Prevalence of human cosavirus and saffold virus with an emergence of saffold virus genotype 6 in patients hospitalized with acute gastroenteritis in Chiang Mai, Thailand, 2014–2016

Study of Cosavirus, Salivirus, and Bufavirus viruses in children with acute gastroenteritis

Background

Acute gastroenteritis (AGE) in children represents a health problem. Besides common enteric viruses such as rotavirus and adenovirus, new viruses such as cosavirus, salivirus, and bufavirus may be associated with AGE. The objective of the study was to detect cosavirus, salivirus, and bufavirus viruses in children below 5 years with acute gastroenteritis by the use of real-time polymerase chain reaction (PCR) besides detection of rotavirus and adenovirus by enzyme-linked immunosorbent assay (ELISA).

Method

The study included 150 children ≤ 5 years with community-acquired diarrhea. Stool samples from children were subjected for the detection of rotavirus and adenovirus antigens by ELISA and for detection of buvavirus, salivirus, and cosavirus by real-time PCR.

Results

The commonest virus detected in the stool samples of children with AGE was rotavirus 31.3% followed by adenovirus 24%. Among the new viruses studied, salivirus was detected in six samples (4.0%), buvavirus was detected in four samples (2.7%), and cosavirus was detected in two samples (1.3%). The mixed rotavirus detection with studied viruses was 23.4% for adenovirus, 4.3% for calicivirus, and 2.1% for bocavirus, and none of the detected cosavirus was associated with rotavirus. In the studied children, at least one of the new viruses was detected in ten children (6.7%). Buvavirus, salivirus, and cosavirus were detected as a single virus (0.7%) in the children with acute gastroenteritis and buvavirus was detected with cosavirus without other viruses in one sample (0.7%).

Conclusion

The study reports the occurrence of buvavirus, cosavirus, and salivirus in the pediatric patients with community-acquired acute gastroenteritis. There was a high prevalence of rotavirus and adenovirus antigens in those patients with low positivity for buvavirus, cosavirus, and salivirus viruses. There is a need for a large cohort study to study the prevalence of buvavirus, cosavirus, and salivirus in pediatrics with acute gastroenteritis and to validate their association with the disease.

Distribution and molecular characterization of saffold virus and human cosavirus in children admitted to hospitals with acute gastroenteritis in Thailand, 2017-2022

Saffold virus (SAFV) and human cosavirus (HCoSV) are emerging viruses of the Picornaviridae family. They have been shown to associate with gastrointestinal infection and more recently these viruses have also been demonstrated to associate with other clinical infections such as the respiratory tract, cardiovascular system, and the cerebral ventricular system. In this study, 2459 stool specimens collected from pediatric patients admitted to hospitals with acute gastroenteritis from January 2017 to December 2022, were screened for SAFV and HCoSV utilizing reverse transcription-polymerase chain reaction. Positive samples were then characterized into genotypes via nucleotide sequencing and bioinformatic analysis. Of the 2459 samples, 21 and 39 were positive for SAFV (0.9%) and HCoSV (1.6%), respectively. Three genotypes of SAFV were identified-SAFV-1 (38%), SAFV-2 (24%), and SAFV-3 (38%). Two genetic groups of HCoSV were identified-HCoSV-C (97%) and HCoSV-A (3%), demonstrating a large increase of HCoSV-C as compared to those reported previously from the same geographical region in Thailand. This study provides the prevalence of SAFV and HCoSV genotypes in Chiang Mai, Thailand during a period of 6 years from 2017 to 2022.

