Sensitivity to Neutralizing Antibodies and Resistance to Type I Interferons in SARS-CoV-2 R.1 Lineage Variants, Canada.

Isolating and characterizing emerging SARS-CoV-2 variants is key to understanding virus pathogenesis. In this study, we isolated samples of the SARS-CoV-2 R.1 lineage, categorized as a variant under monitoring by the World Health Organization, and evaluated their sensitivity to neutralizing antibodies and type I interferons. We used convalescent serum samples from persons in Canada infected either with ancestral virus (wave 1) or the B.1.1.7 (Alpha) variant of concern (wave 3) for testing neutralization sensitivity. The R.1 isolates were potently neutralized by both the wave 1 and wave 3 convalescent serum samples, unlike the B.1.351 (Beta) variant of concern. Of note, the R.1 variant was significantly more resistant to type I interferons (IFN-α/ß) than was the ancestral isolate. Our study demonstrates that the R.1 variant retained sensitivity to neutralizing antibodies but evolved resistance to type I interferons. This critical driving force will influence the trajectory of the pandemic.

Investigating the impact of quarantine on mental health: insights from the COVID-19 international border surveillance study in Canada.

BACKGROUND: Nations throughout the world are imposing mandatory quarantine on those entering the country. Although such measures may be effective in reducing the importation of COVID-19, the mental health implications remain unclear. AIMS: This study sought to assess mental well-being and factors associated with changes in mental health in individuals subject to mandatory quarantine following travel. METHOD: Travellers arriving at a large, urban international airport completed online questionnaires on arrival and days 7 and 14 of mandated quarantine. Questionnaire items, such as travel history, mental health, attitudes toward COVID-19, and protection behaviours, were drawn from the World Health Organization Survey Tool for COVID-19. RESULTS: There was a clinically significant decline in mental health over the course of quarantine among the 10 965 eligible participants. Poor mental health was reported by 5.1% of participants on arrival and 26% on day 7 of quarantine. Factors associated with a greater decline in mental health were younger age, female gender, negative views toward quarantine measures and engaging in fewer COVID-19 prevention behaviours. For instance, travellers who stated that they rarely wore masks had nearly three times higher odds of developing poor mental health. CONCLUSIONS: Although the widespread use of quarantine may be effective in limiting the spread of COVID-19, the mental health implications are profound and have largely been ignored in policy decisions. Psychiatry has a role to play in contributing to the public policy debate to ensure that all aspects of health and well-being are reflected in decisions to isolate people from others.

COVID-19 international border surveillance at Toronto's Pearson Airport: a cohort study.

OBJECTIVES: The primary objective was to estimate the positivity rate of air travellers coming to Toronto, Canada in September and October 2020, on arrival and on day 7 and day 14. The secondary objectives were to estimate the degree of risk based on country of origin and to assess knowledge and attitudes towards COVID-19 control measures and subjective well-being during the quarantine period. DESIGN: Prospective cohort of arriving international travellers. SETTING: Toronto Pearson Airport Terminal 1, Toronto, Canada. PARTICIPANTS: Participants of this study were passengers arriving on international flights. Inclusion criteria were those aged 18 or older who had a final destination within 100 km of the airport, spoke English or French, and provided consent. Excluded were those taking a connecting flight, had no internet access, exhibited symptoms of COVID-19 on arrival or were exempted from quarantine. MAIN OUTCOME MEASURES: Positive for SARS-CoV-2 virus on reverse transcription PCR with self-administered oral-nasal swab and general well-being using the WHO-5 Well-being Index. RESULTS: Of 16 361 passengers enrolled, 248 (1.5%, 95% CI 1.3% to 1.7%) tested positive. Of these, 167 (67%) were identified on arrival, 67 (27%) on day 7, and 14 (6%) on day 14. The positivity rate increased from 1% in September to 2% in October. Average well-being score declined from 19.8 (out of a maximum of 25) to 15.5 between arrival and day 7 (p<0.001). CONCLUSIONS: A single arrival test will pick up two-thirds of individuals who will become positive by day 14, with most of the rest detected on the second test on day 7. These results support strategies identified through mathematical models that a reduced quarantine combined with testing can be as effective as a 14-day quarantine.

Rapid disappearance of influenza following the implementation of COVID-19 mitigation measures in Hamilton, Ontario.

BACKGROUND: Public health measures, such as physical distancing and closure of schools and non-essential services, were rapidly implemented in Canada to interrupt the spread of the coronavirus disease 2019 (COVID-19). We sought to investigate the impact of mitigation measures during the spring wave of COVID-19 on the incidence of other laboratory-confirmed respiratory viruses in Hamilton, Ontario. METHODS: All nasopharyngeal swab specimens (n=57,503) submitted for routine respiratory virus testing at a regional laboratory serving all acute-care hospitals in Hamilton between January 2010 and June 2020 were reviewed. Testing for influenza A and B, respiratory syncytial virus, human metapneumovirus, parainfluenza I-III, adenovirus, and rhinovirus/enterovirus was done routinely using a laboratory-developed polymerase chain reaction multiplex respiratory viral panel. A Bayesian linear regression model was used to determine the trend of positivity rates of all influenza samples for the first 26 weeks of each year from 2010 to 2019. The mean positivity rate of Bayesian inference was compared with the weekly reported positivity rate of influenza samples in 2020. RESULTS: The positivity rate of influenza in 2020 diminished sharply following the population-wide implementation of COVID-19 interventions. Weeks 12-26 reported 0% positivity for influenza, with the exception of 0.1% reported in week 13. CONCLUSION: Public health measures implemented during the COVID-19 pandemic were associated with a reduced incidence of other respiratory viruses and should be considered to mitigate severe seasonal influenza and other respiratory virus pandemics.

