Viruses Causing Gastroenteritis: The Known, The New and Those Beyond

Munnink, Bas B. Oude; Hoek, Lia van der

doi:10.3390/v8020042

Cited by 81 publications

(52 citation statements)

References 98 publications

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“…Although at least 25 different bacteria and protozoa can cause diarrhoea, more than 75% of cases found to be caused by viruses [16]. Viruses that can cause gastroenteritis include rotavirus, norovirus, enteric adenovirus, human astrovirus, and Sapporo virus [17,18]. Currently, the diagnostic methods used to detect viruses in stool samples are sequence-dependent molecular amplification techniques such as PCR, which cannot identify a pool of viruses and completely new viruses in clinical samples.…”

Section: Introductionmentioning

confidence: 99%

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

Mohammad

Madi

Al‐Nakib

2020

Virol J

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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.

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Section: Introductionmentioning

confidence: 99%

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

Mohammad

Madi

Al‐Nakib

2020

Virol J

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“…). Gastroenteric viruses are important pathogens among the gastroenteritis causing agents(Oude Munnink and van der Hoek ), and since they normally replicate efficiently in the gastrointestinal tract, each gram of stool can arise an amount of 10 13 viral particles (Carter ; Bosch et al . ).…”

Section: Introductionmentioning

confidence: 99%

Human enteric viruses in a wastewater treatment plant: evaluation of activated sludge combined with UV disinfection process reveals different removal performances for viruses with different features

Lizasoain

Tort

González-García

et al. 2018

Lett Appl Microbiol

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“…Algunos de estos ensayos han sido comercializados, mientras que otros solo se realizan en centros de referencia. Todos ellos tienen el inconveniente de no distinguir entre infección actual y pasada, por lo que son más útiles en zonas no endémicas, y con frecuencia tienen problemas de reacciones cruzadas 15,16 . En cuanto al diagnóstico molecular, se han diseñado multitud de protocolos de PCR, tanto convencional como a tiempo real, para el diagnóstico de las helmintiasis 8 .…”

Section: Helmintosunclassified

“…Los principales virus productores de gastroenteritis en el ser humano son los rotavirus, astrovirus, adenovirus y norovirus. Otros como los coronavirus, torovirus, picobirnavirus y picornavirus (virus Aichi) también pueden causar infección del tracto gastrointestinal, pero con una frecuencia mucho menor 16 . El diagnóstico rápido de las gastroenteritis víricas se realiza mediante la detección de antígenos virales (tabla 3) o por métodos moleculares basados en la detección de genes específicos.…”

Section: Diagnóstico De Virusunclassified

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Diagnóstico rápido de las infecciones del tracto gastrointestinal por parásitos, virus y bacterias

Balsalobre-Arenas

Alarcón-Cavero

2017

Enfermedades Infecciosas y Microbiología Clínica

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Rapid diagnostic techniques are valuable tools in the diagnosis of gastrointestinal infections, especially for the detection of some microorganisms and in certain groups of patients. While antigen detection techniques are widely used in Clinical Microbiology laboratories, for the diagnosis of viruses, some parasites and some bacteria, molecular techniques are routinely used only for some pathogens (such as Clostridium difficile). However, molecular techniques are constantly evolving, and they allow a rapid diagnosis for an increasing number of pathogens, with high sensitivity and specificity. In addition, they are also able to detect virulence factors or resistance mechanisms. Syndromic surveillance systems, which detect different pathogens simultaneously, are very promising because they enable the most frequent pathogens to be diagnosed in a few hours and they can be very useful in certain patients. For the diagnosis of Helicobacter pylori infection, molecular techniques are able to detect bacteria and its resistance to clarithromycin and levofloxacin, allowing the most appropriate treatment to be selected for each patient when bacterial culture is not possible.

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Viruses Causing Gastroenteritis: The Known, The New and Those Beyond

Cited by 81 publications

References 98 publications

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

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

Human enteric viruses in a wastewater treatment plant: evaluation of activated sludge combined with UV disinfection process reveals different removal performances for viruses with different features

Diagnóstico rápido de las infecciones del tracto gastrointestinal por parásitos, virus y bacterias

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