Evidence map›Paper›PMID 34616728›Full record

ArticleFrontiers in cell and developmental biology2021

SAS: A Platform of Spike Antigenicity for SARS-CoV-2.

Lu Zhang, Ruifang Cao, Tiantian Mao, Yuan Wang, Daqing Lv, Liangfu Yang, Yuanyuan Tang, Mengdi Zhou, Yunchao Ling, Guoqing Zhang and 2 more

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

Article in Frontiers in cell and developmental biology, 2021. 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
0.1field-weighted citation impact, top 50% 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, 2 citations in OpenAlex.

  1. Review
  2. Review
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

12 authors at 4 institutions in 1 country.

Lu ZhangDepartment of Gastroenterology, Shanghai 10th People's Hospital and School of Life Sciences and Technology, Tongji University, Shanghai, China.
Ruifang CaoCAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Shanghai, China.
Tiantian MaoDepartment of Gastroenterology, Shanghai 10th People's Hospital and School of Life Sciences and Technology, Tongji University, Shanghai, China.
Yuan WangDepartment of Gastroenterology, Shanghai 10th People's Hospital and School of Life Sciences and Technology, Tongji University, Shanghai, China.
Daqing LvCAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Shanghai, China.
Liangfu YangCAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Shanghai, China.
Yuanyuan TangCAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Shanghai, China.
Mengdi ZhouDepartment of Gastroenterology, Shanghai 10th People's Hospital and School of Life Sciences and Technology, Tongji University, Shanghai, China.
Yunchao LingCAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Shanghai, China.
Guoqing ZhangCAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Shanghai, China.
Tianyi QiuShanghai Public Health Clinical Center, Fudan University, Shanghai, China.
Zhiwei CaoDepartment of Gastroenterology, Shanghai 10th People's Hospital and School of Life Sciences and Technology, Tongji University, Shanghai, China.
Shanghai Institute of Nutrition and Health · CNTongji University · CNChinese Academy of Sciences · CNShanghai Public Health Clinical Center · CN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Since the outbreak of SARS-CoV-2, antigenicity concerns continue to linger with emerging mutants. As recent variants have shown decreased reactivity to previously determined monoclonal antibodies (mAbs) or sera, monitoring the antigenicity change of circulating mutants is urgently needed for vaccine effectiveness. Currently, antigenic comparison is mainly carried out by immuno-binding assays. Yet, an online predicting system is highly desirable to complement the targeted experimental tests from the perspective of time and cost. Here, we provided a platform of SAS (Spike protein Antigenicity for SARS-CoV-2), enabling predicting the resistant effect of emerging variants and the dynamic coverage of SARS-CoV-2 antibodies among circulating strains. When being compared to experimental results, SAS prediction obtained the consistency of 100% on 8 mAb-binding tests with detailed epitope covering mutational sites, and 80.3% on 223 anti-serum tests. Moreover, on the latest South Africa escaping strain (B.1.351), SAS predicted a significant resistance to reference strain at multiple mutated epitopes, agreeing well with the vaccine evaluation results. SAS enables auto-updating from GISAID, and the current version collects 867K GISAID strains, 15.4K unique spike (S) variants, and 28 validated and predicted epitope regions that include 339 antigenic sites. Together with the targeted immune-binding experiments, SAS may be helpful to reduce the experimental searching space, indicate the emergence and expansion of antigenic variants, and suggest the dynamic coverage of representative mAbs/vaccines among the latest circulating strains. SAS can be accessed at https://www.biosino.org/sas.

Indexed as

antigenic resistancemAbSARS-CoV-2spike proteinvaccine

Identifiers

PMID34616728
PMCPMC8488377
OpenAlexW3201227123

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.