Vietnamese Strains Research Articles

African swine fever virus vaccine candidate ASFV-G-ΔI177L efficiently protects European and native pig breeds against circulating Vietnamese field strain.

The recent spread of African swine fever (ASF) in the People's Republic of China and neighbouring countries in Asia has had significant economic consequences with an estimated direct cost of $55-$130 billion. This pandemic, originally detected in Republic of Georgia in 2007, has devastated the swine industry in large geographical areas of Southeast Asia with 14 countries reporting ASF outbreaks since the first documented case was confirmed in the city of Shenyang, Liaoning Province, China, on 3 August 2018. In the absence of any available vaccines, the control of ASF relies on the detection and culling of infected animals. The United States Department of Agriculture recently developed a recombinant experimental vaccine candidate, ASFV-G-ΔI177L, by deleting the I177L gene from the genome of the highly virulent pandemic ASFV strain Georgia, which efficaciouly protects pigs from the parental virus. Here, the initial studies were extended demonstrating that ASFV-G-ΔI177L is able to protect pigs against the virulent ASFV isolate currently circulating and producing disease in Vietnam with similar efficacy as reported against the Georgia strain. Comparative studies performed using a large number of pigs of European and Vietnamese origin demonstrated that a minimum protective dose of 102 HAD50 of ASFV-G-ΔI177L equally protects animals of both breeds. In concurrence with those results, the onset of immunity in these animal breed showed appearance of protection in approximately one-third of the animals by the second week post vaccination, with full protection achieved by the fourth week post vaccination. Therefore, results presented here demonstrated that ASFV-G-ΔI177L is able to induce protection against virulent Vietnameese ASFV field strains and is effective in protecting local breeds of pigs as efficiently as previously shown for European cross-bred pigs. To our knowledge, this is the first report showing the efficacy of a Georgia 2007 based vaccine candidate in Asian breed of pigs or challenged with an Asian ASFV strain.

Improved bacterial leaf blight disease resistance in the major elite Vietnamese rice cultivar TBR225 via editing of the OsSWEET14 promoter.

TBR225 is one of the most popular commercial rice varieties in Northern Vietnam. However, this variety is highly susceptible to bacterial leaf blight (BLB), a disease caused by Xanthomonas oryzae pv. oryzae (Xoo) which can lead to important yield losses. OsSWEET14 belongs to the SWEET gene family that encodes sugar transporters. Together with other Clade III members, it behaves as a susceptibility (S) gene whose induction by Asian Xoo Transcription-Activator-Like Effectors (TALEs) is absolutely necessary for disease. In this study, we sought to introduce BLB resistance in the TBR225 elite variety. First, two Vietnamese Xoo strains were shown to up-regulate OsSWEET14 upon TBR225 infection. To investigate if this induction is connected with disease susceptibility, nine TBR225 mutant lines with mutations in the AvrXa7, PthXo3 or TalF TALEs DNA target sequences of the OsSWEET14 promoter were obtained using the CRISPR/Cas9 editing system. Genotyping analysis of T0 and T1 individuals showed that mutations were stably inherited. None of the examined agronomic traits of three transgene-free T2 edited lines were significantly different from those of wild-type TBR225. Importantly, one of these T2 lines, harboring the largest homozygous 6-bp deletion, displayed decreased OsSWEET14 expression as well as a significantly reduced susceptibility to a Vietnamese Xoo strains and complete resistance to another one. Our findings indicate that CRISPR/Cas9 editing conferred an improved BLB resistance to a Vietnamese commercial elite rice variety.

The first outbreak of dengue fever and molecular tracing in Puyang, 2019

Objective: This study retrospectively analyzed an outbreak of dengue fever in Puyang of Henan province in 2019, in order to find the sources of infection. Methods: Dengue virus IgM/IgG and NS1 antigen were tested by colloidal gold method. E gene was amplified by PCR. MegaX was used for sequences alignment to construct evolutionary distance trees. Results: After clinical and laboratory confirmation, there were 81 cases of dengue fever, 17 of which were imported case who were local farmers and worked in Combadia and Thailand, and 64 of which were indigenous cases. The E gene alignment results showed that the pathogen of this epidemic was Vietnamese 1 and highly homologous with the Vietnamese strain. After the local outbreak, dengue virus E gene developed a nucleotide site mutation which can be steadily transmission. Conclusion: The dengue fever outbreak in Puyang was a local outbreak caused by dengue virus type 1, which was associated with imported cases. Gene sequencing showed that the imported pathogen had a relatively stable and transmissible nucleotide mutation after the local epidemic.

