Analysis of viral diversity in stool samples from infants and children with acute gastroenteritis in Kuwait using Metagenomics approach

Abstract

Background: Current molecular target-dependent methods are used to detect only known viruses. However, metagenomics based on next-generation sequencing (NGS) technique is a target-independent assay that enables simultaneous detection and genomic characterisation of all microorganisms present in a sample. In this study, we aimed to develop a metagenomics approach using NGS to identify and characterise viruses in stool samples from infants and children with Acute Gastroenteritis (AGE) in Kuwait. Methods: We have investigated 84 stool samples from infants and children aged one month to ten years old with signs and symptoms of gastroenteritis who attended Mubarak Al-Kabeer and Al-Amiri hospitals in Kuwait from January to December 2017. A metagenomics approach using NGS to characterise viruses in clinical samples was used. Also, the commercial Real-Time PCR assay was used to detect viruses causing gastroenteritis. Results: Metagenomics analysis revealed an average of 280,768 reads in which 5% of the reads were derived from viruses. The analysis of viral sequences verified that single infection of human adenovirus was the leading cause of gastroenteritis among infants and children, which was detected in 23.2% of the patients, followed by a mixed infection of human adenovirus and other viruses, which was detected in 20.9% of patients. Also, the newly discovered viruses known to cause gastroenteritis were detected, such as astrovirus MLB2, primate bocaparvovirus-1, Aichivirus A, cardiovirus, parechovirus A, astrovirus VA4, cosavirus-F, and bufavirus-3. Our results showed 71% agreement (k = 0.445, P = 0.000) between multiplex Real-Time PCR, which is used as a routine diagnostic test and metagenomics approach in the detection of viruses causing gastroenteritis in clinical samples. Conclusion: Despite the difficulties in sample preparation and analysis process, we showed that metagenomics approach is a powerful and promising tool for the detection and characterisation of different viruses in clinical samples.

Demography, life-history trade-offs, and the gastrointestinal virome of wild chimpanzees

“…With the possible exception of astrovirus, which can cause diarrhoea [79] and encephalitis [80], the newly identified viruses are not known to cause disease. Bufaviruses [81], husaviruses [82], porprismacoviruses [83] and saliviruses [84] have all been found in human patients with gastroenteritis, but at present, the relationship between infection and disease remains largely speculative. Importantly, most of the viruses we identified did not exhibit clear associations with either chimpanzee age or sex.…”

Viral gastroenteritis in Tocantins, Brazil: characterizing the diversity of human adenovirus F through next-generation sequencing and bioinformatics

“…In the present study, NGS was used to assess enteric HAdV frequency and diversity in rural and low-income urban areas in northern Brazil. The value of NGS in HAdV detection and characterization has been described before [49][50][51][52], including in Brazil [53]. The frequency of HAdV-F infections detected in this study (n=251; 57.8%) using NGS was higher than that observed in other studies carried out in Ethiopia (n=450; 32 %) [23], Thailand (n=2312; 7.2 %) [54], Kenya (n=278; 37.4 %) [55], Iraq (n=155; 34.2 %) [56], Iran (n=2682; 5.2 %) [57], Bangladesh (n=871; 10.7 %) [58], Albania (n=142; 23.2 %) [59] and PR China (n=2233; 10.9%) [60] using conventional PCR; Tanzania (n=1235; 3.5 %) [27] and the Republic of Congo (n=655; 5.5 %) [61] using an enzyme-linked immunosorbent assay (ELISA); and Turkey (n=1154; 26.2 %) [62] using an immunochromatographic test.…”

Human Protoparvovirus DNA and IgG in Children and Adults with and without Respiratory or Gastrointestinal Infections

“…BuV DNA has worldwide been detected by PCR in low prevalence (0–4%) in diarrheal stool samples, whereas non-diarrheal stools have mainly been BuV-DNA negative [ 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 ]. However, the causative role of BuV in gastroenteritis (GE) remains unclear.…”