Comprehensive virome analysis reveals the complexity and diversity of the viral spectrum in pediatric patients diagnosed with severe and mild hand-foot-and-mouth disease

Wang, Chunhua; Zhou, Shuaifeng; Xue, Wanhua; Shen, Liang; Huang, Wei E.; Zhang, Yi; Li, Xuguang; Wang, Junzhi; Zhang, Hong

doi:10.1016/j.virol.2018.02.004

Cited by 15 publications

(20 citation statements)

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“…While RNA phages are relatively sparse relative to DNA phage in human feces, the situation is generally reversed for mammalian viruses largely due to common picornavirus and calicivirus infections. The dominance of RNA viruses seen here is therefore fairly typical for human enteric virus infections 33 – 39 . The assembly of long viral genome contigs also allowed detailed phylogenetic analyses to reveal the relationships between members of the same viral species and genotype.…”

Section: Discussionmentioning

confidence: 52%

Complex virome in feces from Amerindian children in isolated Amazonian villages

et al. 2018

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The number of viruses circulating in small isolated human populations may be reduced by viral extinctions and rare introductions. Here we used viral metagenomics to characterize the eukaryotic virome in feces from healthy children from a large urban center and from three Amerindian villages with minimal outside contact. Numerous human enteric viruses, mainly from the Picornaviridae and Caliciviridae families, were sequenced from each of the sites. Multiple children from the same villages shed closely related viruses reflecting frequent transmission clusters. Feces of isolated villagers also contained multiple viral genomes of unknown cellular origin from the Picornavirales order and CRESS-DNA group and higher levels of nematode and protozoan DNA. Despite cultural and geographic isolation, the diversity of enteric human viruses was therefore not reduced in these Amazonian villages. Frequent viral introductions and/or increased susceptibility to enteric infections may account for the complex fecal virome of Amerindian children in isolated villages.

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Section: Discussionmentioning

confidence: 52%

Complex virome in feces from Amerindian children in isolated Amazonian villages

et al. 2018

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“…In our study, most of the infected persons were children aged less than 2 years old, which is consistent with the study by Rao et al [ 41 ] that presented the most infected persons with HFMD in India. Wang et al [ 42 ] also supported that children less than 2 years old were the most vulnerable population for HFMD in China. Regarding sex, in our study, more than half of the patients were male (57.4%), which is similar to the study by Zou et al [ 43 ], which reported that most of the HFMD-infected children in China were male, accounting for 60.0% of all cases.…”

Section: Discussionmentioning

confidence: 96%

Molecular epidemiology and clinical features of hand, foot and mouth disease in northern Thailand in 2016: a prospective cohort study

et al. 2018

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BackgroundHand, foot and mouth disease (HFMD) is a major communicable disease in children ≤6 years old, particularly in several countries in the Asia-Pacific Region, including Thailand. HFMD impacts public health and the economy, especially in northern Thailand.MethodsA prospective cohort study was conducted to estimate the incidence rate and to identify the serotype and clinical features of HFMD among children in northern Thailand. A validated questionnaire and throat swab were used for data collection. Polymerase chain reaction (PCR) was used to detect human enterovirus and identify its serotypes. Participants were recruited from 14 hospitals in two provinces in northern Thailand, specifically, Chiang Rai and Pha Yao Province, between January 1, 2016, and December 31, 2016. Chi-square or Fisher’s exact test was used to detect the associations of signs and symptoms with HFMD serotype. Logistic regression was used to detect the associations of variables with a positive enterovirus at alpha = 0.05.ResultIn total, 612 children aged ≤6 years from Chiang Rai and Pha Yao Province who were diagnosed with HFMD by a throat swab were recruited for the analysis. Approximately half of the cohort was male (57.2%), 57.5% was aged < 2 years, and 57.5% lived in rural areas. The incidence rate was 279.72/100,000 person-years in Chiang Rai Province and 321.24 per 100,000 person-years in Pha Yao Province. Additionally, 42.5% of children were positive for human enterovirus; among these children, 56.1% were positive for enterovirus-A (EV-A), 17.7% were positive for coxsackievirus (CV), and 26.2% were positive for other human RNA enteroviruses. During the study period, 21 distinct outbreaks of HFMD were recognized. Four to five patients (total 92 patients) were selected from each outbreak for identifying its serotype; enterovirus-A71 (EV-A71) was detected in 34.8% of HFMD cases, coxsackievirus-A16 (CV-A16) in 26.1%, coxsackivirus-A6 (CV-A6) in 15.2%, coxsackievirus-A10 (CV-A10) in 10.9%, coxsackievirus-A4 (CV-A4) in 2.2%, coxsackievirus-B2 (CV-B2) in 2.2%, human rhinovirus in 2.2%, and unknown serotype in 6.4%. Multivariable analysis demonstrated that a history of breastfeeding for ≤6 months was associated with a higher chance of enterovirus infection than a history of breastfeeding > 6 months, and children who had mother who worked as farmers, daily wage employees, and unprofessional skilled jobs had a greater chance of enterovirus infection than those who had unemployed mothers. Coxsackievirus-infected children had a higher rate of rashes on the buttocks, knee, and elbow and fever but a lower rate of lethargy and malaise than EV-A71-infected children.ConclusionsEV-A71 is a major cause of HFMD in children < 6 years old in northern Thailand, but rash, fever, and mouth ulcers are mostly found in participants with coxsackievirus infection. Breastfeeding should be promoted during early childhood for at least 6 months to prevent HFMD particularly those mother who are working in unprofessional skill jobs.Electronic supplementary materialT...