Coxsackievirus A16 in Southern Vietnam.

Background: Hand, Foot and Mouth Disease (HFMD) is a major public health concern in the Asia-Pacific region. Most recent HFMD outbreaks have been caused by enterovirus A71 (EV-A71), coxsackievirus A16 (CVA16), CVA10, and CVA6. There has been no report regarding the epidemiology and genetic diversity of CVA16 in Vietnam. Such knowledge is critical to inform the development of intervention strategies.Materials and Methods: From 2011 to 2017, clinical samples were collected from in- and outpatients enrolled in a HFMD research program conducted at three referral hospitals in Ho Chi Minh City (HCMC), Vietnam. Throat or rectal swabs positive for CVA16 with sufficient viral load were selected for whole genome sequencing and evolutionary analysis.Results: Throughout the study period, 320 CVA16 positive samples were collected from 2808 HFMD patients (11.4%). 59.4% of patients were male. The median age was 20.8 months (IQR, 14.96–31.41). Patients resided in HCMC (55.3%), Mekong Delta (22.2%), and South East Vietnam (22.5%). 10% of CVA16 infected patients had moderately severe or severe HFMD. CVA16 positive samples from 153 patients were selected for whole genome sequencing, and 66 complete genomes were obtained. Phylogenetic analysis demonstrated that Vietnamese CVA16 strains belong to a single genogroup B1a that clusters together with isolates from China, Japan, Thailand, Malaysia, France and Australia. The CVA16 strains of the present study were circulating in Vietnam some 4 years prior to its detection in HFMD cases.Conclusion: We report for the first time on the molecular epidemiology of CVA16 in Vietnam. Unlike EV-A71, which showed frequent replacement between subgenogroups B5 and C4 every 2–3 years in Vietnam, CVA16 displays a less pronounced genetic alternation with only subgenogroup B1a circulating in Vietnam since 2011. Our collective findings emphasize the importance of active surveillance for viral circulation in HFMD endemic countries, critical to informing outbreak response and vaccine development.

Identification and whole-genome characterization of a novel Porcine Circovirus 3 subtype b strain from swine populations in Vietnam.

Porcine circovirus 3 (PCV3) is a novel circovirus detected in pigs suffering from porcine dermatitis and nephropathy syndrome (PDNS), reproductive failure, and multisystemic infection. In this study, we identified PCV3 infection in aborted fetuses and reported the full-length genome sequence of a PCV3 strain identified from southern Vietnam. The complete genome of this PCV3 strain is 2000 nucleotides in length. We found that it shares 98.5-99.25% sequence identity with other reference sequences and that it clusters with the PCV3b subtype. Several specific mutated sites were found to be unique to this Vietnamese PCV3b strain, including I14M in the Rep protein and K139R, I150F, and P169T in the Cap protein. The sequence data that have been made publically available as part of this study will help investigators to better understand the molecular characteristics, genetic diversity, and evolutionary history of PCV3. Careful and in-depth investigations into the epidemiology, pathogenicity, and the evolution of this novel virus is a matter of urgent economic and agricultural interest in Vietnam.

WGS-Based Analysis of Carbapenem-Resistant Acinetobacter baumannii in Vietnam and Molecular Characterization of Antimicrobial Determinants and MLST in Southeast Asia.

