Palou Theresa, Wilmot Mathilda, Duchene Sebastian, Porter Ashleigh, Kemoi Janlyn, Suarkia Dagwin, Andersson Patiyan, Watt Anne, Sherry Norelle, Seemann Torsten, Sait Michelle, Turharus Charlie, Nguyen Son, Schlebusch Sanmarié, Thompson Craig, McMahon Jamie, Vaccher Stefanie, Lin Chantel, Esoram Danoi, Howden Benjamin P, Susapu Melinda
Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, VIC 3000, Australia.
Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, VIC 3000, Australia.
Virus Evol. 2022 Apr 7;8(1):veac033. doi: 10.1093/ve/veac033. eCollection 2022 Apr.
The coronavirus disease pandemic has highlighted the utility of pathogen genomics as a key part of comprehensive public health response to emerging infectious diseases threats, however, the ability to generate, analyse, 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 severe acute respiratory syndrome coronavirus 2 (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.
冠状病毒病大流行凸显了病原体基因组学作为全面应对新发传染病威胁的公共卫生关键组成部分的作用。然而，世界各地生成、分析和应对病原体基因组数据的能力各不相同。巴布亚新几内亚（PNG）国内基因组学能力有限，曾经历过严重急性呼吸综合征冠状病毒2（SARS-CoV-2）的重大疫情，初步基因组学数据表明，很大一部分病例来自当前命名法中定义不明确的谱系。通过该国国内公共卫生机构与学术组织、行业以及澳大利亚一家公共卫生基因组学参考实验室之间的合作，建立了一个来自巴布亚新几内亚的SARS-CoV-2常规基因组学系统。在此，我们旨在对巴布亚新几内亚第二波疫情的基因组学特征进行描述，并研究一个在西太平洋地区定义不明确但非常普遍的谱系的突然扩张。我们从巴布亚新几内亚的病例中生成了1797个序列，并进行了系统发育和系统动力学分析，以研究疫情并确定当前流行的谱系和簇。我们的结果揭示了B.1.466.2及相关谱系在巴布亚新几内亚境内的迅速扩张，这是由多次传入该国所致。我们还强调了在利用基因组学协助快速确定簇时，不稳定的谱系分类所带来的困难。
