Differences in case-fatality-rate of emerging SARS-CoV-2 variants.

Objects: Variants of Severe-Acute-Respiratory-Syndrome Coronavirus-2 (SARS-CoV-2) has caused tremendous impact globally. It has been widely reported that the Omicron (B.1.1.529) variant is less deadly than the Delta (B.1.617.2) variant, presumably due to immunity from vaccination and previous infection. When measuring the severity of a variant, Case-Fatality-Rate (CFR) is often estimated. The purpose of this work is to calculate the change in CFR of different variants over time from a large number of countries/regions since the start of the pandemic in 2020. Study design: A Cross-sectional study. Methods: We extend the comparison to all previous VOCs in 58 counties/regions. We use reported death divided by reported cases in 30-day sliding window with a two-week shift between reported death and reported cases. Results: The drop from Delta variant to Omicron variant is substantial and the difference between subvariants of Omicron is not evident. Conclusion: We showed that the CFR dropped over time, presumably due to vaccine-induced immune and infection induced immune. Population age structure and prevalence of comorbidity influence CFR.

Modelling of Waning of Immunity and Reinfection Induced Antibody Boosting of SARS-CoV-2 in Manaus, Brazil.

It was reported that the Brazilian city, Manaus, likely exceeded the herd immunity threshold (presumably 60-70%) in November 2020 after the first wave of COVID-19, based on the serological data of a routine blood donor. However, a second wave started in November 2020, when an even higher magnitude of deaths hit the city. The arrival of the second wave coincided with the emergence of the Gamma (P.1) variant of SARS-CoV-2, with higher transmissibility, a younger age profile of cases, and a higher hospitalization rate. Prete et al. (2020 MedRxiv 21256644) found that 8 to 33 of 238 (3.4-13.9%) repeated blood donors likely were infected twice in Manaus between March 2020 and March 2021. It is unclear how this finding can be used to explain the second wave. We propose a simple model which allows reinfection to explain the two-wave pattern in Manaus. We find that the two waves with 30% and 40% infection attack rates, respectively, and a reinfection ratio at 3.4-13.9%, can explain the two waves well. We argue that the second wave was likely because the city had not exceeded the herd immunity level after the first wave. The reinfection likely played a weak role in causing the two waves.

Infection Fatality Rate and Infection Attack Rate of COVID-19 in South American Countries (preprint)

Background: The ongoing COVID-19 pandemic hit South America badly with two waves. Different COVID-19 variants have been storming across the region, leading to more severe infections and deaths even in places with high vaccination coverages. Methods: We use the start-of-the-art iterated filtering likelihood-based inference disease modelling framework. We modify the classical susceptible-exposed-infectious-recovered model with a time-varying transmission rate, and additional delayed class and vaccinations to reported COVID-19 deaths in 12 South American countries with the highest COVID-19 mortalities. Results: We yield biologically reasonable estimates for the infection fatality rate (IFR), the infection attack rate (IAR) and time-varying transmission rate. We observe that the severity, the dynamical patterns of the deaths and the time-varying transmission rates among the countries are highly heterogeneous. Further, our analysis of the model with vaccination highlights that increasing the vaccination rate could effectively suppress the pandemics in South America. Conclusion: This study reveals the possible mechanism behind the two waves of COVID-19 in South America. We observe reductions in the transmission rate corresponding to each wave plausibly due to improvement in nonpharmaceutical interventions (NPIs) measures and human protective behavior reaction to recent deaths. Thus, strategies coupling social distancing and vaccination could substantially suppress the mortality rate of COVID-19 in South America.