Molecular detection of parvovirus in Manchurian chipmunks (Tamias sibiricus asiaticus) captured in Korea

Cross-species transmission of viral diseases alarms our global community for its potential of novel pandemic events. Of various viral pathogens noted recently, parvoviruses have posed public health threats not only to humans but to wild animals. To investigate the prevalence of parvoviruses in wild Manchurian chipmunks, here we detected genetic fragments of the nonstructural protein of parvovirus by polymerase chain reaction in wild Manchurian chipmunk specimens captured in the central and southern regions of South Korea and compared their sequence homology with references. Of a total of 348 specimens examined, chipmunk parvovirus (ChpPV)-specific gene fragments were detected with a 31.32 % rate (109 chipmunks of 348) in their kidney, liver, lung, and spleen samples, and the chipmunks captured in Gangwon Province exhibited the highest positive rate (45.37%), followed by Gyeongsang (35.29%), Gyeonggi (31.03%), Chungcheong (20.00%), and Jeolla (19.70%). When compared with the reference sequences registered in GenBank, a partial ChpPV sequence showed 97.70% identity to the previously reported Korean strain at the nucleic acid level. In the phylogenetic analysis, ChpPV exhibited closer relationship to primate parvoviruses, erythroviruses, and bovine parvovirus than to adeno-associated viruses. Despite limited sample size and genetic sequences examined in this study, our results underline the prevalence of ChpPV in Korea and emphasize the need of close surveillance of parvoviruses in wild animals.

Complete Genome Sequence of Erwinia amylovora Strain TS3128, a Korean Strain Isolated in an Asian Pear Orchard in 2015

Erwinia amylovora causes fire blight, a devastating disease of apples and pears. Here, we report the complete genome sequence and annotation of E. amylovora strain TS3128, which was isolated from Anseong, South Korea, where fire blight first occurred in 2015, using the PacBio RS II system.

Pseudoaliinostoc sejongens gen. & sp. nov. (Nostocales, Cyanobacteria) from floodplain soil of the Geum River in Korea based on polyphasic approach

Three strains of Nostoc-related morphotypes isolated from Geum River, Korea. They were studied based on a polyphasic approach using morphology, ecological and molecular data. Phylogenetic analysis of 16S rRNA gene revealed that the selected eight genera were clearly separated into each taxonomic group, and in them, Korean strains formed a clade with Aliinostoc spp. The Aliinostoc sensu lato were monophyletic but divided two distinct lineages with high genetic distance between them (4.2% p-distance between clades vs. 1.8% within clades). In accordance with the statistical analysis, the Korean strain-belonging clade was significantly divergent to segregate from other Aliinostoc clades compared to those of the relative genera (2.8% p-distance between sister-genera vs. 0.9% within the same genus). In addition, the ITS rDNA sequence of the Korean strains showed unique characteristics in terms of nucleotide compositions and length in comparison to that of the Aliinostoc, including their secondary structures of D1–D1ʹ and Box-B. These results supported the establishment of a new genus, proposing Pseudoaliinostoc gen. nov. with a description of P. sejongens sp. nov. for the Korean strains. Likewise, three previously described Aliinostoc species were proposed to be transferred to P. soli comb. nov., P. tiwarii comb. nov., and P. constrictum comb. nov.

Molecular Characterization and Phylogenetic Analysis of Orf Virus Isolated From Goats in Sokoto Metropolis, Nigeria

Aim: Despite the endemic nature of contagious ecthyma in Nigeria, there is limited report on the molecular characterization of the isolates responsible for disease outbreaks. The aim of this study was to molecularly characterize ORFV isolated from clinical infections in goats in Sokoto metropolis. Materials and Methods: Seronegative embryonated chicken eggs were used to isolate ORFV via the chorio allantoic membrane (CAM) route according to the established protocol. Viral DNA was extracted from infected CAM and the full coding region of B2L gene was amplified by PCR and subsequently sequenced by Sanger’s method. The nucleotide sequence results were blasted for identification and phylogenetically analyzed using MEGA and Bioedit softwares. Results and Discussion: The results showed that B2L gene sequences of the ORFV UDUS/01/19/More strain showed slight variability (96- 98.7%) with the reference sequences. Our isolate clustered within the same clade with Korean strain signifying a close genetic relationship. Unique amino acid substitutions were noted in our isolate when compared with other references. This is arguably the first genetic characterisation of B2L gene of ORFV circulating in Nigeria. Conclusion: Our study has provided in sight into the genetic diversity of ORFV in the study area. This is crucial for the design of effective vaccines against the disease which are currently lacking in the country.

Genetic diversity and evolutionary history of Korean isolates of severe fever with thrombocytopenia syndrome virus from 2013–2016

Severe fever with thrombocytopenia syndrome (SFTS) is caused by SFTS virus (SFTSV). Although SFTS originated in China, it is an emerging infectious disease with prevalence confirmed in Japan, Korea, and Vietnam. The full-length genomes of 51 Korean SFTSV isolates from 2013 to 2016 were sequenced, and the sequences were deposited into a public database (GenBank) and analyzed to elucidate the phylogeny and evolution of the virus. Although most of the Korean SFTSV isolates were closely related to previously reported Japanese isolates, some were closely related to previously reported Chinese isolates. We identified one Korean strain that appears to have resulted from multiple inter-lineage reassortments. Several nucleotide and amino acid variations specific to the Korean isolates were identified. Future studies should focus on how these variations affect virus pathogenicity and evolution.