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Two porcine deltacoronavirus (PDCoV) strains (Binh21 and HaNoi6) were isolated from two pig farms in North Vietnam. Phylogenetic analysis of the complete genomes and the Spike and Membrane genes revealed that the two Vietnam PDCoVs belong to the same lineage as PDCoVs from Thailand and Laos; however, the N genes belonged to the same lineage as PDCoVs from the USA, Korea, China, and Hong Kong. The recombination detection program subsequently identified the major parent (S5011 strain) and minor parent (HKU15-44 strain) of the two Vietnam PDCoV strains (p < 0.01).

Background Porcine epidemic diarrhea (PED) is a highly contagious swine disease caused by the PED virus (PEDV), which is a member of the family Coronaviridae . Since the first outbreaks in Belgium and the United Kingdom were reported in 1971, PED has spread throughout many countries around the world and causing significant economic loss. This study was conducted to investigate the recent distribution of PEDV strains in Vietnam during the 2015–2016 seasons. Methods A total of 30 PED‐specific PCR‐positive intestinal and faecal samples were collected from unvaccinated piglets in Vietnam during the 2015–2016 seasons. The full length of the spike (S) gene of these PEDV strains were analysed to determine their phylogeny and genetic relationship with other available PEDV strains globally. Results Phylogenetic analysis of the complete S gene sequences revealed that the 28 Vietnamese PEDV strains collected in the northern and central regions clustered in the G2 group (both G2a and G2b sub‐groups), while the other 2 PEDV strains (HUA‐PED176 and HUA‐PED254) collected in the southern region were clustered in the G1/G1b group/sub‐group. The nucleotide (nt) and deduced amino acid (aa) analyses based on the complete S gene sequences showed that the Vietnamese PEDV strains were closely related to each other, sharing nt and aa homology of 93.2%–99.9% and 92.6%–99.9%, respectively. The N‐glycosylation patterns and mutations in the antigenic region were observed in Vietnamese PEDV strains. Conclusions This study provides, for the first time, up‐to‐date information on viral circulation and genetic distribution, as well as evidence to assist in the development of effective PEDV vaccines in Vietnam.

Black queen cell virus (BQCV) infection is one of the most common viral infections in honeybees (Apis mellifera). A phylogenetic tree was constructed for 19 partial nucleotide sequences for the capsid region of South Korean BQCV, which were also compared with 10 previously reported BQCV sequences derived from different countries. The Korean BQCV genomes were highly conserved and showed 97-100% identity. They also showed 92-99% similarity with other country genotypes and showed no significant clustering in the phylogenetic tree. In order to investigate this phenomenon in more detail, the complete genome sequence of the Korean BQCV strain was determined and aligned with those from a South African reference strain and European genotypes, Poland4-6 and Hungary10. A phylogenetic tree was then constructed. The Korean BQCV strain showed a high level of similarity (92%) with Hungary10, but low similarity (86%) with the South African reference genotype. Comparison of the Korean and other sequences across different genome regions revealed that the 5'-UTR, the intergenic region, and the capsid regions of the BQCV genome were highly conserved. ORF1 (a non-structural protein coding region) was more variable than ORF2 (a structural protein coding region). The 5'-proximal third of ORF1 was particularly variable and contained several insertions/deletions. This phenomenon may be explained by intra-molecular recombination between the Korean and other BQCV genotypes; this appeared to have happened more with the South African reference strain than with the European genotypes.

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