Evidence map›Paper›PMID 38605705›Full record

ArticleFrontiers in microbiology2024

Characteristics of SARS-CoV-2 Omicron BA.5 variants in Shanghai after ending the zero-COVID policy in December 2022: a clinical and genomic analysis.

Pengcheng Liu, Jiehao Cai, He Tian, Jingjing Li, Lijuan Lu, Menghua Xu, Xunhua Zhu, Xiaomin Fu, Xiangshi Wang, Huaqing Zhong and 5 more

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

Article in Frontiers in microbiology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
0.4field-weighted citation impact, top 43% 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

3 citing papers in PubMed, 1 citations in OpenAlex.

  1. Article
  2. Article
  3. 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

15 authors at 2 institutions in 1 country.

Pengcheng Liu *Department of Clinical Laboratory, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China.
Jiehao Cai *Department of Infectious Diseases, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China.
He TianDepartment of Infectious Diseases, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China.
Jingjing LiDepartment of Infectious Diseases, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China.
Lijuan LuDepartment of Clinical Laboratory, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China.
Menghua XuDepartment of Clinical Laboratory, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China.
Xunhua ZhuDepartment of Clinical Laboratory, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China.
Xiaomin FuDepartment of Infectious Diseases, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China.
Xiangshi WangDepartment of Infectious Diseases, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China.
Huaqing ZhongDepartment of Clinical Laboratory, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China.
Ran JiaDepartment of Clinical Laboratory, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China.
Yanling GeDepartment of Infectious Diseases, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China.
Yanfeng ZhuDepartment of Infectious Diseases, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China.
Mei ZengDepartment of Infectious Diseases, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China.
Jin XuDepartment of Clinical Laboratory, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China.
Children's Hospital of Fudan University · CNFudan University · CN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Introduction: An unprecedented surge of Omicron infections appeared nationwide in China in December 2022 after the adjustment of the COVID-19 response policy. Here, we report the clinical and genomic characteristics of SARS-CoV-2 infections among children in Shanghai during this outbreak. Methods: A total of 64 children with symptomatic COVID-19 were enrolled. SARS-CoV-2 whole genome sequences were obtained using next-generation sequencing (NGS) technology. Patient demographics and clinical characteristics were compared between variants. Phylogenetic tree, mutation spectrum, and the impact of unique mutations on SARS-CoV-2 proteins were analysed in silico. Results: The genomic monitoring revealed that the emerging BA.5.2.48 and BF.7.14 were the dominant variants. The BA.5.2.48 infections were more frequently observed to experience vomiting/diarrhea and less frequently present cough compared to the BF.7.14 infections among patients without comorbidities in the study. The high-frequency unique non-synonymous mutations were present in BA.5.2.48 (N:Q241K) and BF.7.14 (nsp2:V94L, nsp12:L247F, S:C1243F, ORF7a:H47Y) with respect to their parental lineages. Of these mutations, S:C1243F, nsp12:L247F, and ORF7a:H47Y protein were predicted to have a deleterious effect on the protein function. Besides, nsp2:V94L and nsp12:L247F were predicted to destabilize the proteins. Discussion: Further in vitro to in vivo studies are needed to verify the role of these specific mutations in viral fitness. In addition, continuous genomic monitoring and clinical manifestation assessments of the emerging variants will still be crucial for the effective responses to the ongoing COVID-19 pandemic.

Indexed as

childrenCOVID-19genomicsOmicron BA.5 variantsSARS-CoV-2

Identifiers

PMID38605705
PMCPMC11007228
OpenAlexW4393273498

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.