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====3.1.6 Variant testing==== | |||
As the pandemic has progressed, you may have heard talk of a "delta" variant of SARS-CoV-2, which is reportedly more contagious and virulent than the initial strain that kicked off the pandemic.<ref name="CDCDelta21">{{cite web |url=https://www.cdc.gov/coronavirus/2019-ncov/variants/delta-variant.html |title=Delta Variant: What We Know About the Science |author=Centers for Disease Control and Prevention |publisher=Centers for Disease Control and Prevention |date=26 August 2021 |accessdate=18 September 2021}}</ref> One or more variants of a virus are expected as time progresses, and some of those variants can cause significantly more problems than the source virus. As such, analytical testing of the virus over time is vital to public health. | |||
The purpose of variant testing can be described in two ways, one for public health reasons and another for clinical care reasons. On the public health side, analysis of SARS-CoV-2 variants provides an unbiased, population-level view "of the specific viral strains in circulation and monitors changes in the viral genome over time."<ref name="BuchanSARS21">{{cite web |url=https://www.amp.org/AMP/assets/File/clinical-practice/COVID/AMP_RC_VariantTestingforSARSCOV2_4_28_21.pdf |format=PDF |title=SARS-CoV-2 Variant Testing |work=Rapid Communication |author=Buchan, B.W.; Wolk, D.M.; Yao, J.D. |publisher=Association for Molecular Pathology |date=28 April 2021 |accessdate=18 September 2021}}</ref> With enough public health laboratories conducting this type of analysis—typically whole-genome sequencing (WGS) using [[next-generation sequencing]] (NGS) techniques—a clearer picture of how an outbreak spreads is gained, as well as what variants are taking hold and further threatening human populations (even those that are vaccinated). This information is typically shared through the public health system for surveillance and reporting purposes, though the affected patients themselves may never see the data.<ref name="BuchanSARS21" /> | |||
On the clinical care side, analysis of SARS-CoV-2 variants provides further insights into improving COVID-19 patient outcomes. Buchan ''et al.'' identify three potential insights that clinicians may gain, noting that variant testing allows the clinician<ref name="BuchanSARS21" />: | |||
* to distinguish between an existing, persistent infection caused by one viral strain vs. re-infection by a different viral strain; | |||
* to determine whether a patient not responding to a treatment is affected by a specific viral spike protein (S) gene mutation that is "potentially resistant or less susceptible to | |||
neutralizing antibodies or monoclonal antibodies"; and | |||
* to detect in the serum or plasma of a patient post-vaccination "viral S gene substitutions in specific variants that are potentially resistant or less susceptible" to the antibodies the vaccine generates. | |||
If, for example, a patient is diagnosed with a variant that is tied to heightened disease severity, the clinician can opt for additional treatments early on to counteract the variant's effects on the patient. This testing is done in a hospital or reference lab by WGS or by targeting a portion of the genome (e.g., a spike protein) or a specific mutation (using RT-PCR). However, according to Buchan ''et al.'', the contributions a mutation makes to a "variant's attributes is not entirely understood, and there is no definitive evidence that directly links a given mutation to poor outcomes, significantly reduced efficacy of SARS-CoV-2 therapies, or vaccine coverage."<ref name="BuchanSARS21" /> | |||
Revision as of 21:53, 18 September 2021
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This is my primary sandbox page, where I play with features and test MediaWiki code. If you wish to leave a comment for me, please see my discussion page instead. |
Sandbox begins below
3.1.6 Variant testing
As the pandemic has progressed, you may have heard talk of a "delta" variant of SARS-CoV-2, which is reportedly more contagious and virulent than the initial strain that kicked off the pandemic.[1] One or more variants of a virus are expected as time progresses, and some of those variants can cause significantly more problems than the source virus. As such, analytical testing of the virus over time is vital to public health.
The purpose of variant testing can be described in two ways, one for public health reasons and another for clinical care reasons. On the public health side, analysis of SARS-CoV-2 variants provides an unbiased, population-level view "of the specific viral strains in circulation and monitors changes in the viral genome over time."[2] With enough public health laboratories conducting this type of analysis—typically whole-genome sequencing (WGS) using next-generation sequencing (NGS) techniques—a clearer picture of how an outbreak spreads is gained, as well as what variants are taking hold and further threatening human populations (even those that are vaccinated). This information is typically shared through the public health system for surveillance and reporting purposes, though the affected patients themselves may never see the data.[2]
On the clinical care side, analysis of SARS-CoV-2 variants provides further insights into improving COVID-19 patient outcomes. Buchan et al. identify three potential insights that clinicians may gain, noting that variant testing allows the clinician[2]:
- to distinguish between an existing, persistent infection caused by one viral strain vs. re-infection by a different viral strain;
- to determine whether a patient not responding to a treatment is affected by a specific viral spike protein (S) gene mutation that is "potentially resistant or less susceptible to
neutralizing antibodies or monoclonal antibodies"; and
- to detect in the serum or plasma of a patient post-vaccination "viral S gene substitutions in specific variants that are potentially resistant or less susceptible" to the antibodies the vaccine generates.
If, for example, a patient is diagnosed with a variant that is tied to heightened disease severity, the clinician can opt for additional treatments early on to counteract the variant's effects on the patient. This testing is done in a hospital or reference lab by WGS or by targeting a portion of the genome (e.g., a spike protein) or a specific mutation (using RT-PCR). However, according to Buchan et al., the contributions a mutation makes to a "variant's attributes is not entirely understood, and there is no definitive evidence that directly links a given mutation to poor outcomes, significantly reduced efficacy of SARS-CoV-2 therapies, or vaccine coverage."[2]
- ↑ Centers for Disease Control and Prevention (26 August 2021). "Delta Variant: What We Know About the Science". Centers for Disease Control and Prevention. https://www.cdc.gov/coronavirus/2019-ncov/variants/delta-variant.html. Retrieved 18 September 2021.
- ↑ 2.0 2.1 2.2 2.3 Buchan, B.W.; Wolk, D.M.; Yao, J.D. (28 April 2021). "SARS-CoV-2 Variant Testing" (PDF). Rapid Communication. Association for Molecular Pathology. https://www.amp.org/AMP/assets/File/clinical-practice/COVID/AMP_RC_VariantTestingforSARSCOV2_4_28_21.pdf. Retrieved 18 September 2021.
