Development of a one step real-time RT-PCR method for sensitive detection of human astrovirus

Development and validation of a probe hybridization reverse-transcription quantitative PCR for detection of mamastrovirus 2 in domestic cats

Astroviruses are viral pathogens that have been associated with enteric and neurologic disease in a variety of species. The domestic cat is a prominent host, with reports of astroviral infection being both highly prevalent and widely distributed in the feline population. Despite the potential for inducing significant disease, especially within shelter environments, there is currently only one reliable method of detection: standard reverse-transcription PCR using pan-astrovirus degenerate primers (consensus RT-PCR) with product sequencing. Unfortunately, this process is relatively slow and costly. Quantitative real-time PCR (qPCR) represents an efficient, economical alternative, with the added benefit of viral load quantification. We developed a RT-qPCR assay using probe hybridization technique to detect conserved regions of mamastrovirus 2 extracted from fecal samples of domestic cats. Known positive and negative samples were tested, and results were compared with gold standard consensus RT-PCR and sequencing. A standard curve was employed to determine limits of detection. In order to assess analytic specificity, we tested several additional samples that had been collected from non-felid species and were known to contain non-target astroviruses. Discrepant results between consensus RT-PCR and RT-qPCR testing were further analyzed with a validation RT-PCR assay, using mamastrovirus 2-specific primers. Our probe hybridization RT-qPCR assay is reliable and effective for the detection of mamastrovirus 2. This assay will allow rapid, affordable detection and facilitate further research on astroviral infection within domestic cats.

Astrovirus Diagnostics

Various methods exist to detect an astrovirus infection. Current methods include electron microscopy (EM), cell culture, immunoassays, polymerase chain reaction (PCR) and various other molecular approaches that can be applied in the context of diagnostic or in surveillance studies. With the advent of metagenomics, novel human astrovirus (HAstV) strains have been found in immunocompromised individuals in association with central nervous system (CNS) infections. This work reviews the past and current methods for astrovirus detection and their uses in both research laboratories and for medical diagnostic purposes.

DNA microarray for detection of gastrointestinal viruses

Gastroenteritis is a clinical illness of humans and other animals that is characterized by vomiting and diarrhea and caused by a variety of pathogens, including viruses. An increasing number of viral species have been associated with gastroenteritis or have been found in stool samples as new molecular tools have been developed. In this work, a DNA microarray capable in theory of parallel detection of more than 100 viral species was developed and tested. Initial validation was done with 10 different virus species, and an additional 5 species were validated using clinical samples. Detection limits of 1 × 10(3) virus particles of Human adenovirus C (HAdV), Human astrovirus (HAstV), and group A Rotavirus (RV-A) were established. Furthermore, when exogenous RNA was added, the limit for RV-A detection decreased by one log. In a small group of clinical samples from children with gastroenteritis (n = 76), the microarray detected at least one viral species in 92% of the samples. Single infection was identified in 63 samples (83%), and coinfection with more than one virus was identified in 7 samples (9%). The most abundant virus species were RV-A (58%), followed by Anellovirus (15.8%), HAstV (6.6%), HAdV (5.3%), Norwalk virus (6.6%), Human enterovirus (HEV) (9.2%), Human parechovirus (1.3%), Sapporo virus (1.3%), and Human bocavirus (1.3%). To further test the specificity and sensitivity of the microarray, the results were verified by reverse transcription-PCR (RT-PCR) detection of 5 gastrointestinal viruses. The RT-PCR assay detected a virus in 59 samples (78%). The microarray showed good performance for detection of RV-A, HAstV, and calicivirus, while the sensitivity for HAdV and HEV was low. Furthermore, some discrepancies in detection of mixed infections were observed and were addressed by reverse transcription-quantitative PCR (RT-qPCR) of the viruses involved. It was observed that differences in the amount of genetic material favored the detection of the most abundant virus. The microarray described in this work should help in understanding the etiology of gastroenteritis in humans and animals.

Human astroviruses

Human astroviruses (HAtVs) are positive-sense single-stranded RNA viruses that were discovered in 1975. Astroviruses infecting other species, particularly mammalian and avian, were identified and classified into the genera Mamastrovirus and Avastrovirus. Through next-generation sequencing, many new astroviruses infecting different species, including humans, have been described, and the Astroviridae family shows a high diversity and zoonotic potential. Three divergent groups of HAstVs are recognized: the classic (MAstV 1), HAstV-MLB (MAstV 6), and HAstV-VA/HMO (MAstV 8 and MAstV 9) groups. Classic HAstVs contain 8 serotypes and account for 2 to 9% of all acute nonbacterial gastroenteritis in children worldwide. Infections are usually self-limiting but can also spread systemically and cause severe infections in immunocompromised patients. The other groups have also been identified in children with gastroenteritis, but extraintestinal pathologies have been suggested for them as well. Classic HAstVs may be grown in cells, allowing the study of their cell cycle, which is similar to that of caliciviruses. The continuous emergence of new astroviruses with a potential zoonotic transmission highlights the need to gain insights on their biology in order to prevent future health threats. This review focuses on the basic virology, pathogenesis, host response, epidemiology, diagnostic assays, and prevention strategies for HAstVs.

