Surveillance and Testing of SARS-CoV-2
During the COVID-19 pandemic, testing for and surveillance of SARS-CoV-2 viral outbreak has been both important and controversial.
Surveillance
Waterwater Sampling
Starting on March 19, 2020, wastewater in the New Haven, Connecticut area was tracked and tested by Yale University researchers.1) Published results of this program showed such wastewater surveillance to predict percentage of positive tests 0 to 2 days ahead, hospital admissions by 1 to 4 days, and magnitude of positive test results 6 to 8 days ahead of reporting date.2)
Omicron Wave
Boston, Massachusetts wastewater samples show substantially higher infection rates than official case counts.3)
S-Gene Target Failure
During the pandemic, one of the methods for distinguishing between variants has been the proxy testing for “expected” sequences of the S-gene, which encodes for the spike protein.4) This binary test for S-gene target failure (SGTF) makes the implicit assumption that there is only ever one variant at a time that not be detected by comparisons of one or more S-gene sequences used.
- May, 2021 - S-Gene Target Failure as a Marker of Variant B.1.1.7 Among SARS-CoV-2 Isolates in the Greater Toronto Area, December 2020 to March 20215)
Research
- Los Alamos National Laboratory (July 8, 2017): COVID-19 Testing R&D Final Report
1)
September 18, 2020 | Yale School of Engineering & Applied Science | Study: Wastewater Predicts COVID-19 Outbreaks Days Before Diagnostic Testing Results
2)
September 18, 2020 | Peccia et al | Nature Biotechnology | doi.org/10.1038/s41587-020-0684-z
4)
February 5, 2021 | ThermoFisher Scientific | Why S-Gene Sequencing is Key for SARS-CoV-2 Surveillance
5)
May, 2021 | Kevin Brown et al | S-Gene Target Failure as a Marker of Variant B.1.1.7 Among SARS-CoV-2 Isolates in the Greater Toronto Area, December 2020 to March 2021 | DOI: 10.1001/jama.2021.5607