Carbapenem-resistant Acinetobacter baumannii (A. baumannii, CRAb) is an emerging global threat for healthcare systems, particularly in Southeast Asia. Next-generation sequencing (NGS) technology was employed to map genes associated with antimicrobial resistance (AMR) and to identify multilocus sequence types (MLST). Eleven strains isolated from humans in Vietnam were sequenced, and their AMR genes and MLST were compared to published genomes of strains originating from Southeast Asia, i.e., Thailand (n = 49), Myanmar (n = 38), Malaysia (n = 11), Singapore (n = 4) and Taiwan (n = 1). Ten out of eleven Vietnamese strains were CRAb and were susceptible only to colistin. All strains harbored ant(3”)-IIa, armA, aph(6)-Id and aph(3”) genes conferring resistance to aminoglycosides, and blaOXA-51 variants and blaADC-25 conferring resistance to ß-lactams. More than half of the strains harbored genes that confer resistance to tetracyclines, sulfonamides and macrolides. The strains showed high diversity, where six were assigned to sequence type (ST)/2, and two were allocated to two new STs (ST/1411-1412). MLST analyses of 108 strains from Southeast Asia identified 19 sequence types (ST), and ST/2 was the most prevalent found in 62 strains. A broad range of AMR genes was identified mediating resistance to ß-lactams, including cephalosporins and carbapenems (e.g., blaOXA-51-like, blaOXA-23, blaADC-25, blaADC-73, blaTEM-1, blaNDM-1), aminoglycosides (e.g., ant(3”)-IIa, aph(3”)-Ib, aph(6)-Id, armA and aph(3’)-Ia), phenicoles (e.g., catB8), tetracyclines (e.g., tet.B and tet.39), sulfonamides (e.g., sul.1 and sul.2), macrolides and lincosamide (e.g., mph.E, msr.E and abaF). MLST and core genome MLST (cgMLST) showed an extreme diversity among the strains. Several strains isolated from different countries clustered together by cgMLST; however, different clusters shared the same ST. Developing an action plan on AMR, increasing awareness and prohibiting the selling of antibiotics without prescription must be mandatory for this region. Such efforts are critical for enforcing targeted policies on the rational use of carbapenem compounds and controlling AMR dissemination and emergence in general.

Molecular phylogenetics of a recently isolated goat pox virus from Vietnam

BackgroundAfter a decade of silence, an outbreak of the contagious and Asian endemic disease, goat pox re-emerged in North Vietnam affecting more than 1800 heads with a mortality rate of 6.5%. The inevitable impact of goat pox on hide quality, breeding, chevon and milk production has resulted in a significant economic losses to the developing goat industry of Vietnam. In the act of establishing an effective control of this devastating disease, tracing the source of re-emergence via a phylogenetic study was carried out to reveal their genetic relatedness. Either skin scab or papule from the six affected provinces were collected, cultured into Vero cells followed by restricted enzyme digestion of targeted P32 gene DNA encoding. The P32 gene was then cloned and transformed into E.coli competent cells for further sequencing.ResultsThe isolated sequence is deposited into GenBank under Accession No. MN317561/VNUAGTP1. The phylogenetic tree revealed high similarity of nucleotide and amino acid sequences to references goat pox strains accounting for 99.6 and 99.3, respectively. The Vietnamese strain is clustered together with currently circulating goat pox virus in China, India and Pakistan which suggested the origin of South China.ConclusionsThis Vietnam isolate is clustered together with other Asian goat pox strains indicating the dissemination of a common goat pox virus within this continent.

First investigation of the prevalence of parvoviruses in slaughterhouse pigs and genomic characterization of ungulate copiparvovirus 2 in Vietnam.

