Molecular Identification of Fecal Contamination in the Elks Run Watershed, Jefferson County, West Virginia, 2016–17

Open-File Report 2019-1064
By:  and 



The U.S. Geological Survey conducted a study using modern methods of molecular analysis aimed at attempting to identify the source(s) of fecal contamination that had been identified in previous studies conducted by the West Virginia Conservation Agency in the Elk Run watershed, Jefferson County, West Virginia. Water samples from multiple sites showing elevated fecal coliform counts were analyzed using molecular markers associated with general mammalian fecal contamination (AllBac), human Bacteroides (HF183), bovine Bacteroides (BoBac), and human polyomavirus (HPyV). Samples were also analyzed by quantitative polymerase chain reaction (qPCR) for human and bovine cytochrome b (mitochondrial DNA marker). A headwater site (Elk Branch at Shenandoah Junction) was found to be severely affected by both human and bovine contamination in May 2017. Although many of the molecular marker levels as well as Escherichia coli numbers had declined by a repeat sampling in June 2017, total coliform bacterial numbers remained high. Examination of the data indicated that this site had probably been affected by two separate contamination events, an influx of bovine contamination close to the time of the May sampling and a human contamination event that had occurred earlier. Samples from all sites contained bovine mitochondrial DNA, whereas only one revealed relatively high levels of human mitochondrial DNA. The Elk Run watershed appears to be widely affected by bovine influences with human influence episodically playing a role. Surface runoff caused by rain events exacerbates both.

Suggested Citation

Schill, W.B., and Iwanowicz, D.D., 2019, Molecular identification of fecal contamination in the Elks Run watershed, Jefferson County, West Virginia, 2016–17: U.S. Geological Survey Open-File Report 2019–1064, 9 p.,

ISSN: 2331-1258 (online)

Study Area

Table of Contents

  • Acknowledgments
  • Abstract
  • Introduction
  • Methods
  • Results
  • Summary
  • References Cited
Publication type Report
Publication Subtype USGS Numbered Series
Title Molecular identification of fecal contamination in the Elks Run Watershed, Jefferson County, West Virginia, 2016–17
Series title Open-File Report
Series number 2019-1064
DOI 10.3133/ofr20191064
Year Published 2019
Language English
Publisher U.S. Geological Survey
Publisher location Reston, VA
Contributing office(s) Leetown Science Center
Description 9 p.
Country United States
State West Virginia
County Jefferson County
Online Only (Y/N) Y
Google Analytic Metrics Metrics page
Additional publication details