The Virome of Acute Respiratory Diseases in Individuals at Risk of Zoonotic Infections.

The ongoing coronavirus disease 2019 (COVID-19) pandemic emphasizes the need to actively study the virome of unexplained respiratory diseases. We performed viral metagenomic next-generation sequencing (mNGS) analysis of 91 nasal-throat swabs from individuals working with animals and with acute respiratory diseases. Fifteen virus RT-PCR-positive samples were included as controls, while the other 76 samples were RT-PCR negative for a wide panel of respiratory pathogens. Eukaryotic viruses detected by mNGS were then screened by PCR (using primers based on mNGS-derived contigs) in all samples to compare viral detection by mNGS versus PCR and assess the utility of mNGS in routine diagnostics. mNGS identified expected human rhinoviruses, enteroviruses, influenza A virus, coronavirus OC43, and respiratory syncytial virus (RSV) A in 13 of 15 (86.7%) positive control samples. Additionally, rotavirus, torque teno virus, human papillomavirus, human betaherpesvirus 7, cyclovirus, vientovirus, gemycircularvirus, and statovirus were identified through mNGS. Notably, complete genomes of novel cyclovirus, gemycircularvirus, and statovirus were genetically characterized. Using PCR screening, the novel cyclovirus was additionally detected in 5 and the novel gemycircularvirus in 12 of the remaining samples included for mNGS analysis. Our studies therefore provide pioneering data of the virome of acute-respiratory diseases from individuals at risk of zoonotic infections. The mNGS protocol/pipeline applied here is sensitive for the detection of a variety of viruses, including novel ones. More frequent detections of the novel viruses by PCR than by mNGS on the same samples suggests that PCR remains the most sensitive diagnostic test for viruses whose genomes are known. The detection of novel viruses expands our understanding of the respiratory virome of animal-exposed humans and warrant further studies.

The first 100 days of SARS-CoV-2 control in Vietnam

BackgroundOne hundred days after SARS-CoV-2 was first reported in Vietnam on January 23rd, 270 cases have been confirmed, with no deaths. We describe the control measures used by the Government and their relationship with imported and domestically-acquired case numbers, with the aim of identifying the measures associated with successful SARS-CoV-2 control. MethodsClinical and demographic data on the first 270 SARS-CoV-2 infected cases and the timing and nature of Government control measures, including numbers of tests and quarantined individuals, were captured by Vietnams National Steering Committee for COVID-19 response. Apple and Google mobility data provided proxies for population movement. Serial intervals were calculated from 33 infector-infectee pairs and used to estimate the proportion of pre-symptomatic transmission events and time-varying reproduction numbers. FindingsAfter the first confirmed case on January 23rd, the Vietnamese Government initiated mass communications measures, case-contact tracing, mandatory 14-day quarantine, school and university closures, and progressive flight restrictions. A national lockdown was implemented between April 1st and 22nd. Around 200 000 people were quarantined and 266 122 RT-PCR tests conducted. Population mobility decreased progressively before lockdown. 60% (163/270) of cases were imported; 43% (89/208) of resolved infections remained asymptomatic for the duration of infection. 21 developed severe disease, with no deaths. The serial interval was 3.24 days, and 27.5% (95% confidence interval, 15.7%-40.0%) of transmissions occurred pre-symptomatically. Limited transmission amounted to a maximum reproduction number of 1.15 (95% confidence interval, 0.37-2.36). No community transmission has been detected since April 15th. InterpretationVietnam has controlled SARS-CoV-2 spread through the early introduction of mass communication, meticulous contact-tracing with strict quarantine, and international travel restrictions. The value of these interventions is supported by the high proportion of asymptomatic and imported cases, and evidence for substantial pre-symptomatic transmission. FundingThe Vietnam Ministry of Health and Wellcome Trust, UK. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSVietnam was one of the first countries outside of China to detect imported and human-to-human transmitted SARS-CoV-2 within its borders. Yet, as of May 1st, a total of only 270 cases have been confirmed, no deaths have occurred, and no community transmission has been detected since April 15th despite intensive screening, tracing and testing. We did a PubMed database search to identify studies investigating COVID-19 response in Vietnam using the terms "Vietnam", "COVID-19", and "SARS-CoV-2". All relevant articles were evaluated. Studies describe cases of COVID-19 and their management, aspects of the government response from newspapers and online government sources, but there are no previous reports using national data to describe and investigate the national epidemic and the impact of control measures cases over time. Added value of this studyWe used data from the National Steering Committee for COVID-19 response to give a comprehensive account of the first 100 days of the SARS-CoV-2 epidemic in Vietnam, including case numbers and their symptomatology, the estimated reproductive number by week, and their relation to the multiple control measures instituted by the Vietnam Government over time. We show two distinctive features of Vietnams response. First, the Government took rapid actions to restrict international flights, closed schools and universities, and instituted meticulous case-contact tracing and quarantining from late January, well before these measures were advised by WHO. Second, they placed mass communication, education, and the identification, serial testing, and 14-day quarantine of all direct contacts of cases, regardless of symptom development, at the heart of the response. The value of strict contact-tracing and quarantine is supported by the high proportion of asymptomatic cases (43%) and imported cases (60%), and evidence for substantial pre-symptomatic transmission. Implications of all the available evidenceVietnam has had remarkable success in controlling the emergence of SARS-CoV-2. Our report provides a complete picture of the control of SARS-CoV-2 in Vietnam, with lessons for other Governments seeking to extend national SARS-CoV-2 control or prevent future epidemics. Our findings shows the importance of acting early, before the virus becomes established in the community, and before the case numbers overwhelm systems of case-contact tracing and mass quarantine. They also demonstrate the value of effective mass communication in rapidly educating the public in infection prevention measures and providing real-time information on the state of the epidemic.

