CAHFS Weekly Update: Minnesota statewide update on COVID-19 trends; Early national perspective on Omicron: Caution, vigilance, and action; Omicron: The latest SARS-CoV-2 variant of concern
Ilya Slizovskiy


Minnesota statewide update on COVID-19 trends

The Minnesota Department of Health has begun sequencing COVID-19 positive samples for the Omicron variant of the SARS-CoV-2 virus and is continuing to track global reports on Omicron cases and their spread. In the meantime, Minnesota health officials state that new variants are expected to occur and the most important thing that can be done to prepare is to ensure that everyone in the state, 5 years and older, be fully vaccinated, and to continue to wear masks in highly congregant settings.

Just prior to the Thanksgiving holiday, Minnesota and Michigan led the U.S. in daily average cases as colder temperatures in these states forced people to move most of their daily activities indoors where the virus tends to spread more readily. Statewide cases in Minnesota are approaching the total of 900,000 in a matter of days, and COVID-19 hospitalizations remain high while intensive care resources are strained. These trends continue to be a concern in light of the fact that only 64% of Minnesotans are fully vaccinated.

In a more recent development, Minnesota continues to lead (2nd in the U.S.) in the number of booster doses administered, with 31% of vaccinated adults having received their booster to date. The Minnesota Department of Health booster portal can be accessed for additional information on eligibility, finding vaccination locations, and scheduling.


Early national perspective on Omicron: Caution, vigilance, and action

In a statement released on December 1st, 2021 by the U.S. Centers for Disease Control and Prevention (CDC), the California Department of Public Health has confirmed the first case of the Omicron variant in the United States. This case was identified in a mildly symptomatic individual who returned from South Africa on November 22, 2021. The individual who tested positive is self-quarantined and all known close contacts have tested negative for the virus so far. The CDC will continue to monitor variants as part of its surveillance system . The news of Omicron in the U.S. comes at a time when the nation continues to sustain high rates of community transmission, with new cases averaging roughly 95,000 per day, a 25% uptick in a 2 week period prior to the Thanksgiving holiday.

Prompted by the latest COVID-19 trends and initial reports on the appearance of the novel variant, on November 29th,  the U.S. CDC issued a strengthened recommendation on vaccine booster doses for individuals who are eighteen years and older. Moving from “may seek boosters when eligible” in their earlier guidance in late October 2021, to adults “...should get a booster shot”, the CDC Director Rochelle Walensky, MD, MPH stated that, “Based on the compelling evidence, all adults over 18 should now have equitable access to a COVID-19 booster dose”. Dr. Walensky stated that, “Booster shots have demonstrated the ability to safely increase people’s protection against infection and severe outcomes and are an important public health tool to strengthen our defenses against the virus as we enter the winter holidays.” In addition to the update on boosters, the U.S. has also instituted temporary travel restrictions. It is also expected that additional rules will be implemented concerning testing requirements for international travelers.

Health officials note that in the face of existing and new variant strains of the SARS-CoV-2 virus, frequent testing and sequencing are critical. Indeed, the U.S. has administered more COVID-19 tests than any other country, and the U.S. is doing far more sequencing than it was at the start of the pandemic. The recently scaled sequencing strategy nation-wide will allow the U.S. to pivot quickly as new variants arise. However, the U.S. continues to trail behind 20 other nations in the number of sequences generated as a percentage of positive cases. For example, according to the GISAID public access database for epidemic and pandemic virus data, in the past six months, the U.S. sequenced roughly 7% of its positive cases, whereas Sweden sequenced roughly 37%. Based on current CDC reports, the sequencing rate of cases is variable across states and indicates potential gaps in sequencing capacity nationwide.