Pandemic Planning in Homeless Shelters: A Pilot Study of a Coronavirus Disease 2019 (COVID-19) Testing and Support Program to Mitigate the Risk of COVID-19 Outbreaks in Congregate Settings.

We tested 104 residents and 141 staff for coronavirus disease 2019 who failed daily symptom screening in homeless shelters in Hamilton, Canada. We detected 1 resident (1%), 7 staff (5%), and 1 case of secondary spread. Shelter restructuring to allow physical distancing, testing, and isolation can decrease outbreaks in shelters.

Comparison of four COVID-19 screening strategies to facilitate early case identification within the homeless shelter population: A structured summary of a study protocol for a randomised controlled trial.

OBJECTIVES: 1. To compare the effectiveness of four different surveillance strategies in detecting COVID-19 within the homeless shelter population. 2. To assess the participant adherence over time for each surveillance method. TRIAL DESIGN: This is a prospective cluster-randomized study to compare the effectiveness of four different surveillance regimens across eight homeless shelters in the city of Hamilton. PARTICIPANTS: Participants will include both residents of, and the staff working within, the homeless shelters. All participants aged 18 or older who consent to the study and are able to collect a swab sample (where relevant) are eligible for the study. The study will take place across eight homeless shelters (four men-only and four women-only) in the City of Hamilton in Ontario, Canada. INTERVENTION AND COMPARATOR GROUPS: The comparator group will receive active daily surveillance of symptoms and testing will only be completed in symptomatic participants (i.e. those who fail screening or who seek care for potential COVID-19 related symptoms). The three intervention arms will all receive active daily surveillance of symptoms and testing of symptomatic participants (as in the comparator group) in addition to one of the following: 1. Once weekly self-collected oral swabs (OS) regardless of symptoms using written and visual instructions. 2. Once weekly self-collected oral-nares swab (O-NS) regardless of symptoms using written and visual instructions. 3. Once weekly nurse collected nasopharyngeal swab (NPS) regardless of symptoms. Participants will follow verbal and written instructions for the collection of OS and O-NS specimens. For OS collection, participants are instructed to first moisten the swab on their tongue, insert the swab between the cheek and the lower gums and rotate the swab three times. This is repeated on the other side. For O-NS collection, after oral collection, the swab is inserted comfortably (about 2-3 cm) into one nostril, parallel to the floor and turned three times, then repeated in the other nostril. NPS specimens were collected by the nurse following standard of care procedure. All swabs were placed into a viral inactivation medium and transported to the laboratory for COVID-19 testing. Briefly, total nucleic acid was extracted from specimens and then amplified by RT-PCR for the UTR and Envelope genes of SARS-CoV-2 and the human RNase P gene, which is used as a sample adequacy marker. MAIN OUTCOMES: 1. PRIMARY OUTCOME: COVID-19 detection rate, i.e. the number of new positive cases over the study period of 8 weeks in each arm of the study. 2. SECONDARY OUTCOMES: Qualitative assessment of study enrollment over 8 weeks. Percentage of participants who performed 50% or more of the weekly swabs in the intervention arms in the 8 week study period. RANDOMIZATION: We will use a computer-generated random assignment list to randomize the shelters to one of four interventions. Shelters were stratified by gender, and the simple randomization scheme was applied within each stratum. The randomization scheme was created using WinPEPI. BLINDING: This is an open-label study in which neither participants nor assessors are blinded. NUMBERS TO BE RANDOMIZED (SAMPLE SIZE): Since we are including our total sample frame, a sample size estimation at the cluster level is not required. However, if we succeed to enroll 50 participants per shelter from 8 shelters (n=400), and the detection rate is 3 times higher in the intervention groups (0.15) than in the comparator groups (0.05), we will have 90% power to detect a statistically significant and clinically important difference at a type I error rate of alpha=0.05 (one tailed), assuming an intraclass correlation of ~0.008. These computations were done using WinPEPI, and informed by conservative estimates from other studies on respiratory illness in the homeless (see Full protocol). TRIAL STATUS: The protocol version number is 3.0. Recruitment began on April 17, 2020 and is ongoing. Due to low numbers of COVID cases in the community and shelter system during the initial study period, the trial was extended. The estimated date for the end of the extended recruitment period is Feb 1, 2021. TRIAL REGISTRATION: The trial was registered with ClinicalTrials.gov on June 18, 2020 with the identifier NCT04438070 . FULL PROTOCOL: The full protocol is attached as an additional file, accessible from the Trials website (Additional file 1). In the interest in expediting dissemination of this material, the familiar formatting has been eliminated; this Letter serves as a summary of the key elements of the full protocol.

Real-time PCR-based SARS-CoV-2 detection in Canadian laboratories.

With emergence of pandemic COVID-19, rapid and accurate diagnostic testing is essential. This study compared laboratory-developed tests (LDTs) used for the detection of SARS-CoV-2 in Canadian hospital and public health laboratories, and some commercially available real-time RT-PCR assays. Overall, analytical sensitivities were equivalent between LDTs and most commercially available methods.