Multiplex real-time PCR assays for the detection of group C rotavirus, astrovirus, and Subgenus F adenovirus in stool specimens

Group C rotavirus (GCRV), astrovirus (AstV), and adenovirus (subgenus F AdenoV) are etiologic agents of acute nonbacterial gastroenteritis, which often represents community outbreaks. For the efficient detection of GCRV, AstV, and subgenus F AdenoV in stool specimens, a multiplex real-time PCR assay was developed to detect these three viruses simultaneously, with high sensitivity and specificity. In total, 8404 clinical specimens were collected between April 2008 and March 2011 and tested for GCRV, AstV, and subgenus F AdenoV by the multiplex real-time PCR, as well as for norovirus (NoV), sapovirus (SaV), and group A rotavirus (GARV) by non-multiplex real-time PCR. Forty-one specimens were positive for GCRV, AstV, or subgenus F AdenoV, including 15 specimens that were also positive for NoV, SaV, or GARV. Multiple viruses were detected simultaneously in 29 out of 4596 (0.63%) specimens infected with at least one virus. The association rates of AstV and subgenus F AdenoV with other viruses were significantly higher than those of NoV, SaV, GARV, or GCRV.

Evaluation and verification of the Seeplex Diarrhea-V ACE assay for simultaneous detection of adenovirus, rotavirus, and norovirus genogroups I and II in clinical stool specimens

Acute viral gastroenteritis is an intestinal infection that can be caused by several different viruses. Here we describe the evaluation and verification of Seeplex Diarrhea-V ACE (Seeplex DV), a novel commercial multiplex reverse transcription-PCR (RT-PCR) assay that detects 5 diarrheal pathogens, including adenovirus, rotavirus, norovirus genogroup I (GI) and GII, and astrovirus. We describe a retrospective study of 200 clinical specimens of which 177 were stool specimens previously tested for the presence of gastrointestinal viruses by electron microscopy (EM) and/or real-time RT-PCR (rRT-PCR). The remaining 23 specimens comprised other human pathogens of viral or bacterial origin. Discordant norovirus GI and GII results were resolved using a commercial kit; discordant adenovirus and rotavirus results were resolved using a home brew multiplex rRT-PCR assay. Diagnostic sensitivities and specificities were calculated before and after discordant analysis. After discordant analysis, estimated diagnostic sensitivities were 100% for adenovirus, rotavirus, and norovirus GI and 97% for norovirus GII. Diagnostic specificities after discordant analysis were 100% for adenovirus, rotavirus, and norovirus GI and 99.4% for norovirus GII. The 95% limits of detection were 31, 10, 2, and 1 genome equivalent per reaction for adenovirus, rotavirus, and norovirus GI and GII, respectively. The results demonstrate that the Seeplex DV assay is sensitive, specific, convenient, and reliable for the simultaneous detection of several viral pathogens directly in specimens from patients with gastroenteritis. Importantly, this novel multiplex PCR assay enabled the identification of viral coinfections in 12 (6.8%) stool specimens.

Genomic analysis of two ORF2 segments of new porcine astrovirus isolates and their close relationship with human astroviruses

Porcine astrovirus (PAstV) has been poorly studied and has been associated mainly with gastroenteritis. Computational analysis has revealed the close relationship of PAstV with astroviruses of humans (HAstV) and cats (FAstV). In this study, 105 and 171 stool specimens were collected from piglets and children under 5 years of age, respectively, in different Colombian regions during a 1-year period. The stool samples were examined for astroviruses by ELISA and RT-PCR; 23.8% and 4% were found to be positive for PAstV and HAstV, respectively. Additional sequence analysis with partial sequences obtained from ORF2 identified at least 2 probable groups of PAstVs and possible recombination events between porcine and human astroviruses. This study provides preliminary evidence of the high presence of PAstVs in pigs and proposes the existence of multiple PAstV types that are evolutionarily closely related to HAstVs.

Development of a fluorescent quantitative real-time polymerase chain reaction assay for the detection of Goose parvovirus in vivo

BACKGROUND

Goose parvovirus (GPV) is a Dependovirus associated with latent infection and mortality in geese. Currently, it severely affects geese production worldwide. The objective of this study was to develop a fluorescent quantitative real-time polymerase chain reaction (PCR) (FQ-PCR) assay for fast and accurate quantification of GPV DNA in infected goslings, which can aid in the understanding of the regular distribution pattern and the nosogenesis of GPV in vivo.

RESULTS

The detection limit of the assay was 2.8 x 10(1) standard DNA copies, with a sensitivity of 3 logs higher than that of the conventional gel-based PCR assay targeting the same gene. The real-time PCR was reproducible, as shown by satisfactory low intraassay and interassay coefficients of variation.

CONCLUSION

The high sensitivity, specificity, simplicity, and reproducibility of the GPV fluorogenic PCR assay, combined with a high throughput, make this method suitable for a broad spectrum of GPV etiology-related applications.

Detection of viral agents of gastroenteritis: Norovirus, Sapovirus and Astrovirus

Norovirus, Sapovirus and Astrovirus are causative agents of viral gastroenteritis affecting all age groups, but most frequently the young, the elderly and persons in semi-closed communities such as hospitals, nursing homes, military bases and cruise ships. The sensitive and rapid detection of causative agents of viral gastroenteritis is key to the effective implementation of infection control systems. Traditional detection methods such as electron microscopy and antigen detection assays lack sensitivity. The detection of gastrointestinal viruses by molecular methods has resulted in increased levels of detection, and enables the epidemiological investigation of viral strains. The significant diversity of gastrointestinal viruses, in particular Norovirus and Sapovirus, are compounded by increasing reports of virus recombination, and pose an ongoing challenge to the development of sensitive and specific molecular detection assays.