Evidence map›Paper›PMID 40871324›Full record

ArticleMicroorganisms2025

Assessing SARS-CoV-2 Rare Mutations and Transmission in New York City by NGS.

Dakai Liu, Harlan Pietz, George D Rodriguez, Yuexiu Wu, Yihan Cao, Vishnu Singh, Hui Li, Eric Konadu, Keither K James, Calvin Lui and 10 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Microorganisms, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

20 authors.

Dakai LiuDepartment of Pathology and Clinical Laboratories, New York-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA.ORCID 0000-0003-0658-5866
Harlan PietzDepartment of Pathology and Clinical Laboratories, New York-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA.ORCID 0000-0003-4792-5708
George D RodriguezDepartment of Quality and Patient Safety, New York-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA.
Yuexiu WuDivision of Infectious Disease, New York-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA.
Yihan CaoMassachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, MA 02114, USA.ORCID 0000-0001-9486-3365
Vishnu SinghDepartment of Pathology and Clinical Laboratories, New York-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA.
Hui LiDepartment of Pathology and Clinical Laboratories, New York-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA.
Eric KonaduDepartment of Pathology and Clinical Laboratories, New York-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA.
Keither K JamesDepartment of Pathology and Clinical Laboratories, New York-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA.
Calvin LuiDepartment of Pathology and Clinical Laboratories, New York-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA.
Bright VargheseDepartment of Pathology and Clinical Laboratories, New York-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA.
Mingyu ShaoDepartment of Pathology and Clinical Laboratories, New York-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA.
Gary ChenDepartment of Pathology and Clinical Laboratories, New York-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA.
Andrew SchreinerDepartment of Pathology and Clinical Laboratories, New York-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA.
Jiankun TongDepartment of Pathology and Clinical Laboratories, New York-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA.
Carl UrbanWeill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA.ORCID 0000-0002-7322-0245
Nishant PrasadWeill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA.ORCID 0000-0001-6445-3744
Ameer HassounDepartment of Emergency Medicine, New York-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA.ORCID 0000-0003-4524-6664
Manish SharmaDepartment of Emergency Medicine, New York-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA.ORCID 0000-0002-7364-4179
William Harry RodgersDepartment of Pathology and Clinical Laboratories, New York-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA.

Funding

Weill Cornell/Rockefeller/Sloan-Kettering MST ProgramT32GM007739 · NIGMS · WEILL MEDICAL COLL OF CORNELL UNIV · PI HSU, KATHARINE C · 1985 to 2023
$51.1M
Studies of the structural and functional basis of neuroblastoma drug resistanceF30CA257282 · NCI · WEILL MEDICAL COLL OF CORNELL UNIV · PI PIETZ, HARLAN LINVER · 2021 to 2024
$189k
NCI NIH HHS F30 CA257282NIGMS NIH HHS T32 GM007739
6 · The paper itself

Abstract

SARS-CoV-2 undergoes frequent mutations that drive viral evolution and genomic diversity, influencing transmissibility, immune escape, and disease severity. In this study, we performed whole-genome sequencing on SARS-CoV-2 isolates from patients in New York City and identified several globally rare mutations across multiple viral lineages. The isolates analyzed for rare mutations belonged to three lineages: B.1.1.7 (Alpha), B.1.526 (Iota), and B.1.623. We identified 16 rare mutations (global incidence <1000) in non-structural protein genes, including

Indexed as

COVID-19mutationnext-generation sequencingSARS-CoV-2viral variants

Identifiers

PMID40871324
PMCPMC12388554

What OpenQuestion holds

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LicenceCC BY
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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.