2002, which detected GII NoV by nested RT-PCR, and was modified from the previously published primers. This study demonstrates that higher detection can be obtained by either using multiple primer sets or using a sensitive nested RT-PCR assay. It also demonstrates the differences in primer sensitivity for detection of Genogroup II (GII) NoVs in India.

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.

Genetic diversity of noroviruses and sapoviruses in children with acute sporadic gastroenteritis in New Delhi, India

BACKGROUND

Human caliciviruses (HuCVs) cause gastroenteritis throughout the world. Limited information is available on molecular epidemiology of caliciviruses from developing countries including India.

OBJECTIVES

Standardization and evaluation of a two-step multiplex RT-PCR assay for HuCVs and characterization of strains.

STUDY DESIGN

Two hundred and twenty-six stool samples were collected from children with acute gastroenteritis (AGE) over a one and half year to study the prevalence and diversity of HuCVs in children with AGE in New Delhi, India. A multiplex two-step RT-PCR using 3 sets of external and 4 sets of internal primers from the RdRp gene was standardized for detection of NoVs and SaVs. Molecular characterization of some HuCV strains was done by sequencing followed by phylogenetic analysis.

RESULTS

Fifty-nine HuCVs strains were detected in 54 (24%) of the samples; 5 samples had mixed infections. Of these 59 HuCVs, 36 (61%) were norovirus (34 were GGII; 2 were GGI) and 23 (39%) were sapovirus (22 were GGI; 1 was GGII). Phylogenetic analysis of partial RdRp gene of 12 HuCV strains identified three genotypes (GGI/4, GGII/3 and a newly identified GIIb/Hilversum cluster) in NoVs and one genotype (GGI/1) in SaVs.

CONCLUSION

This is one of the few reports from India on detection and characterization of HuCVs by multiplex RT-PCR assay. This assay can be a useful tool for epidemiological studies of HuCV infections.

RECOVIR: An application package to automatically identify some single stranded RNA viruses using capsid protein residues that uniquely distinguish among these viruses

Background

Most single stranded RNA (ssRNA) viruses mutate rapidly to generate large number of strains having highly divergent capsid sequences. Accurate strain recognition in uncharacterized target capsid sequences is essential for epidemiology, diagnostics, and vaccine development. Strain recognition based on similarity scores between target sequences and sequences of homology matched reference strains is often time consuming and ambiguous. This is especially true if only partial target sequences are available or if different ssRNA virus families are jointly analyzed. In such cases, knowledge of residues that uniquely distinguish among known reference strains is critical for rapid and unambiguous strain identification. Conventional sequence comparisons are unable to identify such capsid residues due to high sequence divergence among the ssRNA virus reference strains. Consequently, automated general methods to reliably identify strains using strain distinguishing residues are not currently available.

Results

We present here RECOVIR ("recognize viruses"), a software tool to automatically detect strains of caliciviruses and picornaviruses by comparing their capsid residues with built-in databases of residues that uniquely distinguish among known reference strains of these viruses. The databases were created by constructing partitioned phylogenetic trees of complete capsid sequences of these viruses. Strains were correctly identified for more than 300 complete and partial target sequences by comparing the database residues with the aligned residues of these sequences. It required about 5 seconds of real time to process each sequence. A Java-based user interface coupled with Perl-coded computational modules ensures high portability of the software. RECOVIR currently runs on Windows XP and Linux platforms. The software generalizes a manual method briefly outlined earlier for human caliciviruses.

Conclusion

This study shows implementation of an automated method to identify virus strains using databases of capsid residues. The method is implemented to detect strains of caliciviruses and picornaviruses, two of the most highly divergent ssRNA virus families, and therefore, especially difficult to identify using a uniform method. It is feasible to incorporate the approach into classification schemes of caliciviruses and picornaviruses and to extend the approach to recognize and classify other ssRNA virus families.

