African swine fever is one of the most dangerous diseases of swine. We confirmed the 2019 outbreak in Vietnam by real-time reverse transcription PCR. The causative strain belonged to p72 genotype II and was 100% identical with viruses isolated in China (2018) and Georgia (2007). International prevention and control collaboration is needed.

Six new species of Fusarium associated with soil and plant hosts from ecosystems of minimal anthropogenic disturbance in Australia are described. Fusarium coicis from Coix gasteenii, F. goolgardi from Xanthorrhoea glauca, F. mundagurra from soil and Mangifera indica, F. newnesense from soil, F. tjaetaba from Sorghum interjectum and F. tjaynera from soil, Triodia microstachya, Sorghum interjectum and Sorghum intrans. Morphology and phylogenetic analysis of EF-1α, RPB1 and RPB2 sequence data were used to delineate species boundaries. The new species were phylogenetically distributed in the Fusarium sambucinum, F. fujikuroi, and F. chlamydosporum species complexes, and two novel species complexes. These six new species have particular phylogeographic significance as not only do they provide further insight into the geographic patterns of Fusarium evolution but also challenge current phylogeographic hypotheses.

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.

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BackgroundFoot-and-mouth disease virus (FMDV) is one of the highest risk factors that affects the animal industry of the country. The virus causes production loss and high ratio mortality in young cloven-hoofed animals in Vietnam. The VP1 coding gene of 80 FMDV samples (66 samples of the serotype O and 14 samples of the serotype A) collected from endemic outbreaks during 2006–2014 were analyzed to investigate their phylogeny and genetic relationship with other available FMDVs globally.ResultsPhylogenetic analysis indicated that the serotype O strains were clustered into two distinct viral topotypes (the SEA and ME-SA), while the serotype A strains were all clustered into the genotype IX. Among the study strains, the amino acid sequence identities were shared at a level of 90.1–100, 92.9–100, and 92.8–100% for the topotypes SEA, ME-SA, and genotype IX, respectively. Substitutions leading to changes in the amino acid sequence, which are critical for the VP1 antigenic sites were also identified. Our results showed that the studied strains are most closely related to the recent FMDV isolates from Southeast Asian countries (Myanmar, Thailand, Cambodia, Malaysia, and Laos), but are distinct from the earlier FMDV isolates within the genotypes.ConclusionsThis study provides important evidence of recent movement of FMDVs serotype O and A into Vietnam within the last decade and their genetic accumulation to be closely related to strains causing FMD in surrounding countries.Electronic supplementary materialThe online version of this article (doi:10.1186/s12917-016-0896-0) contains supplementary material, which is available to authorized users.

BackgroundPorcine respiratory and reproductive syndrome (PRRS) virus is one of the most economically significant pathogens in the Vietnamese swine industry. ORF5, which participates in many functional processes, including virion assembly, entry of the virus into the host cell, and viral adaptation to the host immune response, has been widely used in molecular evolution and phylogeny studies. Knowing of molecular evolution of PRRSV fields strains might contribute to PRRS control in Vietnam.ResultsThe results showed that phylogenetic analysis indicated that all strains belonged to sub-lineages 8.7 and 5.1. The nucleotide and amino acid identities between strains were 84.5–100% and 82–100%, respectively. Furthermore, the results revealed differences in nucleotide and amino acid identities between the 2 sub-lineage groups. N-glycosylation prediction identified 7 potential N-glycosylation sites and 11 glycotypes. Analyses of the GP5 sequences, revealed 7 sites under positive selective pressure and 25 under negative selective pressure.ConclusionsPhylogenetic analysis based on ORF5 sequence indicated the diversity of PRRSV in Vietnam. Furthermore, the variance of N-glycosylation sites and position under selective pressure were demonstrated. This study expands existing knowledge on the genetic diversity and evolution of PRRSV in Vietnam and assists the effective strategies for PRRS vaccine development in Vietnam.Electronic supplementary materialThe online version of this article (doi:10.1186/s12917-016-0885-3) contains supplementary material, which is available to authorized users.

The high antigenic diversity of porcine epidemic diarrhea virus (PEDV) means that porcine epidemic diarrhea (PED) is a challenge for the global pig industry. Understanding the circulation of the virus to determine an optimal vaccine strategy is important in controlling the disease. In this study, we describe the genetic diversity of circulating PEDV based on the full sequences of spike genes of eight positive samples collected in Vietnam since 2018. Additionally, we developed a live attenuated vaccine candidate from the cell-adapted PEDV2 strain, which was continuously passaged until level 103 in VERO-CCL81 cells. PEDV2-p103, which belongs to the emerging non-S INDEL cluster, exhibited low virus shedding, did not induce lesions in the small intestine of challenged piglets, and had a high titer in the VERO-CCL81 cell at 48 h post-infection. These results suggest that the PEDV2-p103 strain could be a potential oral attenuated vaccine, and its immunogenicity and efficacy should be further assessed through in vivo tests.