RESEARCH ARTICLE
Ancestral Area Reconstruction of SARS-CoV-2 Indicates Multiple Sources of Entry into Australia
Ngoc Minh Hien Phan1, 2, Helen Faddy1, 2, 3, Robert Flower1, 2, Kirsten Spann1, Eileen Roulis1, 2, *
Article Information
Identifiers and Pagination:
Year: 2021Volume: 14
First Page: 13
Last Page: 20
Publisher ID: TOBIOIJ-14-13
DOI: 10.2174/1875036202114010013
Article History:
Received Date: 9/12/2020Revision Received Date: 18/3/2021
Acceptance Date: 25/4/2021
Electronic publication date: 02/11/2021
Collection year: 2021
open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: https://creativecommons.org/licenses/by/4.0/legalcode. This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Abstract
Background:
The ongoing COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). International travels to Australia during the early stages of the pandemic prior to border closure provided avenues for this virus to spread into Australia. Studies of SARS-CoV-2 biogeographical distribution can contribute to the understanding of the viral original sources to Australia.
Objective:
This study aimed to investigate the clonality and ancestral sources of Australian SARS-CoV-2 isolates using phylogenetic methods.
Methods:
We retrieved 1,346 complete genomes from Australia along with 153 genomes from other countries from the GISAID and NCBI nucleotide databases as of the 14th May 2020. A representative dataset of 270 Australian and international sequences were resulted from performance of nucleotide redundancy reduction by CD-HIT. We then constructed a median-joining network by Network 10.1.0.0, and phylogenies by IQ-Tree, BEAST and FastTree. The Bayesian statistical dispersal-vicariance analysis (S-DIVA) and Bayesian interference for discrete areas (BayArea) built in RASP were used to reconstruct ancestral ranges over the phylogenetic trees.
Results:
Two major clusters, from Europe and from Asia, were observed on the network of 183 haplotypes with distinct nucleotide variations. Analysis of ancestral area reconstruction over the phylogenies indicated most Australian SARS-CoV-2 sequences were disseminated from Europe and East Asia-Southeast Asia.
Conclusion:
The finding is genetic evidence for the geographic origins of the Australian SARS-CoV-2 sequences. Most Australian sequences were genetically similar to those from Europe and East Asia-Southeast Asia, which were also suggested as two main sources of introduction of SARS-CoV-2 to Australia.
