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.
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:
Speed of human to
Susceptibility to therapeutic agents (i.e., monoclonal antibodies)
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.
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.
- Focused NGS solutions for SARS-CoV-2 Research
- Blog: Necessity of sequencing emerging SARS-CoV-2 variants from UK and S. Africa
- Application note: NGS Surveying the Viral Genome
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.
- Sanger sequencing solutions for SARS-CoV-2 Research
- Blog: Solutions for surveillance of the S gene mutation in B.1.1.7 (501.V1) SARS-CoV-2 strain lineage
- Protocol for Sanger sequencing of SARS-CoV-2 B.1.1.7 and B.1.351 strain lineages
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.”
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
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
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
Strategies for Epidemiological Surveillance of SARS-CoV-2 Variants
Date: April 13, 2021
Solutions for SARS-CoV-2 Strain Lineage Surveillance
Date: April 14, 2021