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Asymptomatic transmission was found to be the Achilles' heel of the symptom-based screening strategy, necessitating the implementation of mass testing to efficiently contain the transmission of COVID-19 pandemic. However, the global shortage of molecular reagents and the low throughput of available realtime PCR facilities were major limiting factors.A novel semi-nested and heptaplex (7-plex) RT-PCR assay with melting analysis for detection of SARS-CoV-2 RNA has been established for either individual testing or 96-sample pooled testing. The complex melting spectrum collected from the heptaplex RT-PCR amplicons was interpreted with the support of an artificial intelligence algorithm for the detection of SARS-CoV-2 RNA. The analytical and clinical performance of the semi-nested RT-PCR assay was evaluated using RNAs synthesized in-vitro and those isolated from nasopharyngeal samples.The LOD of the assay for individual testing was estimated to be 7.2 copies/reaction. Clinical performance evaluation indicated a sensitivity of 100% (95% CI: 97.83-100) and a specificity of 99.87% (95% CI: 99.55-99.98). More importantly, the assay supports a breakthrough sample pooling method, which makes possible parallel screening of up to 96 samples in one real-time PCR well without loss of sensitivity. As a result, up to 8,820 individual pre-amplified samples could be screened for SARS-CoV-2 within each 96-well plate of realtime PCR using the pooled testing procedure.The novel semi-nested RT-PCR assay provides a solution for highly multiplex (7-plex) detection of SARS-CoV-2 and enables 96-sample pooled detection for increase of testing capacity. .

As a response to the coronavirus disease 2019 (COVID-19) pandemic, Vietnam enforced strict quarantine, contact tracing and physical distancing policies resulting in one of the lowest numbers of individuals infected with severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) globally. This study aimed to determine the prevalence of SARS-CoV-2 antibody positivity among high-risk populations in Vietnam. A prevalence survey was undertaken within four communities in Vietnam, where at least two COVID-19 cases had been confirmed. Participants were classified according to the location of exposure: household contacts, close contacts, community members, and healthcare workers (HCWs) responsible for treating COVID-19 cases. Participants completed a baseline questionnaire and SARS-CoV-2 IgG antibodies were quantified using a commercial assay. A total of 3049 community members and 149 health care workers consented to the study. Among 13 individuals who were seropositive (0.4%), five household contacts (5/27, 18.5%), one close contact (1/53, 1.9%), and seven community members (7/2954, 0.2%) had detectable SARS-CoV-2 antibodies. All HCWs were negative for SARS-CoV-2 antibodies. Participants were tested a median of 15.1 (interquartile range from 14.9 to 15.2) weeks after exposure. Our study found a low prevalence of SARS-CoV-2 antibodies in high-risk communities and healthcare workers in communities in Vietnam with known COVID-19 cases.

Background: As a response to the coronavirus disease 2019 (COVID-19) pandemic, Vietnam enforced strict quarantine, contact tracing and physical distancing policies. By December 2020, this strategy resulted in one of the lowest numbers of individuals infected with severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) cases globally. This study aimed to determine the prevalence of SARS-CoV-2 antibody positivity among high-risk populations in Vietnam. Methods: A prevalence survey was undertaken within four communities in northern and central Vietnam, where at least two COVID-19 cases had been confirmed. Participants were classified according to the location of exposure: household contacts, close contacts, community members, and healthcare workers (HCWs) responsible for treating COVID-19 cases. Participants completed a baseline questionnaire that evaluated exposure history. SARS-CoV-2 IgG antibodies were quantified using a commercially available assay. Results: 3056 community members and 149 health care workers provided consent to participate. Among enrolled community members, 27 (0·9%) were household contacts and 53 (1·7%) were close contacts. Serology was performed in 3034 individuals. Among 13 individuals who were seropositive (0·4%), five household contacts (5/27, 18·5%), one close contact (1/53, 1·9%), and seven community members (7/2954, 0·2%) had detectable SARS-CoV-2 antibodies. All HCWs were negative for SARS-CoV-2 antibodies. Participants were tested a median of 15·1 (interquartile range 14·9 to 15·2) weeks after exposure. Conclusion: The presence of SARS-CoV-2 antibodies in high-risk communities and healthcare workers was low in communities in Vietnam with known COVID-19 cases. The public health response to the COVID-19 pandemic in Vietnam has been effective in limiting community transmission of SARS-CoV-2. Funding Statement: This project was supported by a grant funded by the Australian Department of Foreign Affairs and Trade, awarded in conjunction with the Australian National Health and Medical Research Council (APP1153346). Declaration of Interests: None declared. Ethics Approval Statement: Ethical approval was obtained from the Human Research Ethics Committees of the University of Sydney (HREC 2020/415) and Biomedical Research Ethics Committee of the National Hospital for Tropical Diseases (No. 10/HDDD-NDTU and No. 18/HDDD-NDTU). Consent was documented electronically using a tablet computer. In accordance with local expectations, all COVID-19 patients and other participants were provided with monetary compensation for their participation, equivalent to approximately US$4·30 and US$2·20, respectively.

BK polyomavirus (BKPyV) is an important pathogen in transplant recipients. We report four draft BKPyV genomes, three of BKPyV genotype I (subtype I-b2) (AUS-105, AUS-106, and AUS-108) and one of genotype II (AUS-107). These draft genomes were identified in longitudinal urine samples collected from a single hematopoietic stem cell transplant recipient.

