How many SARS-CoV-2 samples have been sequenced so far?
We have sequenced more than 1100 samples since March, of which 747 resulted in full-length high quality SARS-CoV-2 genomes. These are deposited in the public database GISAID. (November 17 2020)
Who funds this project?
Our research has no commercial purpose and is supported by the Vienna Science and Technology Fund (WWTF), the Research Center for Molecular Medicine of the Austrian Academy of Sciences (CeMM), the Austrian Agency for Health and Food Safety (AGES), and several other institutions.
Does the virus mutate?
SARS-CoV-2 continuously mutates at a rate of approximately one mutation every two weeks. As comparison, influenza virus mutates two- to threefold faster than SARS-CoV-2.
What is D614G?
This is a coding mutation in the genome of SARS-CoV-2 which alters the spike protein. D614G emerged in January 2020 and since then is found in many virus strains worldwide. The majority of the Austrian SARS-CoV-2 genomes sequenced by us from end of February/March onwards contained this mutation already. Laboratory experiments showed that the mutation stabilises the spike protein, which is present as a trimer on the surface of the virion, and improves the binding to the cellular receptor ACE2. These studies suggest that the mutation may confer increased infectivity to SARS-CoV-2 in the human population.
What is Nextstrain Austria?
On May 26, we launched the platform Nextstrain Austria to provide public access to the viral genomes sequenced in this project and their role in the global pandemic. Nextstrain Austria integrates the information of 8000 viral genomes from all over the world together with the Austrian strains. This interactive tool allows you to do your own research on SARS-CoV-2! You can follow inferred transmission paths and search for the occurence of new mutations in sequences. Moreover, you can explore what we see in the data under the section Narratives where we use Nextstrain Austria to explain fundamental principles of the evolution of SARS-CoV-2 and what we learnt about its sweep over the globe. Nextstrain Austria was built by Jakob-Wendelin Genger using the great open-source tools of Nextstrain.org.
How do SARS-CoV-2 mutations emerge?
RNA viruses are prone to random mutations in their genomes and accumulate continuously new mutations as drivers of their evolution. In our study by Popa, Genger et al., we investigated cases from a transmission chain with 8 transmission events and were able to observe the establishment of a new mutation. We observed that this mutation appeared first as a minority variant with 3.6% in one individual. After transmission, this virus mutant reached a frequency of 25% in one case and established as a “fixed” (100%) mutation in two other infects. The particular observed non-coding mutation has no effect on the protein sequence of the virus but we cannot predict its impact on the overall virus fitness.
What was the role of the Austrian tourism resort Ischgl for early virus spread?
Several epidemiological studies from e.g. Iceland, Denmark and Germany suggested that tourists returning from Austria were infected with SARS-CoV-2. In our study by Popa, Genger et al., we performed phylogenetic studies of the circulating viruses in Ischgl/Paznaun and other places in Austria, reconstructed the genetic cluster structure and validated the epidemiological data obtained through contact tracing.
How large is the transmission bottleneck of SARS-CoV-2?
In our study by Popa, Genger et al., combined virus deep sequencing with information about epidemiologically-confirmed infector-infectee pairs to calculate the likely initial number of virions that led to productive infection. To this end we asked the question how many of the mutations found in the infector are also present in the infectee. Our analyses considered mutations down to low frequencies of 1%. The result of these calculations were that there are on average 1000 virions that give rise to a new infection (“transmission bottleneck”). You find more information about this here Popa, Genger et al.. Importantly, this number is not absolute but we find a considerable range of different transmission bottleneck sizes. Current research aims to understand whether there are certain factors (e.g. specific protection measures, indoor vs. outdoor) that may affect this number. We are also keen on understanding whether the size of the initial virus inoculum may impact the later clinical course of COVID-19 disease.
Who contributes to this project?
Please see the page with our team, which encompasses colleagues from numerous scientific and medical institutions in Austria and abroad.