Genomic reconstruction of the SARS-CoV-2 epidemic in England

Abstract

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COVID-19 pandemic dynamics in South Africa and epidemiological characteristics of three variants of concern (Beta, Delta, and Omicron)

“…The model-inference system estimates a 53.19% (95% CI: 27.61 - 91.87%) attack rate by Delta, despite the large number of infections during the previous two waves. This large attack rate was possible, due to the high transmissibility of Delta, as reported in multiple studies, 16-20 the more conducive winter transmission conditions (Fig 2A), and the immune erosion from Delta relative to both the ancestral and Beta variants. Consistent with this finding, and in particular the estimated immune erosion, studies have reported a 27.5% reinfection rate during the Delta pandemic wave in Delhi, India 21 and reduced ability of sera from Beta-infection recoverees to neutralize Delta.…”

COVID-19 due to the B.1.617.2 (Delta) variant compared to B.1.1.7 (Alpha) variant of SARS-CoV-2: two prospective observational cohort studies

“…Other studies have also identified higher Delta transmissibility, resulting in rising incidence particularly in young unvaccinated age groups, higher re-infection rates, and a higher viral load in infected individuals. 26 Here we note the REACT-1 study report of an exponential increase in infections in children aged 5-17 years in September 2021, coinciding with return-to-school, with most schoolage children unvaccinated at this time.…”

Genome wide association study of human bacteremia Escherichia coli isolates identifies genetic determinants for the portal of entry but not fatal outcome

“…One can then wonder whether these approaches are likely to ever lead to the discovery of previously undescribed genetic variants able to modulate the establishment of disease and its outcomes. We argue that as genomic sequencing of pathogens is becoming a routine part of clinical or epidemiological practice 40–42 , we will likely eventually reach very large sample sizes, similar to what is currently available for human GWAS studies 43 , and possibly larger, as has been recently shown for Sars-Cov-2 genomic epidemiology efforts 44,45 . Apart from increasing the power to discover genetic variants associated with a phenotype, a large sample size would allow for the discovery of rare or ultra-rare variants, which in turn may have a relatively large influence on the phenotype of interest, alone or collectively 23 , as has recently been appreciated in the study of human traits and disease 46 .…”