Ungulate protoparvovirus 1, also known as porcine parvovirus 1 (PPV1), is considered to be one of the major causes of reproductive failure in pig breeding herds. Other parvoviruses have also been identified in pigs, including ungulate tetraparvovirus 3, or PPV2, ungulate tetraparvovirus 2, or PPV3, and ungulate copiparvovirus 2, or PPV4, but their significance for pigs is unknown. In the present study, the prevalence of PPV1-4 was investigated using a total of 231 lung and serum samples collected from slaughterhouses in 13 provinces throughout Vietnam. The overall prevalence was 54.5% (126/231) for PPV1, 28.0% (65/231) for PPV2, 17.7% (41/231) for PPV3, and 7.8% (18/231) for PPV4. While PPV1 and PPV2 were found in 11 provinces, PPV4 was detected in only three provinces. Co-circulation of PPV1, PPV2 and PPV3 was frequently observed, with PPV1/PPV2 coinfection predominating, with 20.8% (48/231). All four PPVs were detected together in only one sample from Thua Thien Hue. Three nearly complete PPV4 genome sequences of 5,453 nt were determined and deposited in the GenBank database. Alignment and comparison of the three genome sequences showed 99.5-99.6% nucleotide sequence identity, and the deduced amino acid sequences of open reading frames 1-3 were 99.6-99.9% identical to each other, 98.9-99.3% identical to those of other Vietnamese strains and 99.4-99.7% identical to those of Chinese strains). Phylogenetic analysis further confirmed a close relationship between Vietnamese and Chinese PPV4 strains. These results are the first to report the prevalence of PPV1, PPV2, PPV3, and PPV4 and nearly complete genomic sequences of PPV4 in pigs from slaughterhouses in Vietnam.

Molecular characterization of bovine foamy virus and its association with bovine leukemia virus infection in Vietnamese cattle.

The detection of bovine foamy virus (BFV) in Vietnamese cattle was performed using conventional PCR targeting pol and gag genes. Out of 243 tested samples, ten (4.1%) and eight (3.3%) samples were positive for BFV gag and pol DNA, respectively. The prevalence of bovine leukemia virus (BLV) estimated by detection of proviral DNA using nested PCR targeting env gene was 26.7% (65/243). The results of nucleotide sequence alignment and the phylogenetic analysis suggested that Vietnamese BFV strains showed high homology to isolates belonging to either European or non-European clades. There was no significant correlation between BLV and BFV. This study provides information regarding BFV infection and confirms the existence of two BFV clades among Vietnamese cattle for the first time.

Coxsackieviruses A6 and A16 associated with hand, foot, and mouth disease in Vietnam, 2008–2017: Essential information for rational vaccine design

Development of multivalent hand, foot, and mouth disease (HFMD) vaccines against enterovirus A71 (EV-A71) and several non-EV-A71 enteroviruses is needed for this life-threatening disease with a huge economic burden in Asia-Pacific countries. Comprehensive studies on the molecular epidemiology and genetic and antigenic characterization of major causative enteroviruses will provide information for rational vaccine design. Compared with molecular studies on EV-A71, that for non-EV-A71 enteroviruses remain few and limited in Vietnam. Therefore, we conducted a 10-year study on the circulation and genetic characterization of coxsackievirus A16 (CV-A16) and CV-A6 isolated from patients with HFMD in Northern Vietnam between 2008 and 2017. Enteroviruses were detected in 2228 of 3212 enrolled patients. Of the 42 serotypes assigned, 28.4% and 22.4% accounted for CV-A6 and CV-A16, being the second and the third dominant serotypes after EV-A71 (31.7%), respectively. The circulation of CV-A16 and CV-A6 showed a wide geographic distribution and distinct periodicity. Phylogenetic analyses revealed that the majority of Vietnamese CV-A6 and CV-A16 strains were located within the largest sub-genotypes or sub-genogroups. These comprised strains isolated from patients with HFMD worldwide during the past decade and the Vietnamese strains have been evolving in a manner similar to the strains circulating worldwide. Amino acid sequences of the putative functional loops on VP1 and other VPs among Vietnamese CV-A6 and CV-A16 isolates were highly conserved. Moreover, the functional loop patterns of VP1 were similar to the dominant patterns found worldwide, except for the T164K substitution on the EF loop in Vietnamese CV-A16. The findings suggest that the development of a universal HFMD vaccine, at least in Vietnam, must target CV-A6 and CV-A16 as two of the three major HFMD-causing serotypes. Vietnamese isolates or their genome sequences can be considered for rational vaccine design.

