Evidence map›Paper›PMID 35637329›Full record

ArticleNature microbiology2022

Platform for isolation and characterization of SARS-CoV-2 variants enables rapid characterization of Omicron in Australia.

Anupriya Aggarwal, Alberto Ospina Stella, Gregory Walker, Anouschka Akerman, Camille Esneau, Vanessa Milogiannakis, Deborah L Burnett, Samantha McAllery, Mariana Ruiz Silva, Yonghui Lu and 32 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature microbiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.

0numbers the graph read from it
0cells of the map it votes in
29citing 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

29 citing papers in PubMed.

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  19. Immunomodulatory Role of Interferons in Viral and Bacterial Infections.International journal of molecular sciences · 2023
    Review
  20. Real-world experience of tixagevimab-cilgavimab pre-exposure prophylaxis in orthotopic heart transplant recipients.Transplant infectious disease : an official journal of the Transplantation Society · 2023
    Article
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

42 authors.

Anupriya Aggarwal *The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia.
Alberto Ospina Stella *The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia.
Gregory Walker *Serology and Virology Division (SAViD), NSW Health Pathology, Sydney, New South Wales, Australia.
Anouschka AkermanThe Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia.
Camille EsneauHunter Medical Research Institute, University of Newcastle, Callaghan, New South Wales, Australia.
Vanessa MilogiannakisThe Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia.
Deborah L BurnettGarvan Institute of Medical Research, Sydney, New South Wales, Australia.
Samantha McAlleryThe Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia.
Mariana Ruiz SilvaThe Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia.ORCID http://orcid.org/0000-0002-4330-6523
Yonghui LuSerology and Virology Division (SAViD), NSW Health Pathology, Sydney, New South Wales, Australia.
Charles S P FosterSerology and Virology Division (SAViD), NSW Health Pathology, Sydney, New South Wales, Australia.
Fabienne BrilotBrain Autoimmunity Group, Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, School of Medical Sciences, Sydney University of Sydney, Sydney Institute for Infectious Diseases, Sydney, New South Wales, Australia.
Aleha PillayBrain Autoimmunity Group, Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, School of Medical Sciences, Sydney University of Sydney, Sydney Institute for Infectious Diseases, Sydney, New South Wales, Australia.
Sabastiaan Van HalRoyal Prince Alfred Hospital, Sydney, New South Wales, Australia.ORCID http://orcid.org/0000-0001-5852-4155
Vennila MathivananThe Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia.
Christina FichterThe Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia.
Andrea KindingerThe Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia.
Alexandra Carey HoppeThe Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia.
Mee Ling MunierThe Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia.ORCID http://orcid.org/0000-0002-6419-142X
Supavadee Amatayakul-ChantlerDepartment of Bioanalytical Sciences, Plasma Product Development, Research and Development, CSL Behring, Broadmeadows, Melbourne, Victoria, Australia.ORCID http://orcid.org/0000-0003-3510-7476
Nathan RothDepartment of Bioanalytical Sciences, Plasma Product Development, Research and Development, CSL Behring AG, Bern, Switzerland.
Germano CoppolaDepartment of Bioanalytical Sciences, Plasma Product Development, Research and Development, CSL Behring, Broadmeadows, Melbourne, Victoria, Australia.
Geoff P SymondsGene Therapy Research, Sydney, New South Wales, Australia.
Peter SchofieldGarvan Institute of Medical Research, Sydney, New South Wales, Australia.
Jennifer JacksonGarvan Institute of Medical Research, Sydney, New South Wales, Australia.
Helen LenthallGarvan Institute of Medical Research, Sydney, New South Wales, Australia.
Jake Y HenryGarvan Institute of Medical Research, Sydney, New South Wales, Australia.
Ohan MazigiGarvan Institute of Medical Research, Sydney, New South Wales, Australia.
Hans-Martin JäckUniversity of Erlangen-Nürnberg, Erlangen, Germany.
Miles P DavenportThe Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia.
David R DarleySt Vincent's Hospital, Sydney, New South Wales, Australia.ORCID http://orcid.org/0000-0002-9721-101X
Gail V MatthewsThe Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia.
David S KhouryThe Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia.
Deborah CromerThe Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia.
Christopher C GoodnowGarvan Institute of Medical Research, Sydney, New South Wales, Australia.
Daniel ChristGarvan Institute of Medical Research, Sydney, New South Wales, Australia.
Roselle RobosaMolecular Diagnostic Medicine Laboratory, Sydpath, St Vincent's Hospital, Sydney, New South Wales, Australia.ORCID http://orcid.org/0000-0002-7886-8219
Damien J StarckMolecular Diagnostic Medicine Laboratory, Sydpath, St Vincent's Hospital, Sydney, New South Wales, Australia.
Nathan W BartlettSerology and Virology Division (SAViD), NSW Health Pathology, Sydney, New South Wales, Australia.
William D RawlinsonHunter Medical Research Institute, University of Newcastle, Callaghan, New South Wales, Australia.
Anthony D KelleherThe Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia.
Stuart G TurvilleThe Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia. sturville@kirby.unsw.edu.au.ORCID http://orcid.org/0000-0003-1918-5343

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Genetically distinct variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have emerged since the start of the COVID-19 pandemic. Over this period, we developed a rapid platform (R-20) for viral isolation and characterization using primary remnant diagnostic swabs. This, combined with quarantine testing and genomics surveillance, enabled the rapid isolation and characterization of all major SARS-CoV-2 variants circulating in Australia in 2021. Our platform facilitated viral variant isolation, rapid resolution of variant fitness using nasopharyngeal swabs and ranking of evasion of neutralizing antibodies. In late 2021, variant of concern Omicron (B1.1.529) emerged. Using our platform, we detected and characterized SARS-CoV-2 VOC Omicron. We show that Omicron effectively evades neutralization antibodies and has a different entry route that is TMPRSS2-independent. Our low-cost platform is available to all and can detect all variants of SARS-CoV-2 studied so far, with the main limitation being that our platform still requires appropriate biocontainment.

Indexed as

COVID-19SARS-CoV-2AustraliaHumansPandemics

Identifiers

PMID35637329
PMCPMC9159941

What OpenQuestion holds

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Registered trials

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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.