This study analyses the evolutionary relatedness of 16 Japanese encephalitis virus (JEV) isolates (nine from Vietnam and seven from Japan) to previously published JEV strains using E gene sequence data. Vietnamese and Japanese strains isolated between 1986 and 1990 were found to cluster in genotype 3. However, more recent Vietnamese and Japanese strains isolated between 1995 and 2002 grouped within genotype 1, now a dominant though previously unreported genotype in Vietnam. In addition, in this study, strains isolated between 1995 and 2002 were more closely related to those isolated in the 1990s than to the older genotype 1 strains. Recently, the introduction of JEV genotype 1 into Japan and Korea has also been reported. Hence this genotype shift phenomenon may be occurring throughout all East Asia. Further studies on JEV ecology are needed to clarify the mechanism of JEV genotype 1 spread to new territories.

Understanding global influenza migration and persistence is crucial for vaccine strain selection. Using 240 new human influenza A virus whole genomes collected in Vietnam during 2001–2008, we looked for persistence patterns and migratory connections between Vietnam and other countries. We found that viruses in Vietnam migrate to and from China, Hong Kong, Taiwan, Cambodia, Japan, South Korea, and the United States. We attempted to reduce geographic bias by generating phylogenies subsampled at the year and country levels. However, migration events in these phylogenies were still driven by the presence or absence of sequence data, indicating that an epidemiologic study design that controls for prevalence is required for robust migration analysis. With whole-genome data, most migration events are not detectable from the phylogeny of the hemagglutinin segment alone, although general migratory relationships between Vietnam and other countries are visible in the hemagglutinin phylogeny. It is possible that virus lineages in Vietnam persisted for >1 year.

Mutation and reassortment of highly pathogenic avian influenza A(H5N1) viruses at the animal-human interface remain a major concern for emergence of viruses with pandemic potential. To understand the relationship of H5N1 viruses circulating in poultry and those isolated from humans, comprehensive phylogenetic and molecular analyses of viruses collected from both hosts in Vietnam between 2003 and 2010 were performed. We examined the temporal and spatial distribution of human cases relative to H5N1 poultry outbreaks and characterized the genetic lineages and amino acid substitutions in each gene segment identified in humans relative to closely related viruses from avian hosts. Six hemagglutinin clades and 8 genotypes were identified in humans, all of which were initially identified in poultry. Several amino acid mutations throughout the genomes of viruses isolated from humans were identified, indicating the potential for poultry viruses infecting humans to rapidly acquire molecular markers associated with mammalian adaptation and antiviral resistance.

A cluster of severe acute respiratory syndrome coronavirus 2 infections in Danang, Vietnam, began July 25, 2020, and resulted in 551 confirmed cases and 35 deaths as of February 2021. We analyzed 26 sequences from this cluster and identified a novel shared mutation in nonstructural protein 9, suggesting a single introduction into Vietnam.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing novel coronavirus disease 2019 (COVID-19) appeared in Wuhan, Hubei province, China in late December 2019 and has rapidly spread worldwide. In this study, a total of 267 genomes of SARS CoV-2 viruses collected from 28 Center for Diseases Controls and hospitals in different provinces in Northern and Central Vietnam from January 2020 to April 2021 were sequenced and analyzed their diversity using the iSeq 100 platform. Results showed that most of the virus samples originated from domestic community patients (84.3%). Variable variants of SARS CoV-2 virus were detected within the three pandemic waves. The very first variant of SARS-CoV-2 in Viet Nam in January 2020 was 19B (Nextstrain Clade), 3/8 of the variants were from the international arrival samples group. In the first and second pandemic waves, lineage 20B was the most prevalent and this variant was found in Da Nang, Hai Duong and Thai Binh with a large number of patients. In the third wave of the COVID-19 pandemic, lineage 20I was the most dominant and detected in all provinces where the outbreak occurred. Five COVID-19 clusters caused by SARS-CoV-2 variant 20I were also found during this time.

No abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was appeared in Wuhan, Hubei province, Chinain late December 2019. Rapidly, COVID-19 (disease caused by SARS-CoV-2) then spread rapidly to more than 200countries and regions around the world in April 2020. Since Vietnam is one of the frst countries to detect COVID-19patients, diagnostic methods and outbreak management are essentially needed for the national guidelines. The NationalInstitute of Hygiene and Epidemiology (NIHE) decided to conduct a study by collecting nasal swab from suspectedpeoples. These specimens were screened and inoculated the positive specimens. From January to August 2020, 40 positive specimens of clinical symptoms which Ct < 30 and 27 isolated specimens were sequencing. All the specimens weresequenced the frst time on the Illumina iSeq 100 platform in Vietnam. After 15 operations (12 complete and othersincomplete ones), the entire genome virus of 27 viral strains and 12 clinical specimens were listed. Based on GISAID,these sequences were grouped into three big groups (S, V, G) with dominance of subclade GR (17 isolates and 9 clinicalsamples). Eight isolated sequences were uploaded to Genbank to share data with other researchers in worldwide.

From January to August 2020, Northern Viet Nam faced a COVID-19 outbreak, up to September 2020, there were 1122 confrmed cases of SARS-CoV-2, of which 465 cases were imported from Europe, America and Asia, 657 cases were identifed domestically. A total of 30,686 samples were collected during the SARS-CoV-2 outbreak in Northern Viet Nam and examined by Real-time RT-PCR using primers and probe from Charite - Berlin protocol. This study showed the initial results of SARS-CoV-2 detection and RNA quantitative in positive samples. The positive rate was 0.8%, ranging from 0.4 to 3.5% according to collection sites. Out of 251 positive samples, the mean Ct value was 28 (IQR: 22.3-32; range 14 - 38). The positive samples had a Ct value below 30 was 68.5%, there was no signifcant difference between the Ct value of the group ≤ 30 and > 30. The mean of the RNA copies/µl was 8.4.107, (IQR: 2.29.106 - 1.83.109 RNA copies/µl, range: 1.95.103 – 4.95.1011). In the group of imported COVID-19 cases, the rate of virus at low level was 29%, an average was 56% and at high level was 15%. In the community groups, the viral load data showed that the average rate at low, intermediate and high level were 20%, 63% and 17% respectively. The proportion of high-level viral load may raise an alert to start the quarantine process to reduce the transmission of SARS-CoV-2