Genomic Characterisation Reveals a Dominant Lineage of SARS-CoV-2 in Papua New Guinea | Zendy

Theresa Palou | Zendy; Mathilda Wilmot | Zendy; Sebastián Duchêne | Zendy; Ashleigh F. Porter | Zendy; Janlyn Kemoi | Zendy; Dagwin Suarkia | Zendy; Patiyan Andersson | Zendy; A. Watt | Zendy; Norelle L. Sherry | Zendy; Torsten Seemann | Zendy; Michelle Sait | Zendy; Charlie Turharus | Zendy; Son Hoang Nguyen | Zendy; Sanmarié Schlebusch | Zendy; Craig Thompson | Zendy; Jamie McMahon | Zendy; Stefanie Vaccher | Zendy; Chantel Lin | Zendy; Danoi Esoram | Zendy; Benjamin P. Howden | Zendy; Melinda Susapu | Zendy

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Genomic Characterisation Reveals a Dominant Lineage of SARS-CoV-2 in Papua New Guinea

Author(s) -

Theresa Palou,

Mathilda Wilmot,

Sebastián Duchêne,

Ashleigh F. Porter,

Janlyn Kemoi,

Dagwin Suarkia,

Patiyan Andersson,

A. Watt,

Norelle L. Sherry,

Torsten Seemann,

Michelle Sait,

Charlie Turharus,

Son Hoang Nguyen,

Sanmarié Schlebusch,

Craig Thompson,

Jamie McMahon,

Stefanie Vaccher,

Chantel Lin,

Danoi Esoram,

Benjamin P. Howden,

Melinda Susapu

Publication year - 2022

Publication title -

virus evolution

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 2.231

H-Index - 23

ISSN - 2057-1577

DOI - 10.1093/ve/veac033

Subject(s) - genomics , lineage (genetic) , outbreak , phylogenetic tree , pandemic , biology , evolutionary biology , comparative genomics , public health , genome , phylogenetics , computational biology , genetics , geography , disease , infectious disease (medical specialty) , virology , covid-19 , gene , medicine , pathology , nursing

The COVID-19 pandemic has highlighted the utility of pathogen genomics as a key part of a comprehensive public health response to emerging infectious diseases threats, however the ability to generate, analyses and respond to pathogen genomic data varies around the world. Papua New Guinea (PNG), which has limited in-country capacity for genomics, has experienced significant outbreaks of SARS-CoV-2 with initial genomics data indicating a large proportion of cases were from lineages that are not well-defined within the current nomenclature. Through a partnership between in-country public health agencies and academic organisations, industry, and a public health genomics reference laboratory in Australia a system for routine SARS-CoV-2 genomics from PNG was established. Here we aim to characterise and describe the genomics of PNG’s second wave and examine the sudden expansion of a lineage that is not well defined but very prevalent in the Western Pacific region. We generated 1797 sequences from cases in PNG and performed phylogenetic and phylodynamic analyses to examine the outbreak and characterise the circulating lineages and clusters present. Our results reveal the rapid expansion of the B.1.466.2 and related lineages within PNG, from multiple introductions into the country. We also highlight the difficulties that unstable lineage assignment causes when using genomics to assist with rapid cluster definitions.

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