Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil (preprint)

Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite high levels of previous infection there. Through genome sequencing of viruses sampled in Manaus between November 2020 and January 2021, we identified the emergence and circulation of a novel SARS-CoV-2 variant of concern, lineage P.1, that acquired 17 mutations, including a trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor. Molecular clock analysis shows that P.1 emergence occurred around early November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.4–2.2 times more transmissible and 25-61% more likely to evade protective immunity elicited by previous infection with non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness. One-Sentence Summary We report the evolution and emergence of a SARS-CoV-2 lineage of concern associated with rapid transmission in Manaus.

Frequent testing and immunity-based staffing will help mitigate outbreaks in nursing home settings (preprint)

Background: Nursing homes and other long term care facilities have been disproportionately impacted by the COVID-19 pandemic. Strategies are urgently needed to reduce transmission in these vulnerable populations. We aimed to evaluate the reduction in transmission in nursing homes achieved through contact-targeted interventions and testing and to evaluate the effectiveness of two types of screening tests conducted with varying frequency: 1) rapid antigen testing and 2) PCR testing. Methods: We developed an agent-based Susceptible-Exposed-Infectious(Asymptomatic/Symptomatic)-Recovered (SEIR) model to examine SARS-CoV-2 transmission in nursing homes. Residents and staff are modelled individually; residents are split into two cohorts based on COVID-19 diagnosis. In the resident cohorting intervention, recovered residents are moved back from the COVID (infected) cohort to the non-COVID (susceptible/uninfected) cohort. In the immunity-based staffing intervention, recovered staff, who we assume have protective immunity, are assigned to work in the non-COVID cohort, while susceptible staff work in the COVID cohort and are assumed to have high levels of protection from personal protective equipment. These interventions aim to reduce the fraction of people's contacts that are presumed susceptible (and therefore potentially infected) and replace them with recovered (immune) contacts. Results: The frequency and type of testing has a larger impact on the size of outbreaks than the cohorting and staffing interventions. The most effective testing strategies modeled are daily antigen testing of everyone and daily antigen testing of staff with weekly PCR testing for residents. Under all screening testing strategies, the immunity-based staffing intervention reduces the final size of the outbreak. The resident cohorting intervention reduces the final outbreak size under some, but not all, testing scenarios. Conclusions: Increasing the frequency of screening testing of all residents and staff, or even staff alone, in nursing homes has the potential to greatly reduce outbreaks in this vulnerable setting. Immunity-based staffing can further reduce spread at little or no additional cost and becomes particularly important when daily testing is not feasible.