Global Status of Bufavirus, Cosavirus, and Saffold Virus in Gastroenteritis: A Systematic Review and Meta-Analysis

Background: Bufavirus (BuV), Human Cosavirus (HCoSV), and Saffold (SAFV) virus are three newly discovered viruses and have been suggested as possible causes of gastroenteritis (GE) in some studies. The aim of the present study was to estimate the overall prevalence of viruses and their association with GE. Methods: A comprehensive systematic search was conducted in Scopus, Web of Science, PubMed, and Google scholar between 2007 and 2021 to find studies on the prevalence of BuV, HCoSV, and SAFV viruses. Result: Meta-analysis of the 46 included studies showed the low prevalence of BuV (1.%, 95% CI 0.6-1.5%), HCoSV (0.8%, 95% CI 0.4-1.5%), and SAFV (1.9%, 95% CI 1.1-3.1%) worldwide. Also, no significant association between these viruses and GE was observed. BuV was isolated from patients with GE in Africa, while SAFV was more common in Europe. BuV1 and BuV2 have the same prevalence between the three identified genotypes of BuV. HCoSV-C was the most prevalent genotype of HCoSV, and SAFV2 was the commonest genotype of SAFV. All of these viruses were more prevalent in children older than 5 years of age. Conclusion: This was the first meta-analysis on the prevalence and association of BuV, HCoSV, and SAFV with GE. While no significant association was found between infection with these viruses and GE, we suggest more studies, especially with case-control design and from different geographical regions in order to enhance our knowledge of these viruses.

First Human Cosavirus Detection From Cerebrospinal Fluid in Hospitalized Children With Aseptic Meningitis and Encephalitis in Iran

OBJECTIVE

Human cosavirus (HCosV) is a newly recognized virus that seems to be partly related to nonpolio flaccid paralysis and acute gastroenteritis in pediatric patients. However, the relationship between HCosV and diseases in humans is unclear. To assess an investigation for the occurrence of HCosV among pediatric patients involved in meningitis and encephalitis, we implemented a real-time quantitative polymerase chain reaction assay for detection and quantification of HCosV in stool specimens.

MATERIALS AND METHODS

In this study, a total of 160 cerebrospinal fluid samples from September 2019 to October 2020 were collected from presenting pediatric patients with meningitis and encephalitis in a Karaj hospital, Iran. After viral RNA extraction, the real-time quantitative polymerase chain reaction was performed to amplify the 5'Un-Translated Region region of the HCosV genome and viral load was analyzed.

RESULTS

Of the 160 samples tested, the HCosV genomic RNA was detected in 2/160 (1.25%) of samples. The minimum viral load of HCosV was 3.5 × 103 copies/mL from 4 years male patient. The maximum viral load was determined to be 2.4 × 105 copies/mL in one sample obtained from 3.5 years female patient.

CONCLUSIONS

This is the first documentation of HCosV detection in cerebrospinal fluid samples that better demonstrates relation of HCosV with neurologic diseases including meningitis and encephalitis. Also, these results indicate that HCosV has been circulating among Iranian pediatric patients.

Persistent Detection of Cosavirus and Saffold Cardiovirus in Riachuelo River, Argentina

Cosaviruses (CoSV) and Saffold cardiovirus (SAFV) are novel members of the Picornaviridae family. The Matanza-Riachuelo river basin covers a total area of 2200 km² with approximately 60 km long. Its last section is called Riachuelo River. The aim of this study was to describe the circulation of both picornaviruses and their relationship with the environmental situation of the Riachuelo River using 274 samples collected from 2005 to 2015. CoSV and SAFV were investigated in samples available by two periods: 2005-2006 and 2014-2015 (103 and 101, respectively). Physicochemical and bacteriological parameters confirmed very high levels of human fecal contamination during the 11 years evaluated. CoSV was detected in 85.7% (66/77) and 65.4% (17/26) of the samples collected in 2005-2006 and 2014-2015 periods, respectively. Species A and D were identified, the first one being widely predominant: 74.1% (20/27) and 75.0% (3/4) in both periods. SAFV virus was detected in 47.1% (32/68) and 52.6% (10/19) in periods 2005-2006 and 2014-2015, respectively. SAFV-6 was the most identified genotype in the entire study, while SAFV-3 was predominant in 2005-2006. The contribution of genotypes 1, 2, 4 and 8 was minor. The high prevalence of CoSV and SAFV suggests that both viruses have been circulating in Argentina at least since 2005. Our results show that a watercourse with high rates of human fecal contamination can become a persistent source of new viruses which capacity to produce human diseases is unknown.

