We aimed to determine the effects of Lactobacillus strains against rotaviral infections. Rotaviruses are the major causative agent of acute gastroenteritis in infants and children worldwide. However, to date, no specific antiviral drugs for the treatment of rotavirus infection have been developed. We identified 263 Lactobacillus strains from 35 samples of the traditional Korean fermented vegetable food kimchi. Among them, Lactobacillus plantarum LRCC5310, more specifically the exopolysaccharides produced by these cells, were shown to have an antiviral effect against human rotavirus Wa strain in vitro. In vivo, the oral administration of exopolysaccharides for 2 d before and 5 d after mouse infection with the murine rotavirus epidemic diarrhea of infant mice strain led to a decrease in the duration of diarrhea and viral shedding and prevented the destruction of enteric epithelium integrity in the infected mice. We demonstrated here that the exopolysaccharides extracted from L. plantarum LRCC5310 can be used for the effective control of rotavirus infection.

Of 1,050 fecal specimens collected from January 2013 to August 2015 from children with acute gastroenteritis, 149 (14.2%) were found to be positive for norovirus. Norovirus GII was the most predominant genogroup (98.65%; 147 of 149). The genotypes detected in this study were GI (2; 1.3%), GII.Pe-GII.4 (109; 73.1%), GII.P17-GII.17 (16; 10.7%), GII.P12-GII.3 (8; 5.4%), GII.P12-GII.12 (8; 5.4%), GII.P4-GII.4 (5; 3.4%), and the recombinant GII.Pe-GII.17 (1; 0.7%). Of these, the novel GII.17 strain was the second most predominant, and the number of affected children appeared to continuously increase over time (2013 [2; 4.4%], 2014 [4; 9.3%], and 2015 [10; 16.4%]). Phylogenetic analysis of the full genome and ORF1, ORF2, and ORF3 nucleotide sequences showed that GII.17 was grouped in cluster III with other strains isolated from 2013 to 2015 and had a different evolutionary history from strains collected in 1978 to 2002 and 2005 to 2009 formed clusters I and II. However, the phylogenetic trees also showed that cluster III was divided into subclusters IIIa (CAU-55 and CAU-85) and IIIb (Kawasaki 2014) (CAU-193, CAU-265, CAU-267, CAU-283, and CAU-289). Comparative analysis of the VP1 capsid protein using 15 complete amino acid sequences from noroviruses isolated from 1978 to 2015 showed 99 amino acid changes. These results could be helpful for epidemiological studies to understand circulating norovirus genotypes in population.

After the introduction of two global rotavirus vaccines, RotaTeq in 2007 and Rotarix in 2008 in South Korea, G1[P8] rotavirus was the major rotavirus genotype in the country until 2012. However, in this study, an emergence of G2P[4] as the dominant genotype during the 2013 to 2015 season has been reported. Genetic analysis revealed that these viruses had typical DS-1-like genotype constellation and showed evidence of re-assortment in one or more genome segments, including the incorporation of NSP4 genes from strains B-47/2008 from a cow and R4/Haryana/2007 from a buffalo in India, and the VP1 and VP3 genes from strain GO34/1999 from a goat in Bangladesh. Compared to the G2 RotaTeq vaccine strain, 17–24 amino acid changes, specifically A87T, D96N, S213D, and S242N substitutions in G2 epitopes, were observed. These results suggest that multiple interspecies re-assortment events might have contributed to the emergence of G2P[4] rotaviruses in the post-vaccination era in South Korea.

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H5N1 highly pathogenic avian influenza (HPAI) viruses are considered a threat to national animal industries, causing production losses and high mortality in domestic poultry. In recent years, quail has become a popular terrestrial poultry species raised for production of meat and eggs in Asia. In this study, to better understand the roles of quail in H5N1 viral evolution, two H5N1-positive samples, designated A/quail/Vietnam/CVVI-49/2010 (CVVI-49/2010) and A/quail/Vietnam/CVVI-50/2014 (CVVI-50/2014), were isolated from quail during H5N1 outbreaks in Vietnam, and their whole genome were analyzed. The phylogenetic analysis reveals new evolutionary variation in the worldwide H5N1 viruses. The quail HA genes were clustered into clades 1.1.1 (CVVI-49/2010) and clade 2.3.2.1c (CVVI-50/2014), which may have evolved from viruses circulating from chickens and/or ducks in Cambodia, mainland of China, Taiwan, Indonesia, and South Korea in recent years. Interestingly, the M2 gene of the CVVI-49/2010 strain contained amino acid substitutions at position 26L-I and 31S-N that are related to amantadine-resistance. In particular, the CVVI-50/2014 strain revealed evidence of multiple intersubtype reassortment events between virus clades 2.3.2.1c, 2.3.2.1b, and 2.3.2.1a. Data from this study supports the possible role of quail as an important intermediate host in avian influenza virus evolution. Therefore, additional surveillance is needed to monitor these HPAI viruses both serologically and virologically in quail.

Lactococcus garvieae, the pathogenic species in the genus Lactococcus, is recognized as an emerging pathogen in fish, animals, and humans. Despite the widespread distribution and emerging clinical significance of L. garvieae, little is known about the genomic content of this microorganism. Suppression subtractive hybridization was performed to identify the genomic differences between L. garvieae and Lactococcus lactis ssp. lactis, its closest phylogenetic neighbor, and the type species of the genus Lactococcus. Twenty-seven clones were specific to L. garvieae and were highly different from Lactococcus lactis in their nucleotide and protein sequences. Lactococcus garvieae primer sets were subsequently designed for two of these clones corresponding to a pyrH gene and a novel DNA signature for application in the specific detection of L. garvieae. The primer specificities were evaluated relative to three previously described 16S rRNA gene-targeted methods using 32 Lactococcus and closely related strains. Both newly designed primer sets were highly specific to L. garvieae and performed better than did the existing primers. Our findings may be useful for developing more stable and accurate tools for the discrimination of L. garvieae from other closely related species.

Lactococcus garvieae is an important foodborne pathogen causing lactococcosis associated with hemorrhagic septicemia in fish worldwide. A real-time quantitative polymerase chain reaction (qPCR) protocol targeting the 16S-23S rRNA intergenic spacer (ITS) region was developed for the detection and enum-eration of L. garvieae. The specificity was evaluated using genomic DNAs extracted from 66 cocci strains. Fourteen L. garvieae strains tested were positive, whereas 52 other strains including Lactococcus lactis ssp. lactis, Lactococcus lactis ssp. hordniae and Lactococcus lactis ssp. cremoris did not show a specific signal. The minimal limit of detection was 2.63 fg of purified genomic DNA, equivalent to 1 genome of L. garvieae. The optimized protocol was applied for the survey of L. garvieae in naturally contaminated fish samples. Our results suggest that the qPCR protocol using ITS is a sensitive and efficient tool for the rapid detection and enumeration of L. garvieae in fish and fish-containing foods.