Sample descriptors linked to metagenomic sequencing data from human and animal enteric samples from Vietnam

Abstract

There is still limited information on the diversity of viruses co-circulating in humans and animals. Here, we report data obtained from a large field collection of enteric samples taken from humans, pigs, rodents and other mammal hosts in Vietnam between 2012 and 2016. Each of 2100 stool or rectal swab samples was subjected to virally-enriched agnostic metagenomic sequencing; the short read sequence data are accessible from the European Nucleotide Archive (ENA). We link the sequence data to metadata on host type and demography and geographic location, distinguishing hospital patients, members of a cohort identified as a high risk of zoonotic infections (e.g. abattoir workers, rat traders) and animals. These data are suitable for further studies of virus diversity and virus discovery in humans and animals from Vietnam and to identify viruses found in multiple hosts that are potentially zoonotic.

Fig. 1

Map indicating approximate geographical locations of subjects and sampling points within Dong Thap province. Inset shows position of Dong Thap province within Vietnam.

Fig. 2

Age and gender distribution of participants in the high-risk and hospital based study. Age (years) and genders (male (blue), female (green)) were recorded for each participant in the hospital based study on the day of sampling. The age of participants in the high-risk cohort was recoded on the day of sampling. The genders of participants in the high-risk cohort were not disclosed.

Fig. 3

Distribution of log₁₀(read count per sample) grouped by sample collection method and host type. For each sample, the total number of reads produced by metagenomic sequencing were calculated. Samples were split into four categories based on sample collection method (faecal sample or rectal swab) and host type (human or non-human animal).

Fig. 4

Average read quality grouped by sample collection method and host type. The average read quality for each read was calculated using FastQC. Reads were split into four categories based on collection method (faecal sample or rectal swab) and host type (human or non-human animal) of the sample they belong to.