Virological, serological, and clinical features of an outbreak of acute gastroenteritis due to recombinant genogroup II norovirus in an infant home

Norovirus (NV) is an important cause of acute nonbacterial gastroenteritis worldwide. Recently, several sporadic cases due to naturally occurring recombinant NVs have been reported. In January 2000, there was an outbreak of gastroenteritis in an infant home in Sapporo, Japan. Of 34 residents of the home that were less than 2 years old, 23 developed gastrointestinal symptoms and NV infection was confirmed by conventional reverse transcription-PCR to detect the RNA polymerase region of genogroup II NV. In this virus, the RNA polymerase region shared 86% nucleotide identity with Hawaii virus but only 77% with Mexico virus; however, its capsid region shared only 70% identity with Hawaii virus but 90% with Mexico virus. On the other hand, both regions shared a higher 96% nucleotide identity with Arg320 virus, which was found in Mendoza, Argentina, in 1995 and considered to be a recombinant of Hawaii and Mexico viruses. The findings indicate that the virus involved in the outbreak was similar and may have evolved from the Arg320 virus. Clinically the cases were more severe than those of previously reported sporadic or outbreak cases of NV infection.

Reverse transcription-booster PCR for detection of noroviruses in shellfish

The methods commonly used for norovirus (NV) detection are based on reverse transcription-PCR (RT-PCR) followed by confirmation of the amplified sequence. To increase sensitivity, an RT-booster PCR was developed. The proposed method showed an increase in sensitivity at least 2 log units for all the NV strains tested compared with the standard RT-PCR method. Higher sensitivity was confirmed in tests on experimentally and naturally contaminated shellfish.

Development and evaluation of a new commercial test allowing the simultaneous detection of noroviruses and sapoviruses by reverse transcription-PCR and microplate hybridization

This work describes the design and initial evaluation of a commercial test allowing the detection of noroviruses and sapoviruses by reverse transcription-PCR (RT-PCR) in a single tube followed by microplate hybridization, as well as the detection of PCR inhibitors. The test was shown to be broadly reactive (except for Melksham-like strains), sensitive, and specific and thus should be useful for calicivirus detection in clinical practice.

Detection and characterization of norovirus outbreaks in Germany: application of a one-tube RT-PCR using a fluorogenic real-time detection system

Outbreaks of gastroenteritis caused by Norovirus are an increasing public health problem worldwide. The virus is transmitted by contaminated food and by person-to-person. In Germany, a new health reporting system including Norovirus infections has been introduced in 2001. Norovirus outbreaks (73%) diagnosed in our lab occurred in the first half of the year. Phylogenetic analysis shows that 90% belonged to genogroup II (GGII) with the majority related to prototypes Lordsdale/93 and Tarragona/2001. To date, PCR is the most sensitive and specific method for the detection but several procedures are needed to evaluate the amplification product. To minimize the risk of product carryover, a fast and simple procedure with a minimal number of steps are required. A one-tube RT-PCR method is described using the real-time TaqMan-PCR system. Primer sets and probes for both genogroup I (GGI) and genogroup II (GGII) sequences were developed. The specificity and sensitivity of this method was evaluated on 70 Norovirus positive stool samples of 70 outbreaks in Germany and 34 European samples by comparing the detection rate to those of an in-house RT-nested PCR. Overall, 93% of the PCR positive samples have been detected by the TaqMan-PCR including isolates of four different GGI and seven different GGII genotypes. Using plasmid standards for quantitation, virus loads between 10(2) and 10(10) genomic equivalents/ml stool suspension were found. The advantages of the one-step RT/TaqMan-PCR system for detection and quantitation of Norovirus are the high throughput of clinical samples and a decrease of the risk of contamination.

Detection and differentiation of Norwalk virus by reverse transcription-polymerase chain reaction and enzyme-linked immunosorbent assay

We have developed a reverse transcription-polymerase chain reaction and enzyme-linked immunosorbent assay (RT-PCR-ELISA), using genetic cluster-specific probes in a microtiter plate format, for the detection and differentiation of Norwalk virus (NV) in stool samples. The specificity of the RT-PCR-ELISA was confirmed by testing 76 stool specimens and 15 tissue culture fluids derived from growths of unrelated viruses. The sensitivity of the RT-PCR-ELISA was compared with conventional PCR and Southern hybridization by testing the four cDNA clones derived from the RNA-dependent RNA polymerase region of the NV68 (NV/GI) virus and viruses in the NV/GII/P1B, the NV/GII/P2A, and the NV/GII/P2B cluster. This assay was as sensitive as the conventional RT-PCR with Southern hybridization regardless of primer pairs and probes used in the experiments. However, the actual sensitivity of this method was higher when clinical stool samples were examined because this assay examines all the samples irrespective of the RT-PCR results. The RT-PCR-ELISA format is simple, time saving, and suitable for testing many samples. It should be reliable for large-scale epidemiological studies of NV.

