Global Expansion of SARS-CoV-2 Variants of Concern: Dispersal Patterns and Influence of Air Travel

In many regions of the world, the Alpha, Beta and Gamma SARS-CoV-2 Variants of Concern (VOCs) co-circulated during 2020-21 and fueled waves of infections. During 2021, these variants were almost completely displaced by the Delta variant, causing a third wave of infections worldwide. This phenomenon of global viral lineage displacement was observed again in late 2021, when the Omicron variant disseminated globally. In this study, we use phylogenetic and phylogeographic methods to reconstruct the dispersal patterns of SARS-CoV-2 VOCs worldwide. We find that the source-sink dynamics of SARS-CoV-2 varied substantially by VOC, and identify countries that acted as global hubs of variant dissemination, while other countries became regional contributors to the export of specific variants. We demonstrate a declining role of presumed origin countries of VOCs to their global dispersal: we estimate that India contributed <15% of all global exports of Delta to other countries and South Africa <1-2% of all global Omicron exports globally. We further estimate that >80 countries had received introductions of Omicron BA.1 100 days after its inferred date of emergence, compared to just over 25 countries for the Alpha variant. This increased speed of global dissemination was associated with a rebound in air travel volume prior to Omicron emergence in addition to the higher transmissibility of Omicron relative to Alpha. Our study highlights the importance of global and regional hubs in VOC dispersal, and the speed at which highly transmissible variants disseminate through these hubs, even before their detection and characterization through genomic surveillance. HighlightsO_LIGlobal phylogenetic analysis reveals relationship between air travel and speed of dispersal of SARS-CoV-2 variants of concern (VOCs) C_LIO_LIOmicron VOC spread to 5x more countries within 100 days of its emergence compared to all other VOCs C_LIO_LIOnward transmission and dissemination of VOCs Delta and Omicron was primarily from secondary hubs rather than initial country of detection during a time of increased global air travel C_LIO_LIAnalysis highlights highly connected countries identified as major global and regional exporters of VOCs C_LI

Context-specific emergence and growth of the SARS-CoV-2 Delta variant

The Delta variant of concern of SARS-CoV-2 has spread globally causing large outbreaks and resurgences of COVID-19 cases1-3. The emergence of Delta in the UK occurred on the background of a heterogeneous landscape of immunity and relaxation of non-pharmaceutical interventions4,5. Here we analyse 52,992 Delta genomes from England in combination with 93,649 global genomes to reconstruct the emergence of Delta, and quantify its introduction to and regional dissemination across England, in the context of changing travel and social restrictions. Through analysis of human movement, contact tracing, and virus genomic data, we find that the focus of geographic expansion of Delta shifted from India to a more global pattern in early May 2021. In England, Delta lineages were introduced >1,000 times and spread nationally as non-pharmaceutical interventions were relaxed. We find that hotel quarantine for travellers from India reduced onward transmission from importations; however the transmission chains that later dominated the Delta wave in England had been already seeded before restrictions were introduced. In England, increasing inter-regional travel drove Deltas nationwide dissemination, with some cities receiving >2,000 observable lineage introductions from other regions. Subsequently, increased levels of local population mixing, not the number of importations, was associated with faster relative growth of Delta. Among US states, we find that regions that previously experienced large waves also had faster Delta growth rates, and a model including interactions between immunity and human behaviour could accurately predict the rise of Delta there. Deltas invasion dynamics depended on fine scale spatial heterogeneity in immunity and contact patterns and our findings will inform optimal spatial interventions to reduce transmission of current and future VOCs such as Omicron.

The impact of seasonal respiratory virus transmission on syndromic surveillance for COVID-19 in Ontario, Canada

BackgroundSyndromic surveillance systems for COVID-19 are being increasingly used to track and predict outbreaks of confirmed cases. Seasonal circulating respiratory viruses share syndromic overlap with COVID-19, and it is unknown how they will impact the performance of syndromic surveillance tools. Here we investigated the role of non-SARS-CoV-2 respiratory virus test positivity on COVID-19 two independent syndromic surveillance systems in Ontario, Canada. MethodsWe compared the weekly number of reported COVID-19 cases reported in the province of Ontario against two syndromic surveillance metrics: 1) the proportion of respondents with a self-reported COVID-like illness (CLI) from COVID Near You (CNY) and 2) the proportion of emergency department visits for upper respiratory conditions from the Acute Care Enhanced Surveillance (ACES) system. Separately, we plotted the percent positivity for other seasonal respiratory viruses over the same time period and reported Pearsons correlation coefficients before and after the uncoupling of syndromic tools to COVID-19 cases. ResultsThere were strong positive correlations of both CLI and ED visits for upper respiratory causes with COVID-19 cases up to and including a rise in entero/rhinovirus (r = 0.86 and 0.87, respectively). There was a strong negative correlation of both CLI and ED visits for upper respiratory causes with COVID-19 cases (r = -0.85 and -0.91, respectively) during a fall in entero/rhinovirus. InterpretationTwo methods of syndromic surveillance showed strong positive correlations with COVID-19 confirmed case counts before and during a rise in circulating entero/rhinovirus. However, as positivity for enterovirus/rhinovirus fell in late September 2020, syndromic signals became uncoupled from COVID-19 cases and instead tracked the fall in entero/rhinovirus. This finding provides proof-of-principle that regional transmission of seasonal respiratory viruses may complicate the interpretation of COVID-19 surveillance data. It is imperative that surveillance systems incorporate other respiratory virus testing data in order to more accurately track and forecast COVID-19 disease activity.

