Evidence map›Paper›PMID 35875697›Full record

ArticleVirus evolution2022

Genomic characterisation reveals a dominant lineage of SARS-CoV-2 in Papua New Guinea.

Theresa Palou, Mathilda Wilmot, Sebastian Duchene, Ashleigh Porter, Janlyn Kemoi, Dagwin Suarkia, Patiyan Andersson, Anne Watt, Norelle Sherry, Torsten Seemann and 11 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Virus evolution, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

21 authors.

Theresa Palou
Mathilda WilmotMicrobiological 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.
Sebastian DucheneDepartment of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, VIC 3000, Australia.
Ashleigh PorterDepartment of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, VIC 3000, Australia.
Janlyn KemoiCentral Public Health Laboratory, 3 Mile, Taurama Road, Port Moresby National Captial District 111, Papua New Guinea.
Dagwin SuarkiaInstitute of Medical Research, Homate street, Goroka, Eastern Highlands Province 441, Papua New Guinea.
Patiyan AnderssonMicrobiological 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.
Anne WattMicrobiological 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.
Norelle SherryMicrobiological 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.
Torsten SeemannMicrobiological 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.
Michelle SaitMicrobiological 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.
Charlie TurharusOk Tedi Mining Limited, 1 Dakon Road, Tabubil, Western Province 332, Papua New Guinea.
Son NguyenForensic and Scientific Services, Queensland Health, 39 Kessels Road, Coopers Plains, Brisbane, QLD 4108, Australia.
Sanmarié SchlebuschForensic and Scientific Services, Queensland Health, 39 Kessels Road, Coopers Plains, Brisbane, QLD 4108, Australia.
Craig ThompsonForensic and Scientific Services, Queensland Health, 39 Kessels Road, Coopers Plains, Brisbane, QLD 4108, Australia.
Jamie McMahonForensic and Scientific Services, Queensland Health, 39 Kessels Road, Coopers Plains, Brisbane, QLD 4108, Australia.
Stefanie VaccherIndependant consultant, Papua New Guinea.
Chantel LinMicrobiological 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.
Danoi EsoramNational Control Centre, Ministry of Health, AOPI Building Centre, Waigani Drive, Tower One. Waigani, Port Moresby 121, Papua New Guinea.
Benjamin P HowdenMicrobiological 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.ORCID https://orcid.org/0000-0003-0237-1473
Melinda SusapuNational Control Centre, Ministry of Health, AOPI Building Centre, Waigani Drive, Tower One. Waigani, Port Moresby 121, Papua New Guinea.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

AU.1AU.3B.1.459B.1.466.2genomic sequencing capacityPacific Islands SARS-CoV-2Pacific lineagePapua New Guinea SARS-CoV-2PNG Covid-19PNG genomic sequencingPNG lineagePNG SARS-CoV-2

Identifiers

PMID35875697
PMCPMC9278129

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.