JC polyomavirus (JCPyV) may cause clinical syndromes such as progressive multifocal leukoencephalopathy in immunocompromised patients. Here, we report seven complete genome sequences of JCPyV genotype 7A, generated directly from urine samples from Vietnamese renal transplant recipients by using rolling-circle amplification and next-generation sequencing.

Acinetobacter calcoaceticus–baumannii complex is a common cause of hospital-acquired infections (HAIs) globally, remarkable for its high rate of antibiotic resistance, including to carbapenems. There are few data on the resistance of A. baumannii in Vietnam, which are essential for developing evidence-based treatment guidelines for HAIs. Antibiotic susceptibility testing was conducted by VITEK®2, and pulsed-field gel electrophoresis (PFGE) was performed on 66 clinical A. baumannii complex isolates recovered during 2009 at the National Hospital of Tropical Diseases (NHTD), a referral hospital in Hanoi, Vietnam. Basic demographic and clinical data were collected and analysed using descriptive statistics. Most isolates came from lower respiratory tract specimens (59; 89.4%) from intensive care unit (ICU) patients [64/65 (98.5%) with available data] who had been admitted to NHTD for ≥2 days [42/46 (91.3%) with available data]. More than 90% of the isolates were resistant to the tested β-lactamase/β-lactamase inhibitors, cephalosporins, carbapenems, fluoroquinolones and trimethoprim/sulfamethoxazole. Moreover, 25.4% (16/63) were resistant to all tested β-lactams, quinolones and aminoglycosides. All isolates remained sensitive to colistin and 58.7% were susceptible to tigecycline. Of the 66 isolates, 49 could be classified into eight PFGE types (A–H). Every PFGE type, except D, had cluster(s) of three or more isolates with a temporal relationship. In conclusion, these data suggest a significant rise in A. baumannii antibiotic resistance in Vietnam. Clustering within PFGE types supports cross-transmission of A. baumannii within the ICU at NHTD. Increased research and resources in optimising treatment, infection control and antibiotic stewardship are needed.

Background Prior to 2007, highly pathogenic avian influenza (HPAI) H5N1 viruses isolated from poultry and humans in Vietnam were consistently reported to be clade 1 viruses, susceptible to oseltamivir but resistant to amantadine. Here we describe the re-emergence of human HPAI H5N1 virus infections in Vietnam in 2007 and the characteristics of the isolated viruses. Methods and Findings Respiratory specimens from patients suspected to be infected with avian influenza in 2007 were screened by influenza and H5 subtype specific polymerase chain reaction. Isolated H5N1 strains were further characterized by genome sequencing and drug susceptibility testing. Eleven poultry outbreak isolates from 2007 were included in the sequence analysis. Eight patients, all of them from northern Vietnam, were diagnosed with H5N1 in 2007 and five of them died. Phylogenetic analysis of H5N1 viruses isolated from humans and poultry in 2007 showed that clade 2.3.4 H5N1 viruses replaced clade 1 viruses in northern Vietnam. Four human H5N1 strains had eight-fold reduced in-vitro susceptibility to oseltamivir as compared to clade 1 viruses. In two poultry isolates the I117V mutation was found in the neuraminidase gene, which is associated with reduced susceptibility to oseltamivir. No mutations in the M2 gene conferring amantadine resistance were found. Conclusion In 2007, H5N1 clade 2.3.4 viruses replaced clade 1 viruses in northern Vietnam and were susceptible to amantadine but showed reduced susceptibility to oseltamivir. Combination antiviral therapy with oseltamivir and amantadine for human cases in Vietnam is recommended.

Acinetobacter calcoaceticus–baumannii complex is a common cause of hospital-acquired infections (HAIs) globally, remarkable for its high rate of antibiotic resistance, including to carbapenems. There are few data on the resistance of A. baumannii in Vietnam, which are essential for developing evidence-based treatment guidelines for HAIs. Antibiotic susceptibility testing was conducted by VITEK®2, and pulsed-field gel electrophoresis (PFGE) was performed on 66 clinical A. baumannii complex isolates recovered during 2009 at the National Hospital of Tropical Diseases (NHTD), a referral hospital in Hanoi, Vietnam. Basic demographic and clinical data were collected and analysed using descriptive statistics. Most isolates came from lower respiratory tract specimens (59; 89.4%) from intensive care unit (ICU) patients [64/65 (98.5%) with available data] who had been admitted to NHTD for ≥2 days [42/46 (91.3%) with available data]. More than 90% of the isolates were resistant to the tested β-lactamase/β-lactamase inhibitors, cephalosporins, carbapenems, fluoroquinolones and trimethoprim/sulfamethoxazole. Moreover, 25.4% (16/63) were resistant to all tested β-lactams, quinolones and aminoglycosides. All isolates remained sensitive to colistin and 58.7% were susceptible to tigecycline. Of the 66 isolates, 49 could be classified into eight PFGE types (A–H). Every PFGE type, except D, had cluster(s) of three or more isolates with a temporal relationship. In conclusion, these data suggest a significant rise in A. baumannii antibiotic resistance in Vietnam. Clustering within PFGE types supports cross-transmission of A. baumannii within the ICU at NHTD. Increased research and resources in optimising treatment, infection control and antibiotic stewardship are needed.