A Recombinant Lipl21 Protein Vaccine from Five Leptospira interrogans Strains Against

Leptospirosis is an emerging zoonotic disease with globally public health problem in both animals and humans. Currently, there is no effective vaccine to prevent most of the circulating serovars in Vietnam because ofthe diversity of among leptospiral serovars. In this study, a highly immunogenic epitopes from LipL21 were designed using an in-silico approach. The recombinant protein was constructed from conserved sequences of five Leptospira interrogans isolated Vietnamese strains. Immunization of mice with multi-epitope protein resulted in the antibodies production, as evidenced by MAT. Recombinant proteins can also significantly reduce Leptospire severity in animal hosts. In conclusion, rLipL21 can act as a vaccine capable of effectively and safely against the infection of five strains of Leptospira interrogans in Vietnam

Genetic evolution and epidemiological analysis of Seneca Valley virus (SVV) in China

Seneca Valley virus (SVV) is a novel Picornaviridae that is closely associated with porcine idiopathic vesicular disease (PIVD). Here, a novel SVV strain (CH-GX-01-2019) was detected and isolated from swine in Guangxi Province, China. The complete genomic sequence of CH-GX-01-2019 exhibited 93.3–98.9 % identify with other SVV isolates at the nucleotide level. CH-GX-01-2019 showed the highest level of similarity (98.9 %) with Vietnamese strains. And CH-GX-01-2019 exhibited two consecutive amino acid mutations in VP1 gene. Phylogenetic analysis based on the complete genome and the VP1 gene showed that Chinese SVV isolates can be divided into three clusters. We analyzed the geographical distributions of SVV strains in China and found that the epidemiology of SVV in China is complicated; most strains are distributed predominantly in south and central China. Between 2015 and 2019, the dominant epidemic SVV isolates in China have changed from clusters 1 and 3 to cluster 2. CH-GX-01-2019 (cluster 3) is a recombinant strain from Colombia-2016 (cluster 2) and HB-CH-2016 (cluster 1). Our findings will enhance our understanding of the prevalence and genetic variation of SVV in the swine herds of China and provide important insights into the molecular epidemiology of SVV.

Genome analysis and phylogenetic characterization of two deformed wing virus strains from Apis cerana in Vietnam.

BackgroundDeformed wing virus (DWV) is a virulent virus that causes honeybee disease. DWV can exist as a latent infection in honeybees, outbreak into epidemics, and cause serious damage to beekeeping cross the world, including Vietnam.MethodsThe two DWV strains circulating in Vietnamese honeybee, Apis cerana, were first isolated from adult honeybees in North Vietnam (DWV-NVN) and South Vietnam (DWV-SVN). Their complete nucleotide sequences were determined, aligned, and compared with other DWV strains.ResultsThe two Vietnamese DWV strains comprised 10,113 bp and contained a large single open reading frame (ORF) of 2,893 amino acids, initiating at nucleotide 1,130 and terminating at nucleotide 9,812. Multiple nucleotide sequence alignment between these two DWV-VN strains and DWV strains in A. mellifera was performed. The DWV-VN strains showed a low genetic identity (from 91.4% to 92.0%) with almost of these strains, but lower identities (89.2% and 89.4%) with UK2 and (89.6%) with the China2 strain. Low identities (91.7% and 91.9%) were also observed between the China3 strain (in A. cerana) and the DWV-VN strains, respectively. The deduced amino acid sequence alignment showed high genetic similarities (97.0%–97.9%) when the USA1, Chile, Italy1, France, UK1, UK2, Japan, Korea2, China1, China2 and China3 strains were compared to the DWV-VN strains. This ratio was 96.7% and 96.8% when the Korea1 strain was compared to the DWV-SVN and DWV-NVN strains, respectively. Numerous amino acid substitutions were identified in the L, VP3, and RdRp sequences. Notably, we observed six substitutions positioned at amino acids 27 (E > I), 98 (S > T), 120 (A > V), 153 (M > T), 170 (D > F), and 174 (Y > F) in the L protein, two amino acid changes at positions 980 (S > A) and 1032 (E > T) in VP3, and one amino acid change at position 2627 (R > C) unique to the DWV-VN strains. Phylogenetic analysis based on complete genome sequences, RdRp sequences and Simplot analysis indicated that there was a significant difference between DWV-VN strains in A. cerana and DWV strains in A. mellifera. The results suggested that the genetic variations of the DWV-VN strains in A. cerana help them to adapt geographical conditions and may lead to change the viral pathogenicity of DWV-VN strains.

