Why Strain Surveillance is Important for Public Health
CDC has been conducting SARS-CoV-2 strain surveillance to build a collection of SARS-CoV-2 specimens and sequences to support public health response. Routine analysis of the available genetic sequence data will enable CDC and its public health partners to identify variant viruses for further characterization.
Viruses generally acquire mutations over time, giving rise to new variants. For instance, another variant recently emerged in Nigeria. CDC also is monitoring this strain but, at this time, it has shown no concerning characteristics to public health experts.
Some of the potential consequences of emerging variants are the following:
- Ability to spread more quickly in people. There is already evidence that one mutation, D614G, confers increased ability to spread more quickly than the wild-type SARS-CoV-2. In the laboratory, 614G variants propagate more quickly in human respiratory epithelial cells, outcompeting 614D viruses. There also is epidemiologic evidence that the 614G variant spreads more quickly than viruses without the mutation.
- Ability to cause either milder or more severe disease in people. In January 2021, experts in the UK reported that B.1.1.7 variant may be associated with an increased risk of death compared to other variants. More studies are needed to confirm this finding.
- Ability to evade detection by specific viral diagnostic tests. Most commercial reverse-transcription polymerase chain reaction (RT-PCR)-based tests have multiple targets to detect the virus, such that even if a mutation impacts one of the targets, the other RT-PCR targets will still work.
- Decreased susceptibility to therapeutic agents such as monoclonal antibodies.
- Ability to evade natural or vaccine-induced immunity. Both vaccination against and natural infection with SARS-CoV-2 produce a “polyclonal” response that targets several parts of the spike protein. The virus would likely need to accumulate multiple mutations in the spike protein to evade immunity induced by vaccines or by natural infection.
Among these possibilities, the last—the ability to evade vaccine-induced immunity—would likely be the most concerning because once a large proportion of the population is vaccinated, there will be immune pressure that could favor and accelerate emergence of such variants by selecting for “escape mutants.” There is no evidence that this is occurring, and most experts believe escape mutants are unlikely to emerge because of the nature of the virus.
 Analysis of sequences from the African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Nigeria, identified two SARS-CoV-2 sequences belonging to the B.1.1.207 lineage. These sequences share one non-synonymous mutation in the spike protein (P681H) in common with the B.1.1.7 lineage but does not share any of the other 22 unique mutations of B.1.1.7 lineage. The P681H residue is near the S1/S2 furin cleavage site, a site with high variability in coronaviruses. At this time, it is unknown when this variant may have first emerged. Currently there is no evidence to indicate this variant has any impact on disease severity or is contributing to increased transmission of SARS-CoV-2 in Nigeria.
 “Wild-type” refers to the strain of virus – or background strain – that contains no major mutations.