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Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2.

ABSTRACT: Superspreading events shaped the coronavirus disease 2019 (COVID-19) pandemic, and their rapid identification and containment are essential for disease control. Here, we provide a national-scale analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) superspreading during the first wave of infections in Austria, a country that played a major role in initial virus transmissions in Europe. Capitalizing on Austria's well-developed epidemiological surveillance system, we identified major SARS-CoV-2 clusters during the first wave of infections and performed deep whole-genome sequencing of more than 500 virus samples. Phylogenetic-epidemiological analysis enabled the reconstruction of superspreading events and charts a map of tourism-related viral spread originating from Austria in spring 2020. Moreover, we exploited epidemiologically well-defined clusters to quantify SARS-CoV-2 mutational dynamics, including the observation of low-frequency mutations that progressed to fixation within the infection chain. Time-resolved virus sequencing unveiled viral mutation dynamics within individuals with COVID-19, and epidemiologically validated infector-infectee pairs enabled us to determine an average transmission bottleneck size of 10³ SARS-CoV-2 particles. In conclusion, this study illustrates the power of combining epidemiological analysis with deep viral genome sequencing to unravel the spread of SARS-CoV-2 and to gain fundamental insights into mutational dynamics and transmission properties.

SUBMITTER: Popa A

PROVIDER: S-EPMC7857414 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2.

Popa Alexandra A Genger Jakob-Wendelin JW Nicholson Michael D MD Penz Thomas T Schmid Daniela D Aberle Stephan W SW Agerer Benedikt B Lercher Alexander A Endler Lukas L Colaço Henrique H Smyth Mark M Schuster Michael M Grau Miguel L ML Martínez-Jiménez Francisco F Pich Oriol O Borena Wegene W Pawelka Erich E Keszei Zsofia Z Senekowitsch Martin M Laine Jan J Aberle Judith H JH Redlberger-Fritz Monika M Karolyi Mario M Zoufaly Alexander A Maritschnik Sabine S Borkovec Martin M Hufnagl Peter P Nairz Manfred M Weiss Günter G Wolfinger Michael T MT von Laer Dorothee D Superti-Furga Giulio G Lopez-Bigas Nuria N Puchhammer-Stöckl Elisabeth E Allerberger Franz F Michor Franziska F Bock Christoph C Bergthaler Andreas A

Science translational medicine 20201123 573

Superspreading events shaped the coronavirus disease 2019 (COVID-19) pandemic, and their rapid identification and containment are essential for disease control. Here, we provide a national-scale analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) superspreading during the first wave of infections in Austria, a country that played a major role in initial virus transmissions in Europe. Capitalizing on Austria's well-developed epidemiological surveillance system, we identified ...[more]

PMID: 33229462

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Project description:With the progression of the global SARS-CoV-2 pandemic, the new variants have become more infectious and continue spreading at a higher rate than pre-existing ones. Thus, we conducted a study to explore the epidemiology of emerging variants of SARS-CoV-2 that circulated in Bangladesh from December 2020 to September 2021, representing the 2nd and 3rd waves. We collected new cases and deaths per million daily data with the reproduction rate. We retrieved 928 SARS-CoV-2 sequences from GISAID and performed phylogenetic tree construction and mutation analysis. Case counts were lower initially at the end of 2020, during January-February and April-May 2021, whereas the death toll reached the highest value of 1.587 per million on the first week of August and then started to decline. All the variants (α, β, δ, η) were prevalent in the capital city, Dhaka, with dispersion to large cities, such as Sylhet and Chattogram. The B.1.1.25 lineage was prevalent during December 2020, but the B.1.617.2/δ variant was later followed by the B.1.351/β variant. The phylogeny revealed that the various strains found in Bangladesh could be from numerous countries. The intra-cluster and inter-cluster communication began in Bangladesh soon after the virus arrived. The prominent amino acid substitution was D614G from December 2020 to July 2021 (93.5 to 100%). From February-April, one of the VOC's important mutations, N501Y substitution, was also estimated at 51.8%, 76.1%, and 65.1% for the α, β and γ variants, respectively. The γ variant's unique mutation K417T was detected only at 1.8% in February. Another frequent mutation was P681R, a salient feature of the δ variant, detected in June (88.2%) and July (100%). Furthermore, only one γ variant was detected during the entire second and third wave, whereas no η variant was observed in this period. This rapid growth in the number of variants identified across Bangladesh shows virus adaptation and a lack of strict quarantine, prompting periodic genomic surveillance to foresee the spread of new variants, if any, and to take preventive measures as soon as possible.

Dataset Information

Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2.

Publications

Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2.

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