Prevalence and phylogenetic analysis of hepatitis E virus in pigs in Vietnam

BackgroundHepatitis 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.ResultsA 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.ConclusionsThis 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.

Molecular and phylogenetic analysis of Vietnamese canine parvovirus 2C originated from dogs reveals a new Asia-IV clade.

Canine parvovirus type 2 (CPV-2) is a small, single-stranded DNA virus causing fatal haemorrhagic enteritis in dogs. Currently, CPV-2 is classified into CPV-2a, CPV-2b and CPV-2c based on genetic variation in the VP2 gene. The CPV-2c variant has become ubiquitous worldwide and gained attention for monitoring parvoviral evolution. In this study, we characterized the full-length genome sequences of CPV-2c strains obtained from 59 dogs in Vietnam. Molecular analysis revealed that Vietnamese CPV-2c shared a common evolutionary pattern with the Asian CPV-2 clade, which is marked by genetic signature patterns in the structural and nonstructural proteins. In addition, these Vietnamese CPV-2c strains exhibited unique Thr112Ile and Ile447Met mutations in the VP1 and VP2 sequence, respectively. Interestingly, phylogenetic analysis indicated that the mutations of amino acid residues in both the structural and nonstructural genes have contributed to the emergence of a new clade, designated here as the Asia-IV clade. The substitution rates, estimated from a dataset containing 199 sequences over the last 42years, confirmed that CPV-2 showed a high rate of nucleotide substitution, at about 2.49×10-4 nucleotide substitutions per site per year (nt/s/y), with VP1/2 and NS1/2 estimates of 3.06×10-4 and 3.16×10-4 nt/s/y, respectively. Even though no evidence of genetic recombination in these Vietnamese CPV-2c strains was established, potential positive selection sites were observed in both the structural and nonstructural genes, suggesting the viral evolutionary process has occurred in both the structural and nonstructural proteins. Genetic and evolutionary analysis of the full-length genome sequence is necessary to gain evolutionary insight of CPV-2.

O/SEA/Mya-98 lineage foot-and-mouth disease virus was responsible for an extensive epidemic that occurred in late 2018 in Vietnam.

Since late 2018, foot-and-mouth disease (FMD) has reemerged and rapidly swept through pig farms in North and Central Vietnam, despite widespread use of commercial FMD vaccines. To investigate the FMD virus (FMDV) strains responsible for the current epidemics, 40 FMDV samples were collected from 17 provinces during November-December 2018, and the VP1 coding genes were sequenced and analyzed. Phylogenetic analysis and sequence comparisons revealed that all of the reemerging Vietnamese FMDVs belonged to the Mya-98 lineage of the O/Southeast Asia topotype (O/SEA/Mya-98) and shared high nucleotide (99.06-100% identity) and amino acid (97.65-100% identity) sequence similarity with each other. The study results suggested that the reemerging FMDVs originated from local Vietnamese strains. Field viruses had different amino acids in the antigenic sites of VP1 when compared to the strains used in the vaccines. The present study provides an important basis for vaccine selection in the battle against FMD in Vietnam.

Analyzing 16S rRNA sequences from Vietnamese pathogenic Leptospira strains and in-silico prediction of potential antigenic epitopes on LipL21, LipL32 outer membrane lipoproteins

