====== 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.((September 18, 2020 | Yale School of Engineering & Applied Science | [[https://seas.yale.edu/news-events/news/study-wastewater-predicts-covid-19-outbreaks-days-diagnostic-testing-results|Study: Wastewater Predicts COVID-19 Outbreaks Days Before Diagnostic Testing Results]])) 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.((September 18, 2020 | Peccia et al | [[:Nature Biotechnology]] | [[https://www.nature.com/articles/s41587-020-0684-z|doi.org/10.1038/s41587-020-0684-z]]))

=== Omicron Wave ===

Boston, Massachusetts wastewater samples show substantially higher infection rates than official case counts.((January 11, 2022 | [[:ZeroHedge]] | [[https://www.zerohedge.com/political/mass-wastewater-data-suggests-covid-19-cases-substantially-higher-reported|Mass. Wastewater Data Suggests Covid-19 Cases Substantially Higher Than Reported]]))

==== 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]].((February 5, 2021 | [[:ThermoFisher Scientific]] | [[https://www.thermofisher.com/blog/behindthebench/why-s-gene-sequencing-is-key-for-sars-cov-2-surveillance/|Why S-Gene Sequencing is Key for SARS-CoV-2 Surveillance]]))
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 2021((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 | [[https://pubmed.ncbi.nlm.nih.gov/33830171/|DOI: 10.1001/jama.2021.5607]]))

===== Research =====

  * [[Los Alamos National Laboratory]] (July 8, 2017): //[[https://permalink.lanl.gov/object/tr?what=info:lanl-repo/lareport/LA-UR-21-26450|COVID-19 Testing R&D Final Report]]//