The Tomato Brown Rugose Fruit Virus Movement Protein Gene Is a Novel Microbial Source Tracking Marker

Area of Science:

• Environmental microbiology
• Virology
• Public health

Background:

• Microbial source tracking (MST) is crucial for identifying fecal contamination sources to mitigate disease transmission.
• Existing viral markers for MST are limited, necessitating the development of new, reliable tools.

Purpose of the Study:

• To design and validate novel viral microbial source tracking (MST) markers based on the tomato brown rugose fruit virus (ToBRFV).
• To assess the sensitivity, specificity, and prevalence of these new markers in various environmental and human samples.

Main Methods:

• Assembled eight near-complete ToBRFV genomes from wastewater and stool samples.
• Developed two probe-based reverse transcription-PCR (RT-PCR) assays targeting conserved ToBRFV regions.
• Tested marker performance using human/non-human animal stool and wastewater samples, comparing with pepper mild mottle virus (PMMoV).

Main Results:

• The novel ToBRFV markers demonstrated high sensitivity and specificity for human fecal contamination.
• ToBRFV markers were more prevalent and abundant in human stool and wastewater than the PMMoV CP gene.
• In urban stormwater, ToBRFV marker prevalence matched the established viral marker crAssphage.

Conclusions:

• Tomato brown rugose fruit virus (ToBRFV) serves as a promising, sensitive, and specific viral marker for human-associated fecal contamination.
• These findings expand the toolkit for viral MST, aiding in environmental monitoring and public health protection.