Molecular detection of cosaviruses in a patient with acute flaccid paralysis and in sewage samples in Germany

Cosaviruses (CoSV) were first identified in stool samples collected from non-polio acute flaccid paralysis (AFP) cases and their healthy contacts in Pakistan in 2003. The clinical importance of CoSV remains unclear as data on epidemiology are scarce and no routine diagnostic testing is done. In this study, we characterized human CoSV (HCoSV) in a child with non-polio AFP and in sewage samples collected in Berlin, Germany. Using unbiased high-throughput sequencing and specific PCR, we characterized a HCoSV-D in stool samples of a three-year-old child hospitalized in Germany with non-polio AFP and travel history to Pakistan. The shedding pattern and absence of other relevant pathogens suggests that HCoSV-D may have been involved in the genesis of AFP. The HCoSV-RNA concentration was high, with 2.57 × 10⁶ copies per mL fecal/suspension, decreasing in follow-up samples. To investigate the possibility of local circulation of HCoSV, we screened Berlin sewage samples collected between 2013 and 2018. Molecular testing of sewage samples has shown the presence of CoSV in several parts of the world, but until now not in Germany. Of our sewage samples, 54.3 % were positive for CoSV, with up to three viral species identified in samples. Phylogenetically, the German sequences clustered intermixed with sequences obtained globally. Together, these findings emphasize the need for further clinical, epidemiological, environmental, pathogenicity and phylogenetic studies of HCoSV.

Near-complete genome of cosavirus A from a child hospitalized with acute gastroenteritis, Brazil

Acute gastroenteritis (AG) is responsible for 525,000 deaths worldwide in children under-5-years and is caused by the Human Cosavirus (HCoSV; family Picornaviridae, Genus Cosavirus). Although its health importance, a significant percentage of diarrhea cases (≈ 40 %) still of unknown etiology. In Brazil, few studies have reported HCoSV-A sequences analyzing partial 5' UTR. This study characterized the first near-complete genome of a Cosavirus A (strain AM326) from a child hospitalized with AG in Amazonas state, Northern Brazil. High throughput sequencing (HTS) was performed using the HiSeq™ 2500 platform (Illumina) in one fecal specimen collected from the Surveillance of Rotavirus Network of the Evandro Chagas Institute collected in 2017. Sequence reads were assembled by the De Novo approach using three distinct algorithmic (IDBA-UD, Spades, and MegaHit). The final contig was recovered from the HCoSV-AM326 sample revealing 7,735 nt in length (SRA number SRR12535029; GenBank MT023104) and the genetic characterization, as well as phylogenetic analysis demonstrated a new variant strain from Brazil, highlighting the association of HCoSV-A as a possible causative agent of AG. This finding demonstrates the importance of the metagenomic approach to elucidate cases of diarrhea without a defined etiology, as well as providing a better understanding about the virus genetics, evolution and epidemiology.

Prevalence of Eleven Infectious Viruses Causing Diarrhea in Korea

Rotavirus and norovirus are well-known causes of viral infectious diarrhea. There are few reports on diarrhea caused by other viruses in Korea, although cases of gastroenteritis attributable to other viruses are increasing worldwide. The aims of this study were to detect various causes of viral diarrhea and to investigate their prevalence. A total of 801 fecal specimens submitted to a clinical microbiology laboratory for the detection of diarrheal viruses were included. We sought to detect rotavirus A/B/C, adenovirus, astrovirus, norovirus GI/GII, sapovirus, Aichi virus, human parechovirus, enterovirus, human cosavirus, human bocavirus, and Saffold virus using multiplex reverse transcription polymerase chain reaction (RT-PCR). At least one diarrheal virus was detected in 223 (27.8%) fecal specimens. Among them, two viruses were detected in 11 specimens. Rotavirus A was most common (17.1%; N = 137), followed by norovirus GII (5.0%; N = 40), enterovirus (4.2%; N = 34), adenovirus (1.0%; N = 8), astrovirus (1.0%; N = 8), human parechovirus (0.6%; N = 5), and human bocavirus (0.2%; N = 2). Rotaviruses B and C, norovirus GI, sapovirus, Aichi virus, human cosavirus, and Saffold virus were not detected. We confirmed that various diarrheal viruses can be detected in fecal specimens. We must consider the possibility of viruses other than rotavirus and norovirus being present in cases of diarrhea.

