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Genomic characterisation reveals a dominant lineage of SARS-CoV-2 in Papua New Guinea.
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.
  • Wilmot M; 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.
  • Duchene S; 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.
  • Porter A; 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.
  • Kemoi J; Central Public Health Laboratory, 3 Mile, Taurama Road, Port Moresby National Captial District 111, Papua New Guinea.
  • Suarkia D; Institute of Medical Research, Homate street, Goroka, Eastern Highlands Province 441, Papua New Guinea.
  • Andersson P; 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.
  • Watt A; 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.
  • Sherry N; 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.
  • Seemann T; 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.
  • Sait M; 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.
  • Turharus C; Ok Tedi Mining Limited, 1 Dakon Road, Tabubil, Western Province 332, Papua New Guinea.
  • Nguyen S; Forensic and Scientific Services, Queensland Health, 39 Kessels Road, Coopers Plains, Brisbane, QLD 4108, Australia.
  • Schlebusch S; Forensic and Scientific Services, Queensland Health, 39 Kessels Road, Coopers Plains, Brisbane, QLD 4108, Australia.
  • Thompson C; Forensic and Scientific Services, Queensland Health, 39 Kessels Road, Coopers Plains, Brisbane, QLD 4108, Australia.
  • McMahon J; Forensic and Scientific Services, Queensland Health, 39 Kessels Road, Coopers Plains, Brisbane, QLD 4108, Australia.
  • Vaccher S; Independant consultant, Papua New Guinea.
  • Lin C; 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.
  • Esoram D; National Control Centre, Ministry of Health, AOPI Building Centre, Waigani Drive, Tower One. Waigani, Port Moresby 121, Papua New Guinea.
  • Howden BP; 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.
  • Susapu M; National Control Centre, Ministry of Health, AOPI Building Centre, Waigani Drive, Tower One. Waigani, Port Moresby 121, Papua New Guinea.
Virus Evol ; 8(1): veac033, 2022 Apr.
Article in English | MEDLINE | ID: covidwho-1937684
ABSTRACT
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.
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Full text: Available Collection: International databases Database: MEDLINE Language: English Journal: Virus Evol Year: 2022 Document Type: Article

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Full text: Available Collection: International databases Database: MEDLINE Language: English Journal: Virus Evol Year: 2022 Document Type: Article