Evidence map›Paper›PMID 42182013›Full record

ArticleFrontiers in microbiology2026

Comprehensive whole-genome characterization of SARS-CoV-2 strains in Jining China 2024-2025.

Haixia Yang, Xiaoyu Wang, Linlin Zhang, Lingming Kong, Wei Liu, Qiang Yin, Yongjian Jia, Huixin Dou, Ting Chen, Feifei He and 4 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Frontiers in microbiology, 2026. 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
–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

1 citing paper in PubMed.

  1. 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

14 authors.

Haixia Yang *College of Medical Imaging and Laboratory Medicine, Jining Medical University, Jining, China.
Xiaoyu Wang *Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China.
Linlin Zhang *Department of Laboratory, Yanzhou District Center for Disease Control and Prevention, Jining, Shandong, China.
Lingming KongDepartment of AI and Bioinformatics, Nanjing Chengshi BioTech (TheraRNA) Co. Ltd., Nanjing, China.
Wei LiuJining Center for Disease Control and Prevention, Jining, China.
Qiang YinDepartment of Laboratory, Jining Center for Disease Control and Prevention, Jining, China.
Yongjian JiaDepartment of Laboratory, Jining Center for Disease Control and Prevention, Jining, China.
Huixin DouDepartment of Laboratory, Jining Center for Disease Control and Prevention, Jining, China.
Ting ChenSchool of Basic Medicine, Jining Medical University, Jining, China.
Feifei HeComputer Information Technology, Northern Arizona University, Flagstaff, AZ, United States.
Lili ZhangDepartment for Chronic Non-communicable Disease Prevention and Control, Jining Center for Disease Control and Prevention, Jining, China.
Tihui WangDepartment of Laboratory, Jining Center for Disease Control and Prevention, Jining, China.
Yajuan JiangDepartment of Laboratory, Jining Center for Disease Control and Prevention, Jining, China.
Boyan JiaoDepartment of Laboratory, Jining Center for Disease Control and Prevention, Jining, China.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Objective: To characterize the whole-genome features and evolutionary variation patterns of severe acute respiratory syndrome coronavirus 2 circulating in Jining City during 2024-2025. Methods: Whole-genome sequencing was performed on clinical specimens collected from SARS-CoV-2-infected cases in Jining City during 2024-2025 using next-generation sequencing technology. Phylogenetic and mutation analyses were conducted using standard bioinformatics tools. Results: A total of 429 complete SARS-CoV-2 genome sequences were obtained between January 2024 and December 2025, including 240 sequences in 2024 and 189 sequences in 2025. In 2024, circulating strains showed a sequential replacement from the XBB.1.9 lineage to the BA.2.86 lineage and subsequently to the XDV.1 lineage. All sequences obtained in 2025 belonged to the XDV.1 lineage and its sublineages. Whole-genome nucleotide similarity between the 429 sequences and the Wuhan-Hu-1 reference strain ranged from 99.64 to 99.81%, with the lowest nucleotide similarity observed in the ORF6 and spike genes. Amino acid mutation analysis revealed that the spike proteins of the XBB.1.9, BA.2.86, and XDV.1 lineages harbored an average of 42.67, 53.61, and 55.15 amino acid mutation, respectively. The XDV.1 lineage and its sublineages showed the greatest number of spike protein amino acid substitutions. In addition, ORF8 G8 stop and ORF8 Q18 stop mutations were identified, and frameshift mutations in ORF8 were detected in 10 sequences. Conclusion: Different Omicron lineages circulated alternately in Jining City during 2024-2025, with XDV.1 and its sublineages becoming the predominant circulating strains in 2025. These findings highlight the critical importance of continuous genomic surveillance for real-time monitoring of viral evolution, and provide key data to support the timely adjustment of vaccines and public health strategies in response to emerging variants. Continuous whole-genome sequencing and analysis of SARS-CoV-2 are essential for timely monitoring of viral evolution and provide a theoretical basis for effective prevention and control strategies.

Indexed as

epidemiologyopen reading frame 8severe acute respiratory syndrome coronavirus 2spike proteinwhole genome sequencing

Identifiers

PMID42182013
PMCPMC13194450

What Socratic 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 Socratic graph.