Detection of both hepatitis A virus and Norwalk-like virus in imported clams associated with food-borne illness

Hepatitis A virus (HAV) and Norwalk-like virus (NLV) were detected by reverse transcription-PCR in clams imported into the United States from China. An epidemiological investigation showed that these clams were associated with five cases of Norwalk-like gastroenteritis in New York State in August 2000 (Food and Drug Administration Import Alert 16-50). They were labeled "cooked" but appeared raw. Viral RNA extraction was performed by using dissected digestive tissues rather than whole shellfish meats; this was followed by glycine buffer elution, polyethylene glycol precipitation, Tri-Reagent treatment, and purification of poly(A) RNA with magnetic beads coupled to poly(dT) oligonucleotides. We identified HAV and NLV as genotype I and genogroup II strains, respectively. Both viruses have high levels of homology to Asian strains. An analysis of fecal coliforms revealed a most-probable number of 93,000/100 g of clam meat, which is approximately 300-fold higher than the hygienic standard for shellfish meats.

Improved detection of human enteric viruses in foods by RT-PCR

Human enteric viruses (including hepatitis A virus (HAV) and Norwalk-like viruses (NLVs)) are now recognized as common causes of foodborne disease. While methods to detect these agents in clinical specimens have improved significantly over the last 10 years, applications to food samples have progressed more slowly. In an effort to improve the sensitivity and speed of virus detection from non-shellfish food commodities by reverse transcription-polymerase chain reaction (RT-PCR), we (i) evaluated multiple RNA extraction methods; (ii) compared alternative NLV primer sets; and (iii) developed a one-step RT-PCR method. Hamburger and lettuce samples, processed for virus concentration using a previously reported filtration-extraction-precipitation procedure, were inoculated with HAV or NV. Several RNA extraction methods (guanidinium isothiocyanate, microspin column, QIAshredder Homogenizer, and TRIzol) and primer pairs were compared for overall RNA yield (microg/ml), purity (A(260)/A(280)), and RT-PCR limits of detection. The use of TRIzol with the QIAshredder Homogenizer (TRIzol/Shred) yielded the best RT-PCR detection limits (<1 RT-PCR amplifiable units/reaction for NV), and the NVp110/NVp36 primer set was the most efficient for detecting NV from seeded food samples. A one-step RT-PCR protocol using the TRIzol/Shred extraction method and the NVp110/NVp36 or HAV3/HAV5 primer sets demonstrated improved sensitivity (>10-fold) over the routinely used two-step method. HAV RNA was detected by RT-PCR at initial inoculum levels corresponding to <10 and <100 PFU per 300 microl sample concentrate (corresponding to 6 g food sample) for hamburger and lettuce, respectively. NV RNA was detected by RT-PCR at initial inoculum levels <5 and <50 RT-PCR amplifiable units per 300 microl concentrate (corresponding to 6 g food sample) for hamburger and lettuce, respectively. Residual RT-PCR inhibitors were effectively removed as evidenced by the ability to detect viral RNA in food concentrates without prior dilution. The methods reported here show promise for rapid, sensitive detection of human enteric viruses in foods.

Prevalence of "Norwalk-like virus" infections in outbreaks of acute nonbacterial gastroenteritis observed during the 1999-2000 season in Osaka City, Japan

We have investigated the incidence of Norwalk-like viruses (NLVs) associated with outbreaks of acute nonbacterial gastroenteritis in Osaka City, Japan, since April 1996 using reverse transcription (RT)-PCR and electron microscopy methods. From the results of the first 3 years, between April 1996 and March 1999, we previously reported that multiple genetic types of NLVs were detected in 71.9% of outbreaks using RT-PCR with Ando's primers except for one outbreak [Iritani et al., 2000]. However, during the 1999-2000 season, NLV outbreak strains, which could not be detected by RT-PCR with Ando's primers, were increased. From probe typing and sequence analysis, 76.9% of these undetectable outbreak strains were classified into the P1-B type and the others were untypable. These untypable strains were closely related with Alphatron type strains detected in the Netherlands. The P2-B probe type of the NLV outbreak strains was predominant (88.2%) in the 1999-2000 season. The phylogram based on the 81 nucleotide sequences from these P2-B outbreak strains formed 2 clusters closely related with Lordsdale virus. The dominant genetic type of the P2-B outbreak strains, during the 1996-1997 season in Osaka City, belonged in one of these 2 clusters. These findings of the emergence of NLVs escaping the RT-PCR method strongly indicated the importance of probe typing and sequence analysis to survey NLV infections. Our surveillance of NLV infection in the outbreaks, for these 4 years, showed that the predominant probe type and dominant genetic type of NLV outbreak strains changed each season.

