SARS-CoV-2 sequencing with cloud-based analysis illustrates expedient co-ordinated surveillance of viral genomic epidemiology across six continents (preprint)

Viral sequencing has been critical in the COVID-19 pandemic response, but sequencing and bioinformatics capacity remain inconsistent. To examine the utility of a cloud-based sequencing analysis platform for SARS-CoV-2 sequencing, we conducted a cross-sectional study incorporating seven countries in July 2022. Sites submitted sequential SARS-CoV-2 sequences over two weeks to the Global Pathogen Analysis Service (GPAS). The GPAS bioinformatics cloud platform performs sequence assembly plus lineage and related sample identification. Users can share information with collaborators while retaining data ownership. Seven sites contributed sequencing reads from 5,346 clinical samples, of which 4,799/5,346 (89.8%) had a lineage identified. Omicron lineages dominated, with the vast majority being BA.5, BA.4 and BA.2, commensurate with contemporary genomic epidemiological observations. Phylogenetic analysis demonstrated low within-lineage diversity, and highly similar sequences present in globally disparate sites. A cloud-based analysis platform like GPAS addresses bioinformatics bottlenecks and facilitates collaboration in pathogen surveillance, enhancing epidemic and pandemic preparedness.

Kinetics of neutralising antibodies against Omicron variant in Vietnamese healthcare workers after primary immunisation with ChAdOx1-S and booster with BNT162b2 (preprint)

We studied the development and persistence of neutralising antibodies against SARS-CoV-2 ancestral strain, and Delta and Omicron (BA.1 and BA.2) variants in Vietnamese healthcare workers (HCWs) up to 15 weeks after booster vaccination. We included 47 HCWs with different pre-existing immune statuses (group 1 (G1): n=21, and group 2 (G2): n=26 without and with prior breakthrough Delta variant infection, respectively). The study participants had completed primary immunisation with ChAdOx1-S and booster vaccination with BNT162b2. Neutralising antibodies were measured using a surrogate virus neutralisation assay. Of the 21 study participants in G1, neutralising antibodies against ancestral strain, Delta variant, BA.1 and BA.2 were (almost) abolished at month 8 after the second dose, but all had detectable neutralising antibodies to the study viruses at week two post booster dose. Of the 26 study participants in G2, neutralising antibody levels to BA.1 and BA.2 were significantly higher than those to the corresponding viruses measured at week 2 post breakthrough infection and before the booster dose. At week 15 post booster vaccination, neutralising antibodies to BA.1 and BA.2 dropped significantly, with more profound changes observed in those without breakthrough Delta variant infection. Booster vaccination enhanced neutralising activities against ancestral strain and Delta variant, as compared to those induced by primary vaccination. These responses were maintained at high levels for at least 15 weeks. Our findings emphasise the importance of the first booster dose in producing cross-neutralising antibodies against Omicron variant. A second booster dose might be needed to maintain long-term protection against Omicron variant.

Transmission of SARS-CoV-2 Delta Variant Among Vaccinated Healthcare Workers, Vietnam (preprint)

Background: Data on breakthrough SARS-CoV-2 Delta variant infections are limited.Methods: We studied breakthrough infections among healthcare workers of a major infectious diseases hospital in Vietnam. We collected demographics, vaccination history and results of PCR diagnosis alongside clinical data. We measured SARS-CoV-2 (neutralizing) antibodies at diagnosis, and at week 1, 2 and 3 after diagnosis. We sequenced the viruses using ARTIC protocol.Findings: Between 11th–25th June 2021 (week 7–8 after dose 2), 69 healthcare workers were tested positive for SARS-CoV-2. 62 participated in the clinical study. 49 were (pre)symptomatic with one requiring oxygen supplementation. All recovered uneventfully. 23 complete-genome sequences were obtained. They all belonged to the Delta variant, and were phylogenetically distinct from the contemporary Delta variant sequences obtained from community transmission cases, suggestive of ongoing transmission between the workers. Viral loads of breakthrough Delta variant infection cases were 251 times higher than those of cases infected with old strains detected between March-April 2020. Time from diagnosis to PCR negative was 8–33 days (median: 21). Neutralizing antibody levels after vaccination and at diagnosis of the cases were lower than those in the matched uninfected controls. There was no correlation between vaccine-induced neutralizing antibody levels and viral loads or the development of symptoms.Interpretation: Breakthrough Delta variant infections are associated with high viral loads, prolonged PCR positivity, and low levels of vaccine-induced neutralizing antibodies, explaining the transmission between the vaccinated people. Physical distancing measures remain critical to reduce SARS-CoV-2 Delta variant transmission.Funding: Wellcome (106680/B/14/Z and 204904/Z/16/Z).Declaration of Interest: None to declare.Ethical Approval: The study was approved by the Institutional Review Board of HTD and the Oxford Tropical Research Ethics Committee, University of Oxford, UK.

