Abstract
Emerging and re-emerging infectious diseases caused by RNA viruses pose a critical public health threat. Next generation sequencing (NGS) is a powerful technology to define genomic sequences of the viruses. Of particular interest is the use of whole genome sequencing (WGS) to perform phylogeographic analysis, that allows the detection and tracking of the emergence of viral infections. Hantaviruses, Bunyaviridae, cause hemorrhagic fever with renal syndrome (HFRS) and hantavirus pulmonary syndrome (HPS) in humans. We propose to use WGS for the phylogeographic analysis of human hantavirus infections. A novel multiplex PCR-based NGS was developed to gather whole genome sequences of Hantaan virus (HTNV) from HFRS patients and rodent hosts in endemic areas. The obtained genomes were described for the spatial and temporal links between cases and their sources. Phylogenetic analyses demonstrated geographic clustering of HTNV strains from clinical specimens with the HTNV strains circulating in rodents, suggesting the most likely site and time of infection. Recombination analysis demonstrated a genome organization compatible with recombination of the HTNV S segment. The multiplex PCR-based NGS is useful and robust to acquire viral genomic sequences and may provide important ways to define the phylogeographical association and molecular evolution of hantaviruses.
Highlights
Emerging and re-emerging infectious diseases caused by RNA viruses pose a critical public health threat
To obtain whole genome sequence of Hantaan virus (HTNV) from the patient samples, HTNV tripartite genomes were amplified by performing HTNVspecific multiplex PCR
The genomic sequence of HTNV L, M, and S segments from ROKA 13-8 was recovered up to 85.9%, 98.2%, and 100% based on full-length of the prototype HTNV 76–118 tripartite genomes, respectively
Summary
Emerging and re-emerging infectious diseases caused by RNA viruses pose a critical public health threat. Hantaviruses are the causative agents of hemorrhagic fever with renal syndrome (HFRS) in Eurasia and hantavirus pulmonary syndrome (HPS) in the Americas[13,14,15] They are a significant public health threat with ~200,000 clinical cases reported annually and a fatality rate ranging from 1 to 35% worldwide[16]. A method based on multiplex PCR-based NGS to achieve whole genome sequencing of HTNV L, M, and S segments from human or mammalian clinical specimens was developed Using this method, the whole genome sequence of HTNV L, M, and S segments from four ROK and US Army military HFRS patients was obtained and compared with genome sequences from natural hosts captured from endemic areas to perform the phylogeographic analysis. Analysis of the HTNV tripartite genomes suggested a recombination of the S segment in nature
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