Working Paper Article Version 1 This version is not peer-reviewed

Ancestral Area Reconstruction of SARS-CoV-2 Indicates Multiple Sources of Entry into Australia

Version 1 : Received: 26 June 2020 / Approved: 28 June 2020 / Online: 28 June 2020 (09:21:49 CEST)

How to cite: Phan, N.M.H.; Faddy, H.; Flower, R.; Spann, K.; Roulis, E. Ancestral Area Reconstruction of SARS-CoV-2 Indicates Multiple Sources of Entry into Australia. Preprints 2020, 2020060329 Phan, N.M.H.; Faddy, H.; Flower, R.; Spann, K.; Roulis, E. Ancestral Area Reconstruction of SARS-CoV-2 Indicates Multiple Sources of Entry into Australia. Preprints 2020, 2020060329

Abstract

The coronavirus disease 2019 (COVID-19) was officially declared a pandemic on the 11th March 2020. It is caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), impacting the lower respiratory tract. International travel to Australia during the early stages of the pandemic prior to border closure provided avenues for this virus to spread into Australia. There is little understanding of the clonality of SARS-CoV-2 isolates in Australia, and where they originated. This study aimed to investigate the clonality and ancestral sources of SARS-CoV-2 isolates in Australia using in silico methods. We retrieved 1,346 complete genomes from Australia along with 153 genomes from other countries from the NCBI nucleotide database and Global Initiative On Sharing All Influenza Data (GISAID). We then constructed a representative population of 270 sequences for downstream phylogenetic analysis and ancestral area reconstruction. Overall, two major clusters, one stemming from Europe and another from Asia, especially East Asia, were observed, implying at least two major transmission events with subsequent clades confirming the multiclonality of Australian isolates. We also identified three potential dissemination routes of SARS-CoV-2 into Australia. This study supports the hypothesis of multiple clonality and dispersals of SARS-CoV-2 isolates into Australia.

Subject Areas

SARS-CoV-2; COVID-19; novel severe acute respiratory syndrome coronavirus 2; ancestral reconstruction; clonality; source of entry; dispersal routes

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