First Occurrence of Saffold Virus in Sewage and River Water Samples in Karaj, Iran

Saffold virus as a newly discovered virus, which seems to be related to acute gastroenteritis as with other enteric viruses and to human airway diseases in children belongs to Cardiovirus genus in picornaviridae family with 11 genotypes. Saffold virus initially was detected in America from infant stool sample. Saffold virus has also been detected in environmental water samples. Until now, two reports have demonstrated that sewage water sources are contaminated with Saffold viruses. Molecular detection of Saffold virus mostly depended on reverse transcription PCR methods and RT-qPCR, which had targeted 5'UTR region of the viral genome. The present study aims to evaluate the molecular detection and quantity of Saffold virus in sewage water and river water specimens by RT-qPCR assay in Karaj, Iran. Fifty samples collected from environmental waters containing treated and untreated sewage water and river water samples were included in this study. After viral RNA extraction, the Real-time PCR was developed to amplify the 5'UTR sequence of Saffold virus genome and viral load was assessed. Out of the 50 samples tested (consisting 28 river water samples and 22 sewage water samples), the Saffold virus genomic RNA was identified in 10/28 (35.7%) of river water samples and in 4/12 (33.3%) of treated and 4/10 (40%) of untreated sewage samples. The maximum viral load was 6.8 × 10⁶ copies/l in untreated sewage water sample in December, and the lower viral load was 1.2 × 10⁶ copies/l related to treated sewage water taken in October. Our results for the first time indicate that Saffold virus has apparently been circulating among Iranian peoples. Also, the viral prevalence of Saffold virus in each of the three sets of tested samples was within moderate to high in range.

Evidence of Saffold virus circulation in Italy provided through environmental surveillance

Saffold virus (SAFV) is an emerging human cardiovirus associated with respiratory and gastrointestinal infection, and, more recently, to symptoms related to the endocrine, cardiovascular, and neurological systems. Information about SAFV circulation in Italy is scarce. In order to provide insights into the epidemiology of SAFV in Italy, 141 raw sewage samples collected throughout Italy were tested using broad-range nested RT-PCR primers targeting the 5'-NC region. Seven samples (5·0%) were confirmed as SAFV in samples collected in North, Centre and Southern Italy. Typing was attempted through amplification of the VP1 coding region, using both published and newly designed primers, and one sample was characterized as SAFV-2. SIGNIFICANCE AND IMPACT OF THE STUDY: Prevalence, genetic diversity and geographic distribution of SAFV in Italy is currently unknown. This study represents the first detection of SAFV in sewage samples in Italy, suggesting that it is circulating in the population despite lack of clinical reporting. Whether the virus is associated with asymptomatic cases or with undetected gastroenteritis or respiratory illness is unknown. Further studies are needed to investigate on the occurrence and persistence of SAFV in water environments and its waterborne transmission potential.

Molecular epidemiology and genetic diversity of human parechoviruses in children hospitalized with acute diarrhea in Thailand during 2011-2016

