Background One hundred days after SARS-CoV-2 was first reported in Vietnam on January 23rd, 270 cases were 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. Methods Clinical 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 analysed. 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. Results 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. 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. Conclusions Vietnam 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.

Outbreaks of emerging coronaviruses in the past two decades and the current pandemic of a novel coronavirus (SARS-CoV-2) that emerged in China highlight the importance of this viral family as a zoonotic public health threat. To gain a better understanding of coronavirus presence and diversity in wildlife at wildlife-human interfaces in three southern provinces in Viet Nam 2013-2014, we used consensus Polymerase Chain Reactions to detect coronavirus sequences. In comparison to previous studies, we observed high proportions of positive samples among field rats (34.0%, 239/702) destined for human consumption and insectivorous bats in guano farms (74.8%, 234/313) adjacent to human dwellings. Most notably among field rats, the odds of coronavirus RNA detection significantly increased along the supply chain from field rats sold by traders (reference group; 20.7% positivity, 39/188) by a factor of 2.2 for field rats sold in large markets (32.0%, 116/363) and 10.0 for field rats sold and served in restaurants (55.6%, 84/151). Coronaviruses were also detected in rodents on the majority of wildlife farms sampled (60.7%, 17/28). These coronaviruses were found in the Malayan porcupines (6.0%, 20/331) and bamboo rats (6.3%, 6/96) that are raised on wildlife farms for human consumption as food. We identified six known coronaviruses in

51Outbreaks of emerging coronaviruses in the past two decades and the current pandemic 52 of a novel coronavirus (SARS-CoV-2) that emerged in China highlight the importance of this 53 viral family as a zoonotic public health threat. To gain a better understanding of coronavirus 54 presence and diversity in wildlife at wildlife-human interfaces in three southern provinces in Viet 55Nam 2013-2014, we used consensus Polymerase Chain Reactions to detect coronavirus 56 sequences. In comparison to previous studies, we observed high proportions of positive samples 57 among field rats (34.0%, 239/702) destined for human consumption and insectivorous bats in 58 guano farms (74.8%, 234/313) adjacent to human dwellings. Most notably among field rats, the 59 odds of coronavirus RNA detection significantly increased along the supply chain from field rats 60 sold by traders (reference group; 20.7% positivity, 39/188) by a factor of 2.2 for field rats sold in 61 large markets (32.0%, 116/363) and 10.0 for field rats sold and served in restaurants (55.6%, 62 84/151). Coronaviruses were detected in the majority of wildlife farms (60.7%, 17/28) and in the 63 Malayan porcupines (6.0%, 20/331) and bamboo rats (6.3%, 6/96) that are farmed. We identified 64 six known coronaviruses in bats and rodents, clustered in three Coronaviridae genera, including 65 the Alpha-, Beta-, and Gammacoronaviruses. Our analysis also suggested either mixing of 66 animal excreta in the environment or interspecies transmission of coronaviruses, as both bat and 67 avian coronaviruses were detected in rodent feces in the trade. The mixing of multiple 68 coronaviruses, and their apparent amplification along the wildlife supply chain into restaurants, 69 suggests maximal risk for end consumers and likely underpins the mechanisms of zoonotic 70 spillover to people. 71 72

Despite their classification as low pathogenicity avian influenza viruses (LPAIV), A/H9N2 viruses cause significant losses in poultry in many countries throughout Asia, the Middle East and North Africa. To date, poultry surveillance in Vietnam has focused on detection of influenza H5 viruses, and there is limited understanding of influenza H9 epidemiology and transmission dynamics. We determined prevalence and diversity of influenza A viruses in chickens from live bird markets (LBM) of 7 northern Vietnamese provinces, using pooled oropharyngeal swabs collected from October to December 2014. Screening by real time RT-PCR revealed 1207/4900 (24.6%) of pooled swabs to be influenza A virus positive; overall prevalence estimates after accounting for pooling (5 swabs/pools) were 5.8% (CI 5.4–6.0). Subtyping was performed on 468 pooled swabs with M gene Ct < 26. No influenza H7 was detected; 422 (90.1%) were H9 positive; and 22 (4.7%) were H5 positive. There was no evidence was of interaction between H9 and H5 virus detection rates. We sequenced 17 whole genomes of A/H9N2, 2 of A/H5N6, and 11 partial genomes. All H9N2 viruses had internal genes that clustered with genotype 57 and were closely related to Chinese human isolates of A/H7N9 and A/H10N8. Using a nucleotide divergence cutoff of 98%, we identified 9 distinct H9 genotypes. Phylogenetic analysis suggested multiple introductions of H9 viruses to northern Vietnam rather than in-situ transmission. Further investigations of H9 prevalence and diversity in other regions of Vietnam are warranted to assess H9 endemicity elsewhere in the country.

Participants with documented prior A(H3N2) virus infection had higher pre-vaccine titres against strains circulating since 2004 compared to those without prior infection. Moreover, they had higher titre rises on days 7, 14, 21 and 280 post-vaccination against vaccine and subsequently circulating strains. Accordingly, 1/72 versus 4/28 of vaccinees with and without documented prior infection experienced illness due to A(H3N2) in the season after vaccination (p = 0.021). The range of A(H3N2) virus clades recognized by vaccine-induced antibodies was associated with the clade that last caused infection, indicating that recalled immunity drove antibody production against shared epitopes. InterpretationThese results suggest that immunological memory from prior infection drives and shapes antibody production induced by inactivated influenza vaccine, and underpins the capacity for vaccine to induce sufficient antibody for protection.