Responding to unknown samples with the presence of SARS-CoV-2

 

How can we better plan for, identify, and respond to mutations we see in our communities?

The pathogen testing communities are coming together to develop a response to emerging mutations of the SARS-CoV-2 virus.

There is a clear need to continue surveillance work to identify these samples. What has emerged recently is an equally important need to sequence SARS-CoV-2 samples to confirm mutations.

What is epidemiological surveillance?

Global epidemiological surveillance is vital for understanding the evolution of viral pathogens and monitoring for changes in transmissibility, virulence, and disease pathology. As such, global surveillance plays a central role in proactively managing pathogens.

Sometimes called genetic surveillance, monitoring mutations in a viral disease has important implications characterizing the virus strains further and monitor the virus spread at the population level in order to assess the effectiveness of containment strategies

Genetic surveillance led to a recent finding in Europe that the B.1.1.7 variant of the SARS-CoV-2 mutation has a “substantial transmission advantage” over the reference strain.

Learn more about emerging SARS-CoV-2 mutations and variants ›

   Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data

 

Surveillance and the impact of variants

 

Surveillance is a powerful tool in our collective fight to slow the spread of the SARS-CoV-2 virus. The increasing number of SARS-CoV-2 variants raises important questions including:

Could a new variant:

  • Evade detection by specific tests?
  • Spread in humans more quickly than the reference strain?
  • Cause milder or more severe disease, like COVID-19, in humans?
  • Show decreased susceptibility to therapeutic agents such as monoclonal antibodies?
  • Evade vaccine-induced immunity?

Epidemiological surveillance requires labs to take extra care in sample tracking and follow through. And that work is essential.

The potential implications of multiple untracked variants are significant:

Variant impact

Speed of human to
human transmission

Disease severity

Susceptibility to therapeutic agents (i.e., monoclonal antibodies)

Vaccine-induced immunity

Evade detection by diagnostic tests

Figure 1. Potential implications of new SARS-CoV-2 variants. Source: US CDC.

The net effect raises concerns around potential impacts related to human-to-human spread, decreased response to existing treatments, vaccine efficacy, and challenges to potential future treatments.

 

Surveillance and the mutation detection process

 

Epidemiological surveillance

Monitor mutational changes in SARS-CoV-2 viral genome to detect emerging mutations and to identify new unknown variants. This can be achieved by sequencing the full viral genome or specific sections or genes of interest.

Next-generation sequencing

Capillary electrophoresis

Mutation verification

Conduct strain identification of positive clinical samples to confirm known mutations associated with specific strains by interrogating specific sections or points on the viral genome to determine the presence or absence of specific mutations.

Capillary electrophoresis

Real-Time PCR

Identify the presence of relevant mutations associated with SARS-CoV-2 variants using real-time PCR: TaqMan SARS-CoV-2 Mutation Panel

A call to action

“Although healthcare providers in the United States perform millions of COVID19 tests weekly, only a few thousand samples receive genomic sequencing suitable for informing researchers about the movement and appearance of virus strains.”

Read full blog post

 

Epidemiological surveillance and sequencing to respond to mutations

 

Whether your lab is running coronavirus testing or you are looking to fill excess sequencing capacity by verifying mutations in sequencing SARS-CoV-2 samples, it is challenging to quickly assess the situation. You may be asking:

  • Which approaches have you considered: CE, NGS, qPCR?
  • Do you need to conduct mutation verification of positive samples?
  • Do you test for genetic surveillance?
  • Do you sequence targeted genes or a larger number of mutations?
  • How many samples do you need to sequence?
  • Do you need to send out samples for sequencing?
     

Epidemiological surveillance infographic

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Upcoming and featured webinars

 

Molecular Multi-Target Assay Design Coupled with Reflex Testing with SARS-CoV-2 Mutations in Mind

Date: March 18, 2021
Time: 10 am PT | 1 pm ET | 7 pm CET

Register now

Think Globally, Act Locally: The Importance of Coordinated Global and Community Genetic Surveillance Programs

Date: March 29, 2021
Time: 10 am PT | 1 pm ET | 7 pm CET

Register now

Strategies for Epidemiological Surveillance of SARS-CoV-2 Variants

Date: April 13, 2021
Time: TBD

Coming soon

Solutions for SARS-CoV-2 Strain Lineage Surveillance

Date: April 14, 2021
Time: TBD

Coming soon

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