Sensitive detection and differentiation of Sapporo virus, a member of the family Caliciviridae, by standard and booster nested polymerase chain reaction

Norwalk virus and Sapporo virus (SV) were approved as type species of the genus Norwalk-like viruses and the genus Sapporo-like viruses, respectively, in the family Caliciviridae. Nested polymerase chain reaction (PCR), using newly designed primers in the RNA-dependent RNA polymerase region, was developed to detect and differentiate viruses in the three genetic groups of SV based on the relative size of the PCR products obtained. In addition, a booster nested PCR that performs nested PCR in a single tube was introduced to reduce the chance of contamination during the procedure of standard nested PCR. The specificity of the newly developed PCR was confirmed by testing 77 stool specimens and 16 tissue culture fluids derived from growth of unrelated viruses. The sensitivity of the nested PCR was compared with the conventional PCR using Sapp35/Sapp36 primer pair by testing the three cDNA clones obtained from viruses in the SV/SV82, the SV/London92, and the SV/Parkville virus, respectively. This assay can detect SV in a more sensitive way than the conventional PCR and Southern hybridization. Sensitive and suitable methods to detect and differentiate SV are required to obtain accurate epidemiological data on these viruses and the standard and booster nested PCR should be a very useful tool for this purpose.

Clinical severity of Norwalk virus and Sapporo virus gastroenteritis in children in Hokkaido, Japan

OBJECTIVE

To clarify the clinical significance and etiologic impact of Norwalk virus (NV) and Sapporo virus (SV) in viral gastroenteritis in Japanese children.

STUDY DESIGN

Two outbreaks each of NV gastroenteritis and SV gastroenteritis occurring in an infant home in Sapporo, Japan, as well as 95 hospitalized children with acute gastroenteritis were retrospectively evaluated using a 0- to 20-point clinical severity scoring system.

RESULTS

The mean severity scores for NV and SV gastroenteritis outbreaks were 7.9 and 5.2, respectively, as compared with 8.4 for rotavirus A gastroenteritis that occurred in the same infant home. Among 95 hospitalized children with acute gastroenteritis, rotavirus A was detected in 47% followed by NV in 18%. SV was not found.

CONCLUSION

Our data indicate that NV can cause severe gastroenteritis and is an important etiologic agent in hospitalized cases, whereas SV causes mild gastroenteritis in Japanese children.

Effect of rotavirus vaccine on Sapporo virus gastroenteritis in Finnish infants

BACKGROUND

Sapporo-like viruses (SLVs) occur worldwide, but there is limited information about the SLV-associated gastroenteritis outside Japan.

METHODS

Stool specimens from 1,432 episodes of gastroenteritis that occurred in children between 2 months and 2 years of age during a rotavirus vaccine trial (776 episodes in placebo-vaccinated and 656 in rotavirus-vaccinated infants) were examined for SLVs using a reverse transcription-PCR assay. The reverse transcription-PCR took advantage of new primers specific for Sapporo virus genetic clusters I, II and III; SV/SV82 (SV/Sapporo virus 82); SV/Lond92 (SV/ London 92); and SV/PV (Parkville virus).

RESULTS

SLVs were detected in association with 132 (9.2%) of all episodes; in 80 (5.6%) episodes SLV was the only gastroenteritis virus detected. The epidemic season of SLVs peaked from March to May concurrently with rotaviruses and astroviruses and overlapping withNorwalk-like viruses. Clinically SLV gastroenteritis was characterized by a mild diarrheal disease, being sharply different from the Norwalk-like virus-associated "winter vomiting disease." Rotavirus vaccination did not have any effect on the number of SLV episodes, but the intensity and duration of SLV-associated diarrhea were reduced in rotavirus-vaccinated children compared with placebo-vaccinated children (P = 0.0008).

CONCLUSIONS

SLVs are common causative agents of acute gastroenteritis in young Finnish children. SLV disease is characterized by diarrhea, which is usually mild but can be severe. By an unknown mechanism rotavirus vaccine seems to reduce the severity of SLV-associated diarrhea.