Absence of SARS-CoV-2 antibodies in pre-pandemic plasma from children and adults in Vietnam (preprint)

We tested pre-pandemic (2015-2019) plasma samples from 148 Vietnamese children, and 100 Vietnamese adults at high risk of zoonotic infections, for antibodies against SARS-CoV-2 nucleocapsid and spike proteins. None was positive, indicating no prior serological cross-reactivity with SARS-CoV-2 that might explain the low numbers of COVID-19 in Vietnam.

Immunogenicity of Oxford-AstraZeneca COVID-19 vaccine in Vietnamese healthcare workers (preprint)

We studied the immunogenicity of Oxford-AstraZeneca vaccine in Vietnamese healthcare workers. We collected blood samples before each dose, at 14 days after each dose, and month 1 and 3 after dose 1 from each participant alongside demographics data. We measured neutralizing antibodies using a surrogate virus neutralization assay. The 554 study participants (136 males and 418 females) were aged between 22-71 years (median: 36 years). 104 and 94 out of 144 selected participants were successfully followed up at 14 days after dose 2 and 3 months after dose 1, respectively. Neutralizing antibodies increased after each dose, with the sero-conversion rate reaching 98.1% (102/104) at 14 days after dose 2. At month 3 after dose 1, neutralizing antibody levels decreased, while 94.7% (89/94) of the study participants remained seropositive. Oxford-AstraZeneca COVID-19 vaccine is immunogenic in Vietnamese healthcare workers. The requirement for a third dose warrants further research.

A novel sample pooling strategy and its application for mass screening of SARS-CoV-2 in an outbreak of COVID-19 in Vietnam (preprint)

We present a sample pooling approach and the results of its application for mass screening of SARS-CoV-2 in >96,000 asymptomatic individuals. Our approach did not compromise the sensitivity of PCR, while increasing the throughput and reducing 77% of the costs. 22/32 asymptomatic cases would have been missed without mass screening.

SARS-CoV-2 detection in nasopharyngeal throat swabs by metagenomics (preprint)

Metagenomics could detect SARS-CoV-2 in all eight nasopharyngeal/throat swabs with high/low viral loads, and rhinovirus in a co-infected patient. The sequenced viruses belonged to lineage B1. Because metagenomics could detect novel pathogen and co-infection, and generate sequence data for epidemiological investigation, it is an attractive approach for infectious-disease diagnosis.

The natural history and transmission potential of asymptomatic SARS-CoV-2 infection (preprint)

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 centre 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.

Duration of viral detection in throat and rectum of a patient with COVID-19 (preprint)

The rapid spread of coronavirus disease 2019 (COVID-19) raises concern about a global pandemic. Knowledge about the duration of viral shedding remains important for patient management and infection control. We report the duration of viral detection in throat and rectum of a COVID-19 patient treated at the Hospital for Tropical Diseases in Ho Chi Minh City, Vietnam. Despite clinical recovery, SARS-CoV-2 RNA remained detectable by real time RT-PCR in throat and rectal swabs until day 11 and 18 of hospitalization, respectively. Because live SARS-CoV-2 has been successfully isolated from a stool sample from a COVID-19 patient in China, the results demonstrate that COVID-19 patients may remain infectious for long periods, and fecal-oral transmission may be possible. Therefore, our finding has important implications for infection control.