Mutational dynamics and transmission properties of SARS-CoV-2 superspreading events in Austria

Abstract

Superspreading events shape the COVID-19 pandemic. Here we provide a national-scale analysis of SARS-CoV-2 outbreaks in Austria, a country that played a major role for virus transmission across Europe and beyond. Capitalizing on a national epidemiological surveillance system, we performed deep whole-genome sequencing of virus isolates from 576 samples to cover major Austrian SARS-CoV-2 clusters. Our data chart a map of early viral spreading in Europe, including the path from low-frequency mutations to fixation. Detailed epidemiological surveys enabled us to calculate the effective SARS-CoV-2 population bottlenecks during transmission and unveil time-resolved intra-patient viral quasispecies dynamics. This study demonstrates the power of integrating deep viral genome sequencing and epidemiological data to better understand how SARS-CoV-2 spreads through populations.Graphical Abstract

Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck

“…Our results further suggest that human SARS-CoV-2 isolates are relatively well-adapted to feline hosts, and that cat models recapitulate key aspects of SARS-CoV-2 evolution in humans. Notably, we estimate narrow bottlenecks in cats, involving transmission of only 2-6 viruses, consistent with the subset of studies in humans that have reported small bottleneck sizes [25][26][27][28] . We posit that the cat transmission model will be useful for investigating within-and between-host evolution of SARS-CoV-2 viruses.…”

“…We find genetic drift and purifying selection shape SARS-CoV-2 genetic diversity within feline hosts, and a stringent bottleneck defines viral transmission. This latter finding is at odds with some recent studies in humans, which have estimated wide and variable SARS-CoV-2 transmission bottlenecks [25][26][27][28] . Our data, however, is in line with other narrow estimates 25 .…”

“…Our data, however, is in line with other narrow estimates 25 . These discordant estimates are likely due to a combination of factors including uncertain sources of infection, difficulty collecting samples which closely bookend the transmission event, and inaccurate variant calls [25][26][27][28] . These studies have commonly identified transmission pairs using intrahousehold infections diagnosed within a defined timeframe.…”

The genomic epidemiology of SARS-CoV-2 in Palestine

“…One of the key challenges in reconstructing the spread, and more formal direct transmissions, of SARS-CoV-2 is its relatively low mutation rate, meaning multiple transmissions can occur before any mutation A possible approach to reconstructing transmission in these settings has been suggested by the use of shared minority variants 18,28 . In our dataset we do identify a set of three identical isolates, two of which share minority variants, suggesting these two samples are more closely related.…”

“…Genomic data can be a rich source of information to inform on a variety of key epidemiological parameters such as the age and geographic origins of epidemics, their relative growth rates, to distinguish persistent infections from reinfections and to inform on the relative contributions of imported cases compared to sustained community or cryptic transmission. A wealth of genomic studies of SARS-CoV-2 from the more local 3,[7][8][9][10][11][12][13][14][15][16] through to continental 17,18 and global scales 1,19 have consistently pointed to most densely sequenced countries around the world having experienced a number of independent introductions, seeding local transmission chains which are subsequently maintained or may go extinct.…”