Omicron: The latest SARS-CoV-2 variant of concern

The U.N.’s World Health Organization (WHO) has listed a novel variant of SARS-CoV-2, previously known as B.1.1.529, as a ‘variant of concern’ (VOC), and designated it as “Omicron ." This is the 13th COVID-19 pandemic viral variant to receive the Greek-lettered designation by the Technical Advisory Group on SARS-CoV-2 Virus Evolution (TAG-VE) convened on the 26th of November, 2021. This independent group of experts, in collaboration with other expert networks, national authorities, institutions and researchers, monitor changes to the virus and assess whether specific mutations or combinations of viral alterations may impact the epidemiology and overall course of the COVID-19 pandemic. The novel variant was first reported to WHO from South Africa on the 24th of November, as steep increases in infections coincided with the detection of the B.1.1.529 variant in almost all provinces of South Africa in recent weeks. As of December 1st 2021, confirmed cases of Omicron have been identified in more than twenty nations.

The specific lineages of the SARS-CoV-2 virus, including Alpha, Beta, Gamma, and the currently predominant Delta variant which still accounts for more than 99% of global COVID-19 prevalence, are given a ’ VOC’ designation because they have a potential to spread more easily, cause more serious disease, or are difficult to control with established public health measures. Early evidence suggests that the Omicron variant possesses a large complement of mutations to its genome linked to enhanced infectivity (i.e. the ability of a pathogen to establish an infection) and evasion of protective immunity. However, the impacts of these mutations have not been fully characterized. At this time, the Omicron specific transmissibility, severity of the resulting disease, and the impact on the countermeasures against SARS-CoV-2 including vaccines and treatments remains unknown.


  • Transmission: It remains unclear whether Omicron has the potential to spread from one individual to another more readily, as compared to other variants, including the ongoing Delta variant. Studies are underway to examine the impacts of the new viral mutations of Omicron on its transmission.

  • Health impact: It is currently unknown whether Omicron infections, relative to other variants, are more severe, have a different clinical presentation, or differentially impact specific groups of people. Although the early cases of the variant have been reported among South African university students who tended to have milder disease, further investigations are underway.

  • Protection: The currently available vaccines and treatment strategies remain critical in reducing COVID-19-associated severe disease and death, including against the dominant circulating Delta variant. Assessments are underway by WHO, national health organizations, and industry members to ascertain the level of protection of available vaccines against Omicron.


All viruses, including the SARS-CoV-2 virus, accumulate alterations in their genomes over time. Most changes have little impact on the properties and health implications of viruses. However, as researchers continue to monitor the evolution of viruses like SARS-CoV-2, emergence of some mutations may pose an increased risk to global public health. In these cases, providing characterizations of variants, such as ‘Variant of Concern’ (VOC), ‘Variant of Interest’ (VOI), or ‘Variant under Monitoring’ (VUM) is done in order to help prioritize global monitoring, research, and prevention efforts. More information on variant designations can be found on the WHO tracking webpage. In this vein, international public health experts continue to call for strengthened surveillance and sequencing capacities, the continued sharing of genomic sequencing information and associated data via public databases, and maintenance of public health preventive measures (e.g. vaccinations, masking, distancing, and frequent testing).    

Star Tribune: Coronavirus
CBC Minnesota
Minnesota Department of Health: Statement on the Omicron variantU.S. Center for Disease Control and Prevention (CDC): Expanding booster recommendations
Johns Hopkins University Coronavirus Resource Center: Testing
GISAID SARS-CoV-2 submission tracking
U.S. Center for Disease Control and Prevention (CDC): COVID Data Tracker
Associated Press
UN (WHO) Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern
UN (WHO) Updates on Omicron
Nature news

Ilya Slizovskiy, DVM, MPH


Ilya Slizovskiy, DVM, MPH

I am a veterinarian with a background in public health and epidemiology. My goal is to advance our understanding of the ways in which ecosystems, agricultural practices, and preventive medical systems influence occurrence of disease in human and animal populations. I bring this focus to specifically address Antimicrobial Resistance (AMR), a major global health problem associated with extensive morbidity and mortality. My research involves developing laboratory, computational, and statistical tools to characterize risks of antimicrobial resistance genes in bacteria at the human-animal interface. My work relies on implementation of high-throughput sequencing technology and microbiome investigations. Current research projects are being conducted in the U.S., Europe, and Africa.