Evidence map›Paper›PMID 36712100›Full record

ArticlebioRxiv : the preprint server for biology2023

Tomato brown rugose fruit virus Mo gene is a novel microbial source tracking marker.

Aravind Natarajan, Brayon J Fremin, Danica T Schmidtke, Marlene K Wolfe, Soumaya Zlitni, Katherine E Graham, Erin F Brooks, Christopher J Severyn, Kathleen M Sakamoto, Norman J Lacayo and 9 more

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. 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, 4 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

19 authors at 2 institutions in 1 country.

Aravind NatarajanDepartment of Genetics, Stanford University, Stanford, CA, USA.
Brayon J FreminDepartment of Genetics, Stanford University, Stanford, CA, USA.
Danica T SchmidtkeDepartment of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
Marlene K WolfeDepartment of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA.
Soumaya ZlitniDepartment of Genetics, Stanford University, Stanford, CA, USA.
Katherine E GrahamDepartment of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA.
Erin F BrooksDepartment of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA.
Christopher J SeverynDepartment of Pediatrics, (Hematology/Oncology/Stem Cell Transplant & Regenerative Medicine), Stanford University, Stanford, CA, USA.
Kathleen M SakamotoDepartment of Pediatrics, (Hematology/Oncology/Stem Cell Transplant & Regenerative Medicine), Stanford University, Stanford, CA, USA.
Norman J LacayoDepartment of Pediatrics, (Hematology/Oncology/Stem Cell Transplant & Regenerative Medicine), Stanford University, Stanford, CA, USA.
Scott KuerstenIllumina, Inc., San Diego, CA.
Jeff KobleIllumina, Inc., San Diego, CA.
Glorianna CavesIllumina, Inc., San Diego, CA.
Inna KaplanDepartment of Medicine (Blood and Marrow Transplantation and Cellular Therapy), Stanford University, Stanford, CA, USA.
Upinder SinghDepartment of Medicine (Infectious Diseases and Geographic Medicine), Stanford University, Stanford, CA, USA.
Prasanna JagannathanDepartment of Medicine (Infectious Diseases and Geographic Medicine), Stanford University, Stanford, CA, USA.
Andrew R RezvaniDepartment of Medicine (Blood and Marrow Transplantation and Cellular Therapy), Stanford University, Stanford, CA, USA.
Ami S BhattDepartment of Genetics, Stanford University, Stanford, CA, USA.
Alexandria B BoehmDepartment of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA.
Stanford University · USIllumina (United States) · US

Funding

Supplement to Enhance Wellness and Resiliency in the Graduate EnvironmentT32GM007276 · NIGMS · STANFORD UNIVERSITY · PI MORRISON, ASHBY J. · 1985 to 2023
$32.9M
Culture-free pathogen tracking in hospitalized patientsR01AI143757 · NIAID · STANFORD UNIVERSITY · PI BHATT, AMI SIDDHARTH · 2020 to 2023
$3.0M
Emerging novel mechanisms of antibiotic resistance in the prevalent foodborne pathogen, SalmonellaR01AI148623 · NIAID · STANFORD UNIVERSITY · PI BHATT, AMI SIDDHARTH · 2019 to 2023
$2.0M
Training in Pediatric Nonmalignant Hematology and Stem Cell BiologyT32DK098132 · NIDDK · STANFORD UNIVERSITY · PI SAKAMOTO, KATHLEEN M · 2014 to 2022
$1.9M
NIAID NIH HHS R01 AI143757NIAID NIH HHS R01 AI148623NIDDK NIH HHS T32 DK098132NIGMS NIH HHS T32 GM007276
6 · The paper itself

Abstract

Microbial source tracking (MST) identifies sources of fecal contamination in the environment using fecal host-associated markers. While there are numerous bacterial MST markers, there are few viral markers. Here we design and test novel viral MST markers based on tomato brown rugose fruit virus (ToBRFV) genomes. We assembled eight nearly complete genomes of ToBRFV from wastewater and stool samples from the San Francisco Bay Area in the United States of America. Next, we developed two novel probe-based RT-PCR assays based on conserved regions of the ToBRFV genome, and tested the markers’ sensitivities and specificities using human and non-human animal stool as well as wastewater. TheToBRFV markers are sensitive and specific; in human stool and wastewater, they are more prevalent and abundant than a currently used marker, the pepper mild mottle virus (PMMoV) coat protein (CP) gene. We applied the assays to detect fecal contamination in urban stormwater samples and found that the ToBRFV markers matched cross-assembly phage (crAssphage), an established viral MST marker, in prevalence across samples. Taken together, ToBRFV is a promising viral human-associated MST marker. Importance: Human exposure to fecal contamination in the environment can cause transmission of infectious diseases. Microbial source tracking (MST) can identify sources of fecal contamination so that contamination can be remediated and human exposures can be reduced. MST requires the use of fecal host-associated MST markers. Here we design and test novel MST markers from genomes of tomato brown rugose fruit virus (ToBRFV). The markers are sensitive and specific to human stool, and highly abundant in human stool and wastewater samples.

Identifiers

PMID36712100
PMCPMC9882089
OpenAlexW4313949109

What OpenQuestion holds

Textmetadata
LicenceCC BY-ND
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.