Background Little is known about the natural history of asymptomatic SARS-CoV-2 infection or its contribution to infection transmission. Methods We conducted a prospective study at a quarantine center for COVID-19 in Ho Chi Minh City, Vietnam. We enrolled quarantined people with RT-PCR-confirmed SARS-CoV-2 infection, collecting clinical data, travel and contact history, and saliva at enrolment and daily nasopharyngeal throat swabs (NTS) for RT-PCR testing. We compared the natural history and transmission potential of asymptomatic and symptomatic individuals. Results Between March 10th and April 4th, 2020, 14,000 quarantined people were tested for SARS-CoV-2; 49 were positive. Of these, 30 participated in the study: 13(43%) never had symptoms and 17(57%) were symptomatic. 17(57%) participants acquired their infection outside Vietnam. Compared with symptomatic individuals, asymptomatic people were less likely to have detectable SARS-CoV-2 in NTS samples collected at enrolment (8/13 (62%) vs. 17/17 (100%) P=0.02). SARS-CoV-2 RNA was detected in 20/27 (74%) available saliva; 7/11 (64%) in the asymptomatic and 13/16 (81%) in the symptomatic group (P=0.56). Analysis of the probability of RT-PCR positivity showed asymptomatic participants had faster viral clearance than symptomatic participants (P<0.001 for difference over first 19 days). This difference was most pronounced during the first week of follow-up. Two of the asymptomatic individuals appeared to transmit the infection to up to four contacts. Conclusions Asymptomatic SARS-CoV-2 infection is common and can be detected by analysis of saliva or NTS. NTS viral loads fall faster in asymptomatic individuals, but they appear able to transmit the virus to others.

248 2 1 Main text: 2788 2 2 Running title: Asymptomatic SARS-CoV-2 infection 2 3 ABSTRACT 2 5 Background 2 6Little is known about the natural history of asymptomatic SARS-CoV-2 infection or its 2 7 contribution to infection transmission. 2 8 Methods 2 9We conducted a prospective study at a quarantine centre for COVID-19 in Ho Chi Minh City, 3 0 Vietnam. We enrolled quarantined people with RT-PCR-confirmed SARS-CoV-2 infection, 3 1 collecting clinical data, travel and contact history, and saliva at enrolment and daily 3 2 nasopharyngeal throat swabs (NTS) for RT-PCR testing. We compared the natural history and 3 3 transmission potential of asymptomatic and symptomatic individuals.3 4 Results 3 5Between March 10 th and April 4 th , 2020, 14,000 quarantined people were tested for SARS-3 6CoV-2; 49 were positive. Of these, 30 participated in the study: 13(43%) never had symptoms 3 7 and 17(57%) were symptomatic. 17(57%) participants acquired their infection outside Vietnam. 3 8 Compared with symptomatic individuals, asymptomatic people were less likely to have 3 9 detectable SARS-CoV-2 in NTS samples collected at enrolment (8/13 (62%) vs. 17/17 (100%) 4 0 P=0.02). SARS-CoV-2 RNA was detected in 20/27 (74%) available saliva; 7/11 (64%) in the 4 1 asymptomatic and 13/16 (81%) in the symptomatic group (P=0.56). Analysis of the probability 4 2 of RT-PCR positivity showed asymptomatic participants had faster viral clearance than 4 3 symptomatic participants (P<0.001 for difference over first 19 days). This difference was most 4 4 pronounced during the first week of follow-up. Two of the asymptomatic individuals appeared 4 5 to transmit the infection to up to four contacts. 4 6 Conclusions 4 7 Asymptomatic SARS-CoV-2 infection is common and can be detected by analysis of saliva or 4 8 NTS. NTS viral loads fall faster in asymptomatic individuals, but they appear able to transmit 4 9 the virus to others. 5 0 Hospitals, located approximately 60 km to the West and East, respectively, of HCMC (Figure 9 7 2A).

Background Data on breakthrough SARS-CoV-2 Delta variant infections in vaccinated individuals are limited. Methods We studied breakthrough infections among Oxford-AstraZeneca vaccinated healthcare workers in an infectious diseases hospital in Vietnam. We collected demographic and clinical data alongside serial PCR testing, measurement of SARS-CoV-2 antibodies, and viral whole-genome sequencing. Findings Between 11 th –25 th June 2021 (7-8 weeks after the second dose), 69 staff tested positive for SARS-CoV-2. 62 participated in the study. Most were asymptomatic or mildly symptomatic and all recovered. Twenty-two complete-genome sequences were obtained; all were Delta variant and were phylogenetically distinct from contemporary viruses obtained from the community or from hospital patients admitted prior to the outbreak. Viral loads inferred from Ct values were 251 times higher than in cases infected with the original strain in March/April 2020. Median time from diagnosis to negative PCR was 21 days (range 8–33). Neutralizing antibodies (expressed as percentage of inhibition) measured after the second vaccine dose, or at diagnosis, were lower in cases than in uninfected, fully vaccinated controls (median (IQR): 69.4 (50.7-89.1) vs. 91.3 (79.6-94.9), p=0.005 and 59.4 (32.5-73.1) vs. 91.1 (77.3-94.2), p=0.002). There was no correlation between vaccine-induced neutralizing antibody levels and peak viral loads or the development of symptoms. Interpretation Breakthrough Delta variant infections following Oxford-AstraZeneca vaccination may cause asymptomatic or mild disease, but are associated with high viral loads, prolonged PCR positivity and low levels of vaccine-induced neutralizing antibodies. Epidemiological and sequence data suggested ongoing transmission had occurred between fully vaccinated individuals. Funding Wellcome and NIH/NIAID

Allopatry is conventionally considered the geographical mode of speciation for continental island organisms. However, strictly allopatric speciation models that assume the lack of postdivergence gene flow seem oversimplified given the recurrence of land bridges during glacial periods since the late Pliocene. Here, to evaluate whether a continental island endemic, the Taiwan hwamei (Leucodioptron taewanus, Passeriformes Timaliidae) speciated in strict allopatry, we used weighted-regression-based approximate Bayesian computation (ABC) to analyse the genetic polymorphism of 18 neutral nuclear loci (total length: 8500 bp) in Taiwan hwamei and its continental sister species, the Chinese hwamei (L. canorum canorum). The nonallopatry model was found to fit better with observed genetic polymorphism of the two hwamei species (posterior possibility = 0.82). We also recovered unambiguous signals of nontrivial bidirectional postdivergence gene flow (N(e)m >> 1) between Chinese hwamei and Taiwan hwamei until 0.5 Ma. Divergence time was estimated to be 3.5 to 2 million years earlier than that estimated from mitochondrial cytochrome b sequences. Finally, using the inferred nonallopatry model to simulate genetic variation at 24 nuclear genes examined showed that the adiponectin receptor 1 gene may be under divergent adaptation. Our findings imply that the role of geographical barrier may be less prominent for the speciation of continental island endemics, and suggest a shift in speciation studies from simply correlating geographical barrier and genetic divergence to examining factors that facilitate and maintain divergence, e.g. differential selection and sexual selection, especially in the face of interpopulation gene flow.