Evidence map›Paper›PMID 36060750›Full record

ArticleFrontiers in microbiology2022

Rapid and sensitive amplicon-based genome sequencing of SARS-CoV-2.

Changwoo Park, Kwan Woo Kim, Dongju Park, Zohaib Ul Hassan, Edmond Changkyun Park, Chang-Seop Lee, Md Tazikur Rahman, Hana Yi, Seil Kim

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Frontiers in microbiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
0.4field-weighted citation impact, top 40% 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

2 citing papers in PubMed, 4 citations in OpenAlex.

  1. Article
  2. 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

9 authors at 6 institutions in 1 country.

Changwoo ParkMicrobiological Analysis Team, Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, South Korea.
Kwan Woo KimDepartment of Public Health Sciences, Graduate School, Korea University, Seoul, South Korea.
Dongju ParkMicrobiological Analysis Team, Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, South Korea.
Zohaib Ul HassanMicrobiological Analysis Team, Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, South Korea.
Edmond Changkyun ParkConvergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology (KRICT), Daejeon, South Korea.
Chang-Seop LeeDepartment of Internal Medicine, Jeonbuk National University Medical School, Jeonju, South Korea.
Md Tazikur RahmanDepartment of Internal Medicine, Jeonbuk National University Medical School, Jeonju, South Korea.
Hana YiDepartment of Public Health Sciences, Graduate School, Korea University, Seoul, South Korea.
Seil KimMicrobiological Analysis Team, Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, South Korea.
Jeonbuk National University · KRKorea Research Institute of Chemical Technology · KRKorea University · KRKorea Basic Science Institute · KRKorea Research Institute of Standards and Science · KRKorea University of Science and Technology · KR

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

As SARS-CoV-2 variants of concern emerged, the genome sequencing of SARS-CoV-2 strains became more important. In this study, SARS-CoV-2 was sequenced using amplicon-based genome sequencing with MinION. The primer panel used in this study consisted of only 11 primer panels and the size of the amplicons was approximately 3 kb. Full genome sequences were obtained with a hundred copies of the SARS-CoV-2 genome, and 92.33% and 75.39% of the genome sequences were obtained with 10 copies of the SARS-CoV-2 genome. The few differences in nucleotide sequences originated from mutations in laboratory cultures and/or mixed nucleotide sequences. The quantification of the SARS-CoV-2 genomic RNA was done using RT-ddPCR methods, and the level of LoD indicated that this sequencing method can be used for any RT-qPCR positive clinical sample. The sequencing results of the SARS-CoV-2 variants and clinical samples showed that our methods were very reliable. The genome sequences of five individual clinical samples were almost identical, and the analysis of the sequence variance showed that most of these nucleotide substitutions were observed in the genome sequences of the other clinical samples, indicating this amplicon-based whole-genome sequencing method can be used in various clinical fields.

Indexed as

amplicon-based genome sequencinglong ampliconMinIONreverse transcription digital droplet PCRSARS-CoV-2

Identifiers

PMID36060750
PMCPMC9428490
OpenAlexW4292265834

What OpenQuestion holds

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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.