Pig Exposure and Health Outcomes in Hospitalized Infectious Disease Patients in Vietnam.

Many infectious diseases have a zoonotic origin, and several have had major public health implications. Contact with animals is a known risk factor for zoonotic infections, although there are limited data on disease symptoms and pathogens associated with contact with different animal species. The rise in pig production in Southeast Asia has contributed to the emergence and re-emergence of zoonotic infections caused by contact with pigs and pig products. To compare the symptom and pathogen profiles of hospitalized patients with and without pig contact, we collected data on disease symptoms, infecting pathogens, and animal contact behaviour from patients attending six hospitals across Vietnam between 2012 and 2016. Patients who had previous contact with pigs were more likely to have enteric disease than respiratory or central nervous system infections and were more likely to grow Escherichia coli and Shigella from stool culture than those without pig contact. Patients with enteric infections who kept pigs were also more likely to have a disease of unknown origin. Public health initiatives that account for differences in animal contact behaviours and offer more comprehensive diagnostics in high-risk individuals are needed if emergence and re-emergence of zoonotic disease is to be monitored and prevented.

Evaluation of the Luminex xTAG Respiratory Viral Panel FAST v2 assay for detection of multiple respiratory viral pathogens in nasal and throat swabs in Vietnam.

BACKGROUND: Acute respiratory infections (ARI) are among the leading causes of hospitalization in children ≤5 years old. Rapid diagnostics of viral pathogens is essential to avoid unnecessary antibiotic treatment, thereby slowing down antibiotic-resistance. We evaluated the diagnostic performance of the Luminex xTAG Respiratory Viral Panel FAST v2 against viral specific PCR as reference assays for ARI in Vietnam. METHODS: Four hundred and forty two nose and throat swabs were collected in viral transport medium, and were tested with Luminex xTAG Respiratory Viral Panel FAST v2. Multiplex RT-PCR and single RT-PCR were used as references.    Results: Overall, viral pathogens were detected in a total count of 270/294 (91.8%, 95% CI 88.1-94.7) by the Luminex among reference assays, whilst 112/6336 (1.8%, 95% CI, 1.4-2.1) of pathogens were detected by the Luminex, but not by reference assays. Frequency of pathogens detected by Luminex and reference assays was 379 and 292, respectively. The diagnostic yield was 66.7% (295/442, 95%CI 62.1-71.1%) for the Luminex assay and 54.1% (239/442, 95% CI, 49.3-58.8%) for reference assays. The Luminex kit had higher yields for all viruses except influenza B virus, respiratory syncytial virus, and human bocavirus. High agreements between both methods [mean (range): 0.91 (0.83-1.00)] were found for 10/15 viral agents. CONCLUSIONS: The Luminex assay is a high throughput multiplex platform for rapid detection of common viral pathogens causing ARI. Although the current high cost may prevent Luminex assays from being widely used, especially in limited resource settings where ARI are felt most, its introduction in clinical diagnostics may help reduce unnecessary use of antibiotic prescription.

Unbiased whole-genome deep sequencing of human and porcine stool samples reveals circulation of multiple groups of rotaviruses and a putative zoonotic infection.

Coordinated and synchronous surveillance for zoonotic viruses in both human clinical cases and animal reservoirs provides an opportunity to identify interspecies virus movement. Rotavirus (RV) is an important cause of viral gastroenteritis in humans and animals. In this study, we document the RV diversity within co-located humans and animals sampled from the Mekong delta region of Vietnam using a primer-independent, agnostic, deep sequencing approach. A total of 296 stool samples (146 from diarrhoeal human patients and 150 from pigs living in the same geographical region) were directly sequenced, generating the genomic sequences of sixty human rotaviruses (all group A) and thirty-one porcine rotaviruses (thirteen group A, seven group B, six group C, and five group H). Phylogenetic analyses showed the co-circulation of multiple distinct RV group A (RVA) genotypes/strains, many of which were divergent from the strain components of licensed RVA vaccines, as well as considerable virus diversity in pigs including full genomes of rotaviruses in groups B, C, and H, none of which have been previously reported in Vietnam. Furthermore, the detection of an atypical RVA genotype constellation (G4-P[6]-I1-R1-C1-M1-A8-N1-T7-E1-H1) in a human patient and a pig from the same region provides some evidence for a zoonotic event.