Affiliation:
1. Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Department of Microbiology, College of Life Sciences, Northwest University , Xi'an 710069 , China
2. College of Marine Science and Environment, Dalian Ocean University , Dalian 116023 , China
3. College of Food Technology and Sciences, Shanghai Ocean University , Shanghai 200093 , China
4. Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology , Qingdao 266237 , China
5. Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture , Shanghai 200093 , China
Abstract
Abstract
Aims
Despite metatranscriptomics becoming an emerging tool for pathogen surveillance, very little is known about the feasibility of this approach for understanding the fate of human-derived pathogens in drinking water sources.
Methods and results
We conducted multiplexed microfluidic cards and metatranscriptomic sequencing of the drinking water source in a border city of North Korea in four seasons. Microfluidic card detected norovirus, hepatitis B virus (HBV), enterovirus, and Vibrio cholerae in the water. Phylogenetic analyses showed that environmental-derived sequences from norovirus GII.17, genotype C of HBV, and coxsackievirus A6 (CA6) were genetically related to the local clinical isolates. Meanwhile, metatranscriptomic assembly suggested that several bacterial pathogens, including Acinetobacter johnsonii and V. cholerae might be prevalent in the studied region. Metatranscriptomic analysis recovered 349 species-level groups with substantial viral diversity without detection of norovirus, HBV, and CA6. Seasonally distinct virus communities were also found. Specifically, 126, 73, 126, and 457 types of viruses were identified in spring, summer, autumn, and winter, respectively. The viromes were dominated by the Pisuviricota phylum, including members from Marnaviridae, Dicistroviridae, Luteoviridae, Potyviridae, Picornaviridae, Astroviridae, and Picobirnaviridae families. Further phylogenetic analyses of RNA (Ribonucleic Acid)-dependent RNA polymerase (RdRp) sequences showed a diverse set of picorna-like viruses associated with shellfish, of which several novel picorna-like viruses were also identified. Additionally, potential animal pathogens, including infectious bronchitis virus, Bat dicibavirus, Bat nodavirus, Bat picornavirus 2, infectious bursal disease virus, and Macrobrachium rosenbergii nodavirus were also identified.
Conclusions
Our data illustrate the divergence between microfluidic cards and metatranscriptomics, highlighting that the combination of both methods facilitates the source tracking of human viruses in challenging settings without sufficient clinical surveillance.
Funder
National Natural Science Foundation of China
Opening Project of Key Laboratory of Environment Controlled Aquaculture
Shaanxi Fundamental Science Research Project for Chemistry & Biology
Publisher
Oxford University Press (OUP)
Subject
Applied Microbiology and Biotechnology,General Medicine,Biotechnology