Highly pathogenic avian influenza virus H5N1 is endemic in poultry in East and Southeast Asia with disease outbreaks recently spreading to parts of central Asia, Europe and Africa. Continued interspecies transmission to humans has been reported in Vietnam, Thailand, Cambodia, Indonesia and China, causing pandemic concern. Here, we genetically characterize 82 H5N1 viruses isolated from poultry throughout Indonesia and Vietnam and 11 human isolates from southern Vietnam together with sequence data available in public databases to address questions relevant to virus introduction, endemicity and evolution. Phylogenetic analysis shows that all viruses from Indonesia form a distinct sublineage of H5N1 genotype Z viruses suggesting this outbreak likely originated from a single introduction that spread throughout the country during the past two years. Continued virus activities in Indonesia were attributed to transmission via poultry movement within the country rather than through repeated introductions by bird migration. Within Indonesia and Vietnam, H5N1 viruses have evolved over time into geographically distinct groups within each country. Molecular analysis of the H5N1 genotype Z genome shows that only the M2 and PB1-F2 genes were under positive selection, suggesting that these genes might be involved in adaptation of this virus to new hosts following interspecies transmission. At the amino acid level 12 residues were under positive selection in those genotype Z viruses, in the HA and PB1-F2 proteins. Some of these residues were more frequently observed in human isolates than in avian isolates and are related to viral antigenicity and receptor binding. Our study provides insight into the ongoing evolution of H5N1 influenza viruses that are transmitting in diverse avian species and at the interface between avian and human hosts.

Background African swine fever (ASF), caused by the ASF virus (ASFV), was first reported in Vietnam in 2019 and spread rapidly thereafter. Better insights into ASFV characteristics and early detection by surveillance could help control its spread. However, the pathogenicity and methods for early detection of ASFV isolates from Vietnam have not been established. Therefore, we investigated the pathogenicity of ASFV and explored alternative sampling methods for early detection. Results Ten pigs were intramuscularly inoculated with an ASFV strain from Vietnam (titer, 103.5 HAD50/mL), and their temperature, clinical signs, and virus excretion patterns were recorded. In addition, herd and environmental samples were collected daily. The pigs died 5–8 days-post-inoculation (dpi), and the incubation period was 3.7 ± 0.5 dpi. ASFV genome was first detected in the blood (2.2 ± 0.8) and then in rectal (3.1 ± 0.7), nasal (3.2 ± 0.4), and oral (3.6 ± 0.7 dpi) swab samples. ASFV was detected in oral fluid samples collected using a chewed rope from 3 dpi. The liver showed the highest viral loads, and ear tissue also exhibited high viral loads among 11 tissues obtained from dead pigs. Overall, ASFV from Vietnam was classified as peracute to acute form. The rope-based oral fluid collection method could be useful for early ASFV detection and allows successful ASF surveillance in large pig farms. Furthermore, ear tissue samples might be a simple alternative specimen for diagnosing ASF infection in dead pigs. Conclusions Our data provide valuable insights into the characteristics of a typical ASFV strain isolated in Vietnam and suggest an alternative, non-invasive specimen collection strategy for early detection.

In Vietnam, serological post H5N1 vaccination surveillance using the HI test is applied to 28 assess the efficiency of the vaccination in addition to virological monitoring. In this paper we 29 report on the evaluations of the performances of the haemagglutination inhibition (HI) test 30 and of a H5-ELISA, using chicken and duck field samples. The evaluations were conducted 31 by comparison with a pseudotyped-based virus neutralization test (H5pp VNT) performed in a 32 reference laboratory and considered as a "gold standard" and also by using methods 33 developed for imperfect reference test. Their global accuracy and best cut-offs were also 34 estimated. Results from the HI test for several haemagglutinin subtypes and from a 35 commercial type A influenza competition ELISA were also compared. 36The results showed that performance of the HI test was very good in comparison with the 37 H5pp VNT. Data also clearly supported the cut-off of ≥4log 2 used for the HI test for chickens 38 but, a 3log 2 positivity cut-off would be more appropriate for ducks. When compared with the 39 VNT, the H5-ELISA showed poor specificity when using the positivity cut-off specified by 40 the manufacturer but could be used as a screening test if confirmed by the HI test or the 41H5ppVNT which presents some interests for large scale testing (no need for biosafety level 3 42 conditions and high performance). 43 A general and highly sensitive pre-screening can also be achieved using the detection of NP-44 specific antibodies with a competition ELISA. This appears of little interest in a context of 45 high subtypes diversity where only a subtype is targeted for surveillance and control.

Background Hepatitis E virus (HEV) is a zoonotic disease and has been reported around the world. The main objective of this study was to evaluate the sero-prevalence and phylogenetic analysis of HEV in Vietnam. Pig blood and fecal pooled samples were collected to assess the prevalence of HEV. We assessed the true prevalence (TP) of HEV from apparent prevalence (AP) by taking into account the sensitivity and specificity of diagnostic tests using a Bayesian approach. For phylogenetic analysis, the data compared with worldwide HEV reference strains including all eight genotypes (G1-G8) which were identified in previous study. Results A total of 475 sera and 250 fecal pooled samples were collected at slaughterhouses and pig farms from five provinces, in Viet Nam. Overall, the sero-AP of HEV was 58.53% (95% confidence interval: 53.95–62.70) while the sero-TP was slightly higher (65.43, 95% credible interval: 47.19–84.70). In terms of pooled samples, overall, the RNA-AP was 6.80% (95% confidence interval: 4.01–10.66). One strain in Hanoi, two strains in Dak Lak, seven strains in An Giang, four strains in Son La and two strains in Nghe An were isolated. The phylogenetic tree demonstrated that 19 Vietnamese strains were clustered into HEV 3 and 4. Conclusions This study provided evidence that HEV is circulating in domestic pigs in Vietnam. From a public health perspective, it is very important to raise public awareness for high-risk groups (e.g. slaughterhouse workers, pig traders, farmers and market sellers) who have more opportunities to come in contact with pig and contaminated meats.

Competing interestsNo potential conflict of interest relevant to this article was reported. Funding sourcesState funding sources (grants, funding sources, equipment, and supplies). Include name and number of grant if available.