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

Ngoc Minh Hien Phan,Robert Flower,Eileen Roulis,Helen Faddy,Kirsten Spann

doi:10.2174/1875036202114010013

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.

Highlights

IntroductionPeople infected with severe acute respiratory syndrome (SARS)-CoV-2 can have mild symptoms such as fever, cough, sore throat, muscle pain or fatigue, or more severe symptoms such as acute respiratory distress syndrome and shortness of breath [2, 9, 10]
Of the 1,499 human severe acute respiratory syndrome (SARS)-CoV-2 complete genomes initially collected from Global Initiative On Sharing All Influenza Data (GISAID) and NCBI nucleotide databases (Table S1), we obtained 1,218 genomes isolated within Australia and 153 genomes outside Australia (Fig. 1) after removing 128 sequences having ≥3% noninformative sites – 124 from the state of VIC, Australia and four from the Northern Territory (NT), Australia
Over 50% of locally acquired cases were reported to be associated with multiple SARS-CoV-2 introductions by these travellers [38]. This investigation contributes to our understanding of multiple clonality and dissemination of SARS-CoV-2 isolates circulating in Australia

Summary

Introduction

People infected with SARS-CoV-2 can have mild symptoms such as fever, cough, sore throat, muscle pain or fatigue, or more severe symptoms such as acute respiratory distress syndrome and shortness of breath [2, 9, 10]. Other symptoms such as shock, diarrhea, and loss of smell/taste have been reported [2, 9, 10]. Studies of SARS-CoV-2 biogeographical distribution can contribute to the understanding of the viral original sources to Australia

Methods

Results

Discussion

Conclusion