Evidence map›Paper›PMID 38632523›Full record

ArticleBMC genomics2024

Comprehensive genomic analysis of the SARS-CoV-2 Omicron variant BA.2.76 in Jining City, China, 2022.

Qiang Yin, Wei Liu, Yajuan Jiang, Qiang Feng, Xiaoyu Wang, Huixin Dou, Zanzan Liu, Feifei He, Yingying Fan, Baihai Jiao and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing 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

7 citing papers in PubMed.

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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

11 authors.

Qiang YinDepartment of Laboratory, Jining Center for Disease Control and Prevention, Jining, China.
Wei LiuDepartment of Laboratory, Jining Center for Disease Control and Prevention, Jining, China.
Yajuan JiangDepartment of Laboratory, Jining Center for Disease Control and Prevention, Jining, China.
Qiang FengDepartment of Laboratory, Rencheng Center for Disease Control and Prevention, Jining, China.
Xiaoyu WangDepartment of Laboratory, Jining Center for Disease Control and Prevention, Jining, China.
Huixin DouDepartment of Laboratory, Jining Center for Disease Control and Prevention, Jining, China.
Zanzan LiuDepartment of Laboratory, Jining Center for Disease Control and Prevention, Jining, China.
Feifei HeComputer Information Technology, Northern Arizona University, Arizona, USA.
Yingying FanDepartment of Laboratory, Jining Center for Disease Control and Prevention, Jining, China. 1269792106@qq.com.
Baihai JiaoDepartment of Medicine, School of Medicine, University of Connecticut Health Center, Farmington, CT, USA. Bjiao@uchc.edu.
Boyan JiaoDepartment of Laboratory, Jining Center for Disease Control and Prevention, Jining, China. j198319831983@126.com.

Funding

Jining City Key Research and Development Plan 2023YXNS026Key Research and Development Funds for Jining Medical and Health 2021018Science and Technology Development Funds for Shandong Medical and Health 202112060725
6 · The paper itself

Abstract

objectiveThis study aims to analyze the molecular characteristics of the novel coronavirus (SARS-CoV-2) Omicron variant BA.2.76 in Jining City, China.

methodsWhole-genome sequencing was performed on 87 cases of SARS-CoV-2 infection. Evolutionary trees were constructed using bioinformatics software to analyze sequence homology, variant sites, N-glycosylation sites, and phosphorylation sites.

resultsAll 87 SARS-CoV-2 whole-genome sequences were classified under the evolutionary branch of the Omicron variant BA.2.76. Their similarity to the reference strain Wuhan-Hu-1 ranged from 99.72 to 99.74%. In comparison to the reference strain Wuhan-Hu-1, the 87 sequences exhibited 77-84 nucleotide differences and 27 nucleotide deletions. A total of 69 amino acid variant sites, 9 amino acid deletions, and 1 stop codon mutation were identified across 18 proteins. Among them, the spike (S) protein exhibited the highest number of variant sites, and the ORF8 protein showed a Q27 stop mutation. Multiple proteins displayed variations in glycosylation and phosphorylation sites.

conclusionSARS-CoV-2 continues to evolve, giving rise to new strains with enhanced transmission, stronger immune evasion capabilities, and reduced pathogenicity. The application of high-throughput sequencing technologies in the epidemic prevention and control of COVID-19 provides crucial insights into the evolutionary and variant characteristics of the virus at the genomic level, thereby holding significant implications for the prevention and control of the COVID-19 pandemic.

Indexed as

COVID-19SARS-CoV-2Amino AcidsChinaGenomicsHumansNucleotidesPandemicsAmino AcidsNucleotidesMolecular featuresOmicronSARS-CoV-2Termination mutationWhole genome sequencing

Identifiers

PMID38632523
PMCPMC11022347

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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.