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

Educational Resources for SARS-CoV-2 Research Using NGS

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

Epidemiological surveillance infographic


"The ability to very quickly run multiple samples and accurately decipher key changes in the virus’ genetic code will be crucial for the global scientific community to stay ahead of SARS-COV-2 and to develop strategies against it that, ultimately, can be leveraged to help solve the pandemic’’

Dr. Maria Rosaria Capobianchi
Head of the Virology Department, National Institute for the Infectious Diseases “L. Spallanzani”, Rome, Italy


Epidemiological 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:

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.

Thermo Fisher Scientific has developed a comprehensive solution to enable labs involved in global, regional, and local SARS-CoV-2 Mutation surveillance efforts. To learn more about how these workflows can be integrated into your laboratory, we can connect you with a local technical specialist.


Epidemiological 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?


Featured webinars


Surveillance Solutions for Detection, Discrimination and Discovery of Emerging SARS-CoV-2 Variants

Watch on-demand

Solutions for SARS-CoV-2 Strain Lineage Surveillance

Watch on-demand

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

Watch on-demand

Strategies for Epidemiological Surveillance of SARS-CoV-2 Variants

Watch on-demand

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

Watch on-demand

Style Sheet for Global Design System
Style Sheet for Komodo Tabs