Development and Validation of an In-House Real-Time Reverse-Transcriptase Polymerase Chain Reaction Assay for SARS-CoV-2 Omicron Lineage Subtyping between BA.1 and BA.2.

David Pham, Susan Maddocks, Dominic E Dwyer, Vitali Sintchenko, Jen Kok, Rebecca J Rockett

Open access · goldAbstract read

In one paragraph

Article in Viruses, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it

0cells of the map it votes in

1citing papers in PubMed

0.1field-weighted citation impact, top 57% of its field

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

1 citing paper in PubMed, 1 citations in OpenAlex.

Use of allele-specific qPCR and PCR-RFLP analysis for rapid detection of the SARS-CoV-2 variants in Tunisia: A cheap flexible approach adapted for developing countries.PloS one · 2025
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

6 authors at 2 institutions in 1 country.

David PhamCentre for Infectious Diseases & Microbiology Laboratory Services, New South Wales Health, Pathology-Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia.ORCID 0000-0002-0953-4063

Susan MaddocksCentre for Infectious Diseases & Microbiology Laboratory Services, New South Wales Health, Pathology-Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia.

Dominic E DwyerCentre for Infectious Diseases & Microbiology Laboratory Services, New South Wales Health, Pathology-Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia.

Vitali SintchenkoCentre for Infectious Diseases & Microbiology Laboratory Services, New South Wales Health, Pathology-Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia.

Jen KokCentre for Infectious Diseases & Microbiology Laboratory Services, New South Wales Health, Pathology-Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia.ORCID 0000-0002-8796-283X

Rebecca J RockettSydney Infectious Diseases Institute, The University of Sydney, Westmead, NSW 2145, Australia.

The University of Sydney · AUWestmead Hospital · AU

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

In order to rapidly differentiate sublineages BA.1 and BA.2 of the SARS-CoV-2 variant of concern Omicron, we developed a real-time reverse-transcriptase polymerase chain reaction to target the discriminatory spike protein deletion at amino acid position 69-70 (S:del69-70). Compared to the gold standard of whole genome sequencing, the candidate assay was 100% sensitive and 99.4% specific. Sublineage typing by RT-PCR can provide a rapid, high throughput and cost-effective method to enhance surveillance as well as potentially guiding treatment and infection control decisions.

Indexed as

COVID-19SARS-CoV-2COVID-19 TestingHumansReverse Transcriptase Polymerase Chain ReactionRNA-Directed DNA PolymeraseRNA, ViralRNA-Directed DNA PolymeraseRNA, ViralCOVID-19Omicronreal-time RT-PCRSARS-CoV-2sublineagevariants of concern

Identifiers

PMID36016382

DOI10.3390/v14081760

PMCPMC9416591

OpenAlexW4292182256

What OpenQuestion holds

Textmetadata

LicenceCC BY

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.