Epidemiological Surveillance and Genomic Characterization of Soochong Virus From Apodemus Species Using Multiplex PCR‐Based Next‐Generation Sequencing, Republic of Korea

Abstract

Orthohantavirus hantanense causes hemorrhagic fever with renal syndrome in Eurasia, posing a substantial public health threat. Although the Hantaan virus is the primary etiological agent in the Republic of Korea (ROK), evidence suggests the potential zoonotic transmission of the Amur virus (AMRV), closely related to the Soochong virus (SOOV), to humans in China and Russia. This study examined 31 Apodemus spp. captured from six regions in Gangwon Province, ROK, between 2015 and 2018. Of these, 5/31 (16.1%) tested positive for anti‐SOOV immunoglobulin G and SOOV RNA, with 3/6 (50%) in Hongcheon‐gun and 2/5 (40%) in Pyeongchang‐gun. Utilizing a multiplex polymerase chain reaction‐based next‐generation sequencing approach, we achieved complete genomic sequencing of SOOV from rodent lung tissues, with coverage rates of 90.3%−98.2% for the S segment, 92.3%−98.1% for the M segment, and 88.1%−93.0% for the L segment. Five novel whole‐genome sequences of SOOV were obtained from rodents in Hongcheon‐gun and Pyeongchang‐gun, representing the first documented SOOV in Pyeongchang‐gun. The evolutionary rate analysis of SOOV tripartite genomes demonstrated lower divergence in the S segment. Phylogenetic analysis revealed a well‐supported divergence of the SOOV and AMRV lineages across the ROK, China, and Russia, with incongruences suggesting differential segment evolution. Co‐divergence analysis indicated the inter‐species transmission of SOOV Aa18‐104 from Apodemus agrarius in Pyeongchang‐gun. The high zoonotic potential of all SOOV strains underscores the need for extensive monitoring and surveillance. This report provides crucial insights for the development of effective control strategies against hantaviral outbreaks in the ROK.