Little is known about human parechovirus (HPeV) infection in Thailand. The genotype distribution of HPeV strains in children admitted to hospitals with acute gastroenteritis was investigated using polymerase chain reaction (PCR) and nucleotide sequencing of the VP1 region as the detection and genotype identification methods, respectively. Of a total of 2,002 stool samples, 49 (2.4%) were positive for HPeV. Of these, HPeV-1 was the most predominant genotype (40.8%), followed by HPeV-3 (16.3%) and HPeV-14 (16.3%), while HPeV-5, -6, -2, -4, and -8 strains were less frequently detected, at 10.2%, 8.2%, 2%, 2%, and 2%, respectively. HPeV infections were detected throughout the year with the biannual peaks of infection in the rainy (Jun-Jul-Aug) and winter (Nov-Dec-Jan) months in Thailand. Based on VP1 amino acid sequence alignment, the arginyl-glycyl-aspartic acid (RGD) motif was found in HPeV-1, -2, -4, and -6 strains. Additionally, an amino acid insertion at the N-terminus of VP1 was observed in HPeV-4 and HPeV-5 strains. Phylogenetic analysis revealed that small clades of HPeV-1 and HPeV-3 strains emerged in 2016 and 2015, respectively, and dominated in the year of their emergence. The HPeV strains detected in Thailand in this study were most closely related to reference strains from Asia and Europe. The evolutionary rate of HPeV strains was 2.87 × 10^-4 (95% highest posterior density (HPD) 0.10-6.14 × 10^-4) substitutions/site/year. These findings provide information about the genetic diversity and evolutionary dynamics of HPeV genotypes circulating in pediatric patients with acute gastroenteritis in Thailand.

Iterative Excretion of Human Cosaviruses from Different Genotypes Associated with Combined Immunodeficiency Disorder

BACKGROUND

Human cosaviruses (HCoSVs) are newly discovered enteric viruses in the Picornaviridae family. They have been described in non-polio acute flaccid paralysis, diarrheal patients, and healthy individuals. They remain rarely documented in immunodeficient patients.

OBJECTIVES

This study reports iterative excretion of HCoSVs in a patient with major histocompatibility complex (MHC) class II combined immunodeficiency, a relatively common primary immunodeficiency in consanguineous settings.

METHODS

A total of 35 samples were collected from a patient followed for oral polio vaccine strains detection in stool samples during a 57-month period. Detection of HCoSVs in stools was performed by nested RT-PCR in the 5' noncoding region. The genotype identification and screening for recombinant strains was performed by sequencing in the VP1 and 3D genomic regions followed by phylogenetic analysis.

RESULTS

The patient was infected with HCoSVs twice at a 3-year interval. The excreted viruses belonged to 2 different genotypes with 2 probable recombinant viruses. During HCoSV infections, the patient was also excreting Sabin-related polioviruses.

CONCLUSIONS

This study describes excretion kinetics and genetic characteristics of HCoSVs in a patient with combined immunodeficiency due to MHC class II expression defect. The patient did not have concomitant symptoms related to the HCoSV infection.

Occurrence and Genetic Diversity of Human Cosavirus in Sewage in Italy

Human Cosavirus (HCoSV) is a newly discovered virus whose role in human enteric diseases is still unknown. In Italy, the prevalence and genetic diversity of HCoSV are unexplored. One hundred forty-one raw sewage samples collected throughout Italy were screened for HCoSV by RT-nested PCR. HCoSV was detected in 25.5% of samples. Species A, C, and D, and a potentially new species were detected. Our results show a significant circulation and heterogeneity of HCoSV in Italy.

Near full length genome of a recombinant (E/D) cosavirus strain from a rural area in the central region of Brazil

In the present article we report the nearly full length genome of a Cosavirus strain (BRTO-83) isolated from a child with acute gastroenteritis, and who is an inhabitant of a rural area in the central region of Brazil. The sample was previously screened and negative for both: common enteric viruses (i.e. rotavirus and norovirus), bacteria, endoparasites and helminthes. Evolutionary analysis and phylogenetic inferences indicated that the Brazilian BRTO-83 Cosavirus strain was a recombinant virus highly related to the E/D recombinant NG385 strain (Genbank JN867757), which was isolated in Nigeria from an acute flaccid paralysis patient. This is the first report of a recombinant E/D Cosavirus strain detected in Brazil, and the second genome described worldwide. Further surveillance and molecular studies are required to fully understand the epidemiology, distribution and evolution of the Cosavirus.