Impact of a public policy restricting staff mobility between long-term care homes in Ontario, Canada during the COVID-19 pandemic

ObjectivesTo assess changes in the mobility of staff between long-term care homes in Ontario, Canada before and after enactment of public policy restricting staff from working at multiple homes. DesignPre-post observational study. Setting and Participants623 long-term cares homes in Ontario, Canada between March 2020 and June 2020. MethodsWe used anonymized mobile device location data to approximate connectivity between all 623 long-term care homes in Ontario during the 7 weeks before (March 1 - April 21) and after (April 22 - June 13) the policy restricting staff movement was implemented. We visualized connectivity between long-term care homes in Ontario using an undirected network and calculated the number of homes that had a connection with another long-term care home and the average number of connections per home in each period. We calculated the relative difference in these mobility metrics between the two time periods and compared within-home changes using McNemars test and the Wilcoxon rank-sum test. ResultsIn the period preceding restrictions, 266 (42.7%) long-term care homes had a connection with at least one other home, compared to 79 (12.7%) homes during the period after restrictions, a drop of 70.3% (p <0.001). The average number of connections in the before period was 3.90 compared to 0.77 in after period, a drop of 80.3% (p < 0.001). In both periods, mobility between long-term care homes was higher in homes located in larger communities, those with higher bed counts, and those part of a large chain. Conclusions and ImplicationsMobility between long-term care homes in Ontario fell sharply after an emergency order by the Ontario government limiting long-term care staff to a single home, though some mobility persisted. Reducing this residual mobility should be a focus of efforts to reduce risk within the long-term care sector during the COVID-19 pandemic.

Establishment & lineage dynamics of the SARS-CoV-2 epidemic in the UK

The UKs COVID-19 epidemic during early 2020 was one of worlds largest and unusually well represented by virus genomic sampling. Here we reveal the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 SARS-CoV-2 genomes, including 26,181 from the UK sampled throughout the countrys first wave of infection. Using large-scale phylogenetic analyses, combined with epidemiological and travel data, we quantify the size, spatio-temporal origins and persistence of genetically-distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in >1000 lineages; those introduced prior to national lockdown were larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, whilst lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.

Defining the role of asymptomatic SARS-CoV-2 transmission: a living systematic review

BackgroundReports suggest that asymptomatic individuals (those with no symptoms at all throughout the infection) with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are infectious, but the extent of asymptomatic transmission requires further understanding. PurposeThis living review aims to critically appraise available data about secondary attack rates from people with asymptomatic and pre-symptomatic SARS-CoV-2 infection. Data sourcesMedline, EMBASE, China Academic Journals full-text database (CNKI), and preprint servers were searched from 30 December 2019 to 3 July 2020 using relevant MESH terms. Study selectionStudies that report on contact tracing of index cases with asymptomatic or pre-symptomatic SARS-CoV-2 infection, in either English or Chinese were included. Data extractionTwo authors independently extracted data and assessed study quality and risk of bias. We calculated the secondary attack rate as the number of contacts with SARS-CoV-2, divided by the number of contacts tested. Data synthesisOf 928 studies identified, 19 were included. Secondary attack rates from asymptomatic index cases ranged from 0% to 2.8% (9 studies). Pre-symptomatic secondary attack rates ranged from 0.7% to 31.8% (10 studies). The highest secondary attack rates were found in contacts who lived in the same household as the index case. Other activities associated with transmission were group activities such as sharing meals or playing board games with the index case. LimitationsWe excluded some studies because the index case or number of contacts were unclear. Owing to the anticipated heterogeneity, we did not produce a summary estimate of the included studies. ConclusionAsymptomatic patients can transmit SARS-CoV-2 to others, but our findings indicate that such individuals are responsible for fewer secondary infections than people with symptoms in the same studies. Systematic review registrationPROSPERO CRD42020188168 FundingNo funding was received

Syndromic Surveillance for COVID-19 in Canada

BackgroundSyndromic surveillance through web or phone-based polling has been used to track the course of infectious diseases worldwide. Our study objective was to describe the characteristics, symptoms, and self-reported testing rates of respondents in three different COVID-19 symptom surveys in Canada. MethodsData sources consisted of two distinct Canada-wide web-based surveys, and phone polling in Ontario. All three sources contained self-reported information on COVID-19 symptoms and testing. In addition to describing respondent characteristics, we examined symptom frequency and the testing rate among the symptomatic, as well as rates of symptoms and testing across respondent groups. ResultsWe found that 1.6% of respondents experienced a symptom on the day of their survey, 15% of Ontario households had a symptom in the previous week, and 44% of Canada-wide respondents had a symptom in the previous month over March-April 2020. Across the three surveys, SARS-CoV-2-testing was reported in 2-9% of symptomatic responses. Women, younger and middle-aged adults (versus older adults) and Indigenous/First nations/Inuit/Metis were more likely to report at least one symptom, and visible minorities were more likely to report the combination of fever with cough or shortness of breath. InterpretationThe low rate of testing among those reporting symptoms suggests significant opportunity to expand testing among community-dwelling residents of Canada. Syndromic surveillance data can supplement public health reports and provide much-needed context to gauge the adequacy of current SARS-CoV-2 testing rates.