Leptospirosis, a zoonosis caused by Leptospira, is recognized as an emergent infectious disease. In currently, the lack of adequate diagnostic tools, vaccines are an attractive intervention strategy. In this experiment, a 550 bp fragment of large ribosomal RNA gene (16S rRNA) was sequenced and constructed phylogenetic tree from a panel of six Vietnamese pathogenic strains of Leptospira spirochetes (e.g., Pomona, Canicola, Mitis, Ictero haemohagiae, Bataviae, and Grippotyphosa). The results showed a close relationship of L.Pomona_VN and L.Hardjo (bootstrap: 99%). L.Canicola_VN and L.Ictero haemohagiae_VN appeared to be weak related to the classic L.Canicola, L. Grippotyphosa, these assemblage have a bootstrap support of 62%. The other strains (L.Mitis_VN and L.Grippotyphosa_VN) were appeared monophyletic, while their sister group (L.Bataviae_VN) relationship found only weak support (bootstrap: 62%). We also selected six genes [e.g. the immunoglobulin like proteins A and B (LigA and LigB genes), outer membrane protein (OmpL1 gene), and lipopolysaccharide (LipL32, LipL41, and LipL21 genes)] and checked gene expression in these Leptospira strains by polymerase chain reaction (PCR) method. There were three genes (e.g., LipL32, LipL21, and LigA genes) expressed in all strains, OmpL1 gene occured in 4 strains (L.Bataviae_VN, L.Canicola_VN, L.Grippotyphosa_VN and L.Mitis_VN), whereas LipL41 and LigB genes did not appear in any Leptospira strains. A multi-antigenic epitope potential of two gene (Lip L21 and Lip L32) was predicted by bioinformatic tools for designing a recombinant vaccine against leptospirosis. There were 3 multi-epitope regions (1 region and 95 antigenic epitope for B and T cells of LipL21 peptide; 2 regions and 124 antigenic epitope for both B and T cells of LipL32 peptide). It should be more of the deeply molecular biology studies to confirm the level agglutinating, antigen cleavage, peptide specificity matrices as well as neutralizing antibodies in the immune responses of DNA vaccine of these genes.

Polymorphism at variable regions (VRs) of porA gene from Neisseria meningitidis strains isolated in Northern Vietnam

Meningococcal bacterium Neisseria meningitidis is one of the major causes of meningitis worldwide. Currently in Vietnam, N. meningitidis B and C are the most prevalent invasive serogroups. N. meningitidis expresses two major transmembrane proteins, PorA and PorB, of which PorA showed high levels of polymorphism among strains and has been studied as one component of vaccines against N. meningitidis B. Polymorphisms in porA gene clustered into three variable regions VR1, VR2 and VR3. In this study, we sequenced the entired porA gene of 19 N. meningitidis strains isolated from military units in northern Vietnam during the period 2008 – 2017 in order to: (1) evaluate the polymorphism of porA gene at nucleotide level and predict its immuno-reactivity from annotated amino acide sequences; and (2) compare porA variants of Vietnamese strains with known strains worldwide. Our results showed a high level of polymorphisms among Vietnamese strains, with the highest polymorphism found in VR1, followed by VR2 and VR3. Notably, 5/19 strains in this study showed novel variants at VR2 with unknown immunological reactivity. This result suggested potential novel immunological characteristics of meningococcal strains from Vietnam.

Epidemiology of Enterobacter cloacae strains producing a carbapenemase or metallo-beta-lactamase in Vietnamese clinical settings in 2014-2017.

Introduction. Little is known about the epidemiology of Enterobacter cloacae strains producing a carbapenemase or metallo-beta-lactamase in Vietnamese hospitals.Aim. This study analysed E. cloacae strains resistant to imipenem or meropenem that had been isolated from patients admitted to one of the largest hospitals in Vietnam in 2014-2017.Methodology. Eighteen Vietnamese (VN) strains were subjected to whole-genome sequencing and their sequences compared with those of 17 E. cloacae strains carrying a carbapenemase or metallo-beta-lactamase in the database (db strains).Results. Although the distribution of virulence factors did not differ significantly between VN and db strains, all 18 VN isolates harboured blaNDM-1, phylogenetic analysis revealed a high clonality of the VN strains. Bayesian phylogenetic analysis suggested that the VN strains speciated relatively recently.Conclusions. Several prevalent clones of carbapenem-resistant E. cloacae have circulated within Vietnamese hospitals. Adequate measures are needed to prevent their further spread.

Genetic characterization of the spike gene of porcine epidemic diarrhea viruses (PEDVs) circulating in Vietnam from 2015 to 2016

BackgroundPorcine 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.MethodsA 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.ResultsPhylogenetic 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.ConclusionsThis 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.