Discovery of a Novel Parahenipavirus, Parahenipavirus_GH, in Shrews in South Korea, 2022

Abstract

Highly pathogenic henipaviruses (Nipah and Hendra viruses) and parahenipaviruses (Langya virus) have demonstrated significant zoonotic potential. We aimed to identify Henipavirus or Parahenipavirus species in rodents and shrews in South Korea to underline the potential zoonotic transmission risk. Kidney and lung tissues from 285 rodents and shrews were screened for Henipavirus and Parahenipavirus using quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) targeting the Gamak virus and Daeryong virus (DARV) sequences. Based on the qRT-PCR results, 75 out of the 285 individuals tested positive, with the highest viral loads in the kidneys of Apodemus agrarius, Crocidura lasiura, and Crocidura shantungensis. A kidney sample from C. shantungensis that exhibited the lowest Ct value was further analyzed using PCR, Sanger sequencing, and metagenomic analysis, yielding a near-complete genome of a novel Parahenipavirus, designated Parahenipavirus_GH (PHNV-GH), which is phylogenetically related to DARV and Jingmen virus but exhibits distinct genomic features. Ixodes granulatus ticks were also identified on the host shrew. The identification of PHNV-GH in southern South Korea expands the known geographical distribution range of parahenipaviruses and highlights the ongoing risk of zoonotic transmission. Given the uncertain transmission dynamics and pathogenic potential of parahenipaviruses, comprehensive environmental surveillance and characterization of emerging parahenipaviruses are essential for preventing future outbreaks.

Keywords: Henipavirus; Parahenipavirus; Paramyxoviridae; shrew; zoonotic.

Figure 1

Map showing the present rodent- and shrew-sampling sites and the sites where parahenipaviruses were previously identified in South Korea. The sampling sites were Goheung-gun and Donghae-si in Gangwon-do; Paju-si, Pocheon-si, and Yeoju-si in Gyeonggi-do; Geoje-si in Gyeongsangnam-do; Cheongdo-gun and Uiseong-gun in Gyeongsangbuk-do; Goseong-gun and Haenam-gun in Jeollanam-do; Jeongeup-si in Jeonbuk-do; Jeju-si and Seogwipo-si in Jeju-do; Boryeong-si in Chungcheongnam-do; and Sejong-si. The blue areas on the map indicate the sampling sites in this study and the magenta star (★) represents the location where Parahenipavirus_GH was detected. The green diamond (◆) and yellow triangles (▲) indicate the sites where Daeryong virus and Gamak virus, respectively, were previously identified [11]. The map was generated using Tableau Public.

Figure 2

Phylogenetic analysis of a novel Parahenipavirus, Parahenipavirus_GH, using VipTree. Phylogenetic trees were constructed based on whole-genome sequences to examine the evolutionary relationships of Parahenipavirus_GH (PHNV-GH) with (a) related single-stranded RNA viral genomes and (b) closely related members of the family Paramyxoviridae. The red star indicates the PHNV-GH sequence identified in this study and the red branches denote input sequences, including PHNV-GH sequence, which were not available in the VipTree database at the time of analysis.

Figure 3

Genome organization of Parahenipavirus_GH and related Henipavirus and Parahenipavirus strains. This schematic diagram illustrates the genome organization of Parahenipavirus_GH compared with that of other reported henipaviruses and parahenipaviruses. The horizontal bars represent viral genomes, with colored segments indicating the coding regions of each gene. A scale bar indicating genome length is shown above the genome structures. Abbreviations: N, nucleocapsid protein; P, phosphoprotein; M, matrix protein; h, hypothetical protein; F, fusion protein; G, glycoprotein; L, large protein. The diagram was illustrated using Adobe Photoshop CS6.