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“…Numerous protocols for viral enrichment and genome amplification have been described in literature [5][6][7]. Commonly employed protocols such as sample filtration [8], nuclease digestion, ultracentrifugation, and random pre-amplification of RNA or DNA in separate reactions would be particularly useful for increasing the signal-to-noise ratio in the viral analysis of biological samples in which the levels of nucleic acid background are high. In principle, these protocols can significantly reduce the proportion of human and bacteria reads and increase the number of viral reads.…”

Section: Introductionmentioning

confidence: 99%

Metagenomic analysis of viral nucleic acid extraction methods in respiratory clinical samples

et al. 2018

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BackgroundNumerous protocols for viral enrichment and genome amplification have been created. However, the direct identification of viral genomes from clinical specimens using next-generation sequencing (NGS) still has its challenges. As a selected viral nucleic acid extraction method may determine the sensitivity and reliability of NGS, it is still valuable to evaluate the extraction efficiency of different extraction kits using clinical specimens directly.ResultsIn this study, we performed qRT-PCR and viral metagenomic analysis of the extraction efficiency of four commonly used Qiagen extraction kits: QIAamp Viral RNA Mini Kit (VRMK), QIAamp MinElute Virus Spin Kit (MVSK), RNeasy Mini Kit (RMK), and RNeasy Plus Micro Kit (RPMK), using a mixed respiratory clinical sample without any pre-treatment. This sample contained an adenovirus (ADV), influenza virus A (Flu A), human parainfluenza virus 3 (PIV3), human coronavirus OC43 (OC43), and human metapneumovirus (HMPV). The quantity and quality of the viral extracts were significantly different among these kits. The highest threshold cycle(Ct)values for ADV and OC43 were obtained by using the RPMK. The MVSK had the lowest Ct values for ADV and PIV3. The RMK revealed the lowest detectability for HMPV and PIV3. The most effective rate of NGS data at 67.47% was observed with the RPMK. The other three kits ranged between 12.1–26.79% effectiveness rates for the NGS data. Most importantly, compared to the other three kits the highest proportion of non-host reads was obtained by the RPMK. The MVSK performed best with the lowest Ct value of 20.5 in the extraction of ADV, while the RMK revealed the best extraction efficiency by NGS analysis.ConclusionsThe evaluation of viral nucleic acid extraction efficiency is different between NGS and qRT-PCR analysis. The RPMK was most applicable for the metagenomic analysis of viral RNA and enabled more sensitive identification of the RNA virus genome in respiratory clinical samples. In addition, viral RNA extraction kits were also applicable for metagenomic analysis of the DNA virus. Our results highlighted the importance of nucleic acid extraction kit selection, which has a major impact on the yield and number of viral reads by NGS analysis. Therefore, the choice of extraction method for a given viral pathogen needs to be carefully considered.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5152-5) contains supplementary material, which is available to authorized users.

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Comprehensive virome analysis reveals the complexity and diversity of the viral spectrum in pediatric patients diagnosed with severe and mild hand-foot-and-mouth disease

Cited by 15 publications

References 44 publications

Complex virome in feces from Amerindian children in isolated Amazonian villages

Complex virome in feces from Amerindian children in isolated Amazonian villages

Molecular epidemiology and clinical features of hand, foot and mouth disease in northern Thailand in 2016: a prospective cohort study

Metagenomic analysis of viral nucleic acid extraction methods in respiratory clinical samples

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