niman

USA/CA-CDC-STM-UNK84/2020 San Diego Co USA/CA-CDC-STM-154/2020 12/31 72F California map update https://www.google.com/maps/d/u/1/edit?mid=1aQDSL2LwQFbuoCAg_nIOPK8D-LIJ5MYd&ll=32.933625656338364%2C-117.3396572064774&z=9

USA/CA-CDC-STM-UNK83/2020 San Diego Co USA/CA-CDC-STM-150/2020 12/31 9F California map update https://www.google.com/maps/d/u/1/edit?mid=1aQDSL2LwQFbuoCAg_nIOPK8D-LIJ5MYd&ll=32.933625656338364%2C-117.3396572064774&z=9

USA/CA-CDC-STM-UNK82/2020 San Diego Co USA/CA-CDC-STM-149/2020 12/31 33M California map update https://www.google.com/maps/d/u/1/edit?mid=1aQDSL2LwQFbuoCAg_nIOPK8D-LIJ5MYd&ll=32.933625656338364%2C-117.3396572064774&z=9

CDC update on B.1.1.7 variants in the US lists 40 for California Six new sequences for San Diego Co will be assigned UNK numbers and updated when sequences released USA/CA-CDC-STM-UNK82/2020 San Diego Co USA/CA-CDC-STM-UNK83/2020 San Diego Co USA/CA-CDC-STM-UNK84/2020 San Diego Co USA/CA-CDC-STM-UNK85/2020 San Diego Co USA/CA-CDC-STM-UNK86/2020 San Diego Co USA/CA-CDC-STM-UNK87/2020 San Diego Co USA/CA-CDC-STM-149/2020 12/31 33M California USA/CA-CDC-STM-150/2020 12/31 9F California USA/CA-CDC-STM-154/2020 12/31 72F California USA/CA-CDC-STM-155/2020 12/31 15M California USA/CA-CDC-STM-156/2020 12/31 40M California https://www.cdc.gov/coronavirus/2019-ncov/transmission/variant-cases.html

USA/NY-Wadsworth-UNK81-01/202 Tompkins Co map update https://www.google.com/maps/d/u/1/edit?mid=1aQDSL2LwQFbuoCAg_nIOPK8D-LIJ5MYd&ll=42.446488526279026%2C-76.68607107539061&z=10

The sequence from Tomkins Co has not been release and will be assigned a UNK number, which will be upgraded upon release. USA/NY-Wadsworth-UNK81-01/202 USA/NY-CU-B1/2021 1/7 Ithaca New York The Tompkins County Health Department is announcing that a positive case of the “UK variant” of COVID-19 has been identified in Tompkins County. The case was sequenced through Cornell University’s COVID-19 testing lab as part of that lab’s testing services for Cayuga Health System and the region. Test results are sequenced for this strain when an individual indicates that they are a close contact of another individual with the variant or indicates relevant travel from the United Kingdom. https://tompkinscountyny.gov/health/covid19-2021-01-15-uk-variant

map update USA/NY-Wadsworth-UNK80-01/2021 Saratoga Co USA/NY-Wadsworth-21009427-01/2021 1/12 42M Saratoga County New York https://www.google.com/maps/d/u/1/edit?mid=1aQDSL2LwQFbuoCAg_nIOPK8D-LIJ5MYd&ll=43.068586405429336%2C-73.96559789530934&z=10

map update USA/NY-Wadsworth-UNK79-01/2021 Saratoga Co USA/NY-Wadsworth-21001578-01/2021 1/5 56F Warren https://www.google.com/maps/d/u/1/edit?mid=1aQDSL2LwQFbuoCAg_nIOPK8D-LIJ5MYd&ll=43.068586405429336%2C-73.96559789530934&z=10

map update USA/NY-Wadsworth-UNK78-01/2021 Saratoga Co USA/NY-Wadsworth-21006028-01/2021 1/5 48M Saratoga https://www.google.com/maps/d/u/1/edit?mid=1aQDSL2LwQFbuoCAg_nIOPK8D-LIJ5MYd&ll=43.068586405429336%2C-73.96559789530934&z=10

Three of the Saratoga Co sequences below have not been released. The will be assigned UNK numbers and updated when released. USA/NY-Wadsworth-78UNK70-01/2021 Saratoga Co USA/NY-Wadsworth-79UNK70-01/2021 Saratoga Co USA/NY-Wadsworth-80UNK70-01/2021 Saratoga Co — Gov. Cuomo Wednesday updated New Yorkers on the state’s progress during the ongoing COVID-19 pandemic. Three additional cases of the UK variant have reportedly been identified in Warren County, bringing the total number of cases in New York to 15. Health officials say four cases in Saratoga County and two cases in Warren County have been identified as part of the cluster connected to a jewelry store in Saratoga Springs. Three additional cases in Warren County are reportedly under investigation for their link to the cluster, but have yet to be confirmed. A second cluster has also reportedly been identified and includes two cases in Suffolk County, two cases from Nassau County and one from Queens. The final case was identified in Manhattan and is said not to be connected to either cluster. https://www.news10.com/health/gov-cuomo-provides-wednesday-coronavirus-update-for-nys-3/?utm_campaign=socialflow&utm_source=t.co&utm_medium=referral

USA/PA_UNK77/2020 map update https://www.google.com/maps/d/u/1/edit?mid=1aQDSL2LwQFbuoCAg_nIOPK8D-LIJ5MYd&ll=39.92914039503186%2C-75.26203434628906&z=11

The sequence of the Philadelphia case has not been released and will be assigned a UNK number USA/PA_UNK77/2020 Health officials say a woman in her 50s, who lives in both Philadelphia and Bucks County, was found to have the UK variant. She became sick at the end of December. She was briefly hospitalized and is now recovering. She had contact with someone who became infected after traveling to England. https://6abc.com/covid-19-variant-new-coronavirus-in-pennsylvania-dauphin-county/9688618/

USA/UT-UPHL-UNK76/2020 USA/UT-UPHL-2101766431/2020 Map update https://www.google.com/maps/d/u/1/edit?mid=1aQDSL2LwQFbuoCAg_nIOPK8D-LIJ5MYd&ll=40.64819348452384%2C-112.05901111015626&z=10

The sequence from Utah has not been released. It will be assigned a UNK number which will updated when released. USA/UT-UPHL-UNK76/2020 USA/UT-UPHL-2101766431/2020 The case is a 25-44 year old male from Salt Lake County who tested positive last month. The case has no known travel outside of Utah and experienced only mild symptoms. https://coronavirus.utah.gov/covid-19-uk-variant-discovered-in-utah/

Jan 15 Early Rel MMWR - Variants B.1.1.7 501.v2 P.1 B.1.1.7 with E484K Recombinant https://recombinomics.co/thedrnimanshow/2021/011521_MMWR_E484K.mp3

Chicago and Illinois Departments of Public Health confirm first Illinois case of the COVID-19 variant first seen in the United Kingdom January 15, 2021 Andy Buchanan [email protected] CHICAGO – The Chicago Department of Public Health (CDPH) and Illinois Department of Public Health (IDPH) today announced the first case in Illinois of the SARS-CoV-2 variant B.1.1.7 first identified in the United Kingdom. The case was identified by the Northwestern University Feinberg School of Medicine through sequencing analysis of a specimen from bio-banked samples of COVID-19 positive tests. The new strain was first identified in the United States about two weeks ago in Colorado and has since been identified in several other states. Evidence suggests that this variant can spread more easily than most currently-circulating strains of COVID-19, but there is no evidence that the new strain affects the sensitivity of diagnostic tests or that it causes more severe illness or increased risk of death. In addition, data suggest current vaccines will be effective and safe in providing protection against the variant. “This news isn’t surprising and doesn’t change our guidance around COVID-19. We must double down on the recommended safety strategies we know help stop the spread of this virus,” said CDPH Commissioner Allison Arwady, M.D. “In order to protect Chicago, please continue to wear a mask, practice social distancing, wash your hands often, do not have outside guests in your home, and get vaccinated when it is your turn.” CDPH, IDPH and the U.S. Centers for Disease Control and Prevention (CDC), in collaboration with various public health agencies, are closely monitoring this strain. “When we learned of this and other COVID-19 variants, we increased our surveillance efforts by performing genomic sequence testing on an increased number of specimens,” said IDPH Director Dr. Ngozi Ezike. “We will continue to collaborate with our academic partners, local health departments like CDPH, hospitals, and the CDC to monitor for additional cases.” A follow-up case investigation by CDPH found that the individual had travelled to the UK and the Middle East in the 14 days prior to the diagnosis. CDPH has worked to identify close contacts of the individual to reinforce the importance of adherence with quarantine and isolation measures. CDPH is also working with the CDC and IDPH to contribute to national SARS-CoV-2 strain surveillance. Building regional capacity and coordination for this more advanced, specialized molecular laboratory public health work is a top priority for CDPH. Last year, prior to the detection of this variant, CDPH awarded $3 million to lay the groundwork for a Regional Innovative Public Health Laboratory, in partnership with Rush University Medical Center and working with laboratories and academic centers across the City, to increase public health surveillance of possible COVID-19 variants in the Chicago region. “It is important to monitor the spread of virus variants,” said Dr. Egon Ozer, an assistant professor of medicine in infectious diseases at Northwestern University Feinberg School of Medicine. “We expected this variant to show up eventually. We will continue to sequence and study these samples.” Some data show a higher concentration of the virus in the respiratory tract for the UK variant that could be related to a higher infectivity and easier spread of the variant, but this needs to be confirmed, Ozer said. Some modeling and molecular data also seem to indicate the variant may attach more strongly to the receptor of the human cell, but this also remains under study. Importantly, no data suggests an increased severity of illness, and early studies have shown the vaccine is still effective against this variant. Dr. Ozer, Dr. Judd Hultquist, Dr. Ramon Lorenzo Redondo and their team in the Northwestern Pathogen Genomics and Bioinformatics Group have been sequencing virus samples obtained from the Northwestern Medicine Diagnostics Molecular Biology Lab and other collaborating institutions. Their goal is to identify populations of SARS-CoV-2 viruses circulating in the city and see how they change over time in their ability to cause disease and spread. In December, the Northwestern team sequenced 180 random residual samples from individuals who came to Northwestern clinics or other sites for COVID-19 testing or screening that would have otherwise been discarded. The COVID-19 virus – also known as SARS-CoV-2 – like other viruses, constantly changes through mutation, and new variants of a virus are expected to occur over time. According to the CDC, this variant is estimated to have first emerged in the UK during September 2020. Other novel variants of SARS-CoV-2, which also might change the way the virus transmits or behaves, have been identified in South Africa, Nigeria, Brazil, Japan and the US. More novel strains are likely to be identified in the coming weeks and months. As a pre-cautionary measure, the CDC earlier this week announced that all international passengers headed to the United States will first need to show proof of a negative coronavirus test, a policy which goes into effect on Jan. 26. The new policy requires all air passengers, regardless of vaccination status, to get a test for current infection within the three days before their flight to the United States departs, and to provide written documentation of their test results or proof of having recovered from Covid-19. Everyday preventive actions by the public can help to slow the spread of all known COVID-19 variants, including wearing a mask, washing hands often, staying six feet away from others and avoiding crowds, avoiding non-essential travel and getting vaccinated when it is your turn. https://www.chicago.gov/city/en/depts/cdph/provdrs/health_protection_and_response/news/2021/january/chicago-and-illinois-departments-of-public-health-confirm-first-.html

References