Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) have been key drivers of new coronavirus disease 2019 (COVID-19) pandemic waves. To better understand variant epidemiologic characteristics, here we apply a model-inference system to reconstruct SARS-CoV-2 transmission dynamics in South Africa, a country that has experienced three VOC pandemic waves (i.e. Beta, Delta, and Omicron BA.1) by February 2022. We estimate key epidemiologic quantities in each of the nine South African provinces during March 2020 to February 2022, while accounting for changing detection rates, infection seasonality, nonpharmaceutical interventions, and vaccination. Model validation shows that estimated underlying infection rates and key parameters (e.g. infection-detection rate and infection-fatality risk) are in line with independent epidemiological data and investigations. In addition, retrospective predictions capture pandemic trajectories beyond the model training period. These detailed, validated model-inference estimates thus enable quantification of both the immune erosion potential and transmissibility of three major SARS-CoV-2 VOCs, that is, Beta, Delta, and Omicron BA.1. These findings help elucidate changing COVID-19 dynamics and inform future public health planning.
Keywords: COVID-19; SARS-CoV-2; epidemiology; global health; immune evasion; none; reinfection rate; transmissibility; variant of concern.
【저자키워드】 COVID-19, SARS-CoV-2, Epidemiology, None, global health, immune evasion, Transmissibility, Variant of concern., reinfection rate, 【초록키워드】 coronavirus disease, severe acute respiratory syndrome coronavirus 2, public health, Coronavirus disease 2019, coronavirus, vaccination, pandemic, VoC, variant, Infection, variants of concern, Delta, risk, Nonpharmaceutical interventions, severe acute respiratory syndrome Coronavirus, omicron, immune, global health, immune evasion, Reinfection, SARS-CoV-2 transmission, South Africa, Characteristics, Transmissibility, African, VOCs, Model, trajectory, Beta, epidemiological data, infection rate, estimate, quantification, disease, New coronavirus, retrospective, acute respiratory syndrome, acute respiratory syndrome coronavirus, help, South, parameter, country, independent, addition, nine, driver, 【제목키워드】 COVID-19 pandemic, variants of concern, Delta, Characteristics, epidemiological,