COVID-19 Health Alert # 25: Surveillance for New Genetic Variants of SARS-CoV-2: Information for Clinicians

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DHS Health Alert Network

COVID-19 Health Alert # 25:

Surveillance for New Genetic Variants of SARS-CoV-2: Information for Clinicians

Bureau of Communicable Diseases, January 4, 2021


  • New variant strains of SARS-CoV-2 have been recently described in numerous countries, and are believed to be more highly transmissible than wild-type SARS-CoV-2. CDC has published a scientific brief about these emerging strains, which is updated regularly as more information becomes available.

  • The first “variant of concern,” referred to as VOC 202012/01 or B.1.1.7, was discovered to be circulating widely in England during November and December of 2020. Several infections with this strain have been detected in Canada and the United States, but it is not currently known how widely the variant is circulating in North America. Additional “variants of concern” will likely be identified in the coming months and will warrant ongoing surveillance.

  • In Wisconsin, several clinical, research and public health laboratories are actively participating in genomic surveillance for novel and emerging strains, in collaboration with DHS and CDC. Clinicians can support this work by notifying DHS of any cases of COVID-19 that are travel-associated, or that occur in patients who previously received antiviral treatment, antibody-based treatment, or vaccination for COVID-19. Information about such cases can be sent to

Dear Colleagues,

In mid-December, 2020, a new variant of the SARS-CoV-2 virus was recognized to be spreading rapidly in London and southeast England. This strain of the virus is notable for having an unusually large number of genetic mutations, including a mutation in the receptor binding domain of the spike protein (N501Y), which is hypothesized to be associated with increased transmissibility. The new strain has been alternatively referred to as “variant of concern (VOC) 202012/01” or “B.1.1.7.”

Based on epidemiologic and modeling studies, researchers believe that the novel strain discovered in the United Kingdom is spreading more rapidly and easily than the original, or wild-type strain of SARS-CoV-2.  The basic reproductive number, R0, has been estimated to be between 1.4 and 1.7 times higher than that of the wild-type strain. Currently, there is no evidence that this variant causes more severe illness or increased risk of death. New information about the virologic, epidemiologic, and clinical characteristics of this variant and other novel strains of SARS-CoV-2 is rapidly emerging.

In Wisconsin, no cases of COVID-19 caused by the B.1.1.7 variant have been detected to date, but it is plausibly already circulating in our region. Wisconsin DHS, the State Laboratory of Hygiene, and other laboratory partners regularly perform whole genome sequencing on a subset of specimens collected from patients who test positive for COVID-19, but only a small proportion (~1%) of cases are able to be sequenced.

Now in the second year of the COVID-19 pandemic, molecular surveillance of SARS-CoV-2 will take on increased importance to quickly identify and understand novel and emerging variants of clinical and public health significance. Wisconsin DHS will communicate new information about COVID-19 epidemiology as it becomes available. At this time, we would like to emphasize the following points to clinical and public health partners:

  • Viruses constantly change through mutation, and new variants of a virus are expected to occur over time. Multiple variants of the SARS-CoV-2 have been documented in the United States and globally during this pandemic. Most variants do not change how the virus behaves and many disappear.

  • The new variant of concern from the UK does not appear to cause more severe disease or death than the previous circulating strain. However, a higher rate of transmission could lead to more cases, which would increase the number of people overall who need clinical care. If a more transmissible variant becomes the predominant stain in circulation, we may also need to achieve higher vaccination coverage to fully disrupt community transmission when vaccines become widely available.

  • Health care and public health leaders must continue to emphasize the importance of wearing a mask, staying at least 6 feet apart from others, avoiding crowds, ventilating indoor spaces, and washing hands frequently. These are our best tools for preventing the spread of this virus, no matter the strain.

  • DHS and its laboratory partners are collaborating with CDC to conduct SARS-CoV-2 Strain Surveillance to build a collection of virus specimens and sequences to support public health research. Routine analysis of these available genetic sequence data enables a targeted approach to identify variant viruses for further characterization. Wisconsin clinicians can support this activity by promptly notifying DHS of individuals who have a positive PCR test result for COVID-19 AND meet any of the following criteria:

    • Have traveled to another country within the previous 30 days

    • Have been in close contact with a person who tested positive for COVID-19 after traveling to another country in the previous 30 days.

    • Prolonged clinical illnesses, including those who are suspected of having protracted SARS-CoV-2 viral replication, are immunocompromised, or who have a recurrence of COVID-19 disease after an initial period of recovery.

    • Suspected repeat infection occurring in patients who received monoclonal antibody therapy, convalescent plasma therapy, or antiviral drugs including remdesivir.

    • Any SARS-CoV-2 infection in an individual who has received a COVID-19 vaccine.

  • Clinicians who wish to obtain whole genome sequencing for cases such as those described above should contact the DHS Bureau of Communicable Diseases via email at

  • In addition to notifying DHS, clinicians should communicate directly with the laboratory that performs COVID-19 testing. Whole genome sequencing can be performed on residual specimens obtained for diagnostic purposes, but testing laboratories must be notified as early as possible about cases of interest, so that specimens can be saved for sequencing before they are discarded. More information about policies and practices related to SARS-CoV-2 molecular surveillance in Wisconsin is described in a DHS Memo from October 2020.


Ryan Westergaard, MD, PhD, MPH Chief Medical Officer and State Epidemiologist for Communicable Diseases Wisconsin Department of Health Services

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