Inferring effects of mutations on SARS-CoV-2 transmission from genomic surveillance data

New and more transmissible variants of SARS-CoV-2 have arisen multiple times over the course of the pandemic. Rapidly identifying mutations that affect transmission could facilitate outbreak control efforts and highlight new variants that warrant further study. Here we develop an analytical epidemiological model that infers the transmission effects of mutations from genomic surveillance data. Applying our model to SARS-CoV-2 data across many regions, we find multiple mutations that strongly affect the transmission rate, both within and outside the Spike protein. We also quantify the effects of travel and competition between different lineages on the inferred transmission effects of mutations. Importantly, our model detects lineages with increased transmission as they arise. We infer significant transmission advantages for the Alpha and Delta variants within a week of their appearances in regional data, when their regional frequencies were only around 1%. Our model thus enables the rapid identification of variants and mutations that affect transmission from genomic surveillance data.

Hospital Outbreak of the SARS-CoV-2 Delta Variant in Partially and Fully Vaccinated Patients and Healthcare Workers in Toronto, Canada

The SARS-CoV-2 Delta variant is highly transmissible and current vaccines may have reduced effectiveness in preventing symptomatic infection. Using epidemiological and genomic analysis, we investigated an outbreak of the variant in an acute care setting amongst partially and fully vaccinated individuals. Effective outbreak control was achieved using standard measures.

Studies of COVID-19 Outbreak Control Using Agent-Based Modeling

An agent-based model was developed to study outbreaks and outbreak control for COVID-19, mainly in urban communities. Rules for people’s interactions and virus infectiousness were derived based on previous sociology studies and recently published data-driven analyses of COVID-19 epidemics. The calculated basic reproduction number of epidemics from the developed model coincided with reported values. There were three control measures considered in this paper: social distancing, self-quarantine and community quarantine. Each control measure was assessed individually at first. Later on, an artificial neural network was used to study the effects of different combinations of control measures. To help quantify the impacts of self-quarantine and community quarantine on outbreak control, both were scaled respectively. The results showed that self-quarantine was more effective than the others, but any individual control measure was ineffective in controlling outbreaks in urban communities. The results also showed that a high level of self-quarantine and general community quarantine, assisted with social distancing, would be recommended for outbreak control.

Factors influencing SARS-CoV-2 transmission and outbreak control measures in densely populated settings

Starting with a handful of SARS-CoV-2 infections in dormitory residents in late March 2020, rapid transmission in their dense living environments ensued and by October 2020, more than 50,000 acute infections were identified across various dormitories in Singapore. The aim of the study is to identify combination of factors facilitating SARS-CoV-2 transmission and the impact of control measures in a dormitory through extensive epidemiological, serological and phylogenetic investigations, supported by simulation models. Our findings showed that asymptomatic cases and symptomatic cases who did not seek medical attention were major drivers of the outbreak. Furthermore, each resident had about 30 close contacts and each infected resident spread to 4.4 (IQR 3.5–5.3) others at the start of the outbreak. The final attack rate of the current outbreak was 76.2% (IQR 70.6–98.0%) and could be reduced by further 10% under a modified dormitory housing condition. These findings are important when designing living environments in a post COVID-19 future to reduce disease spread and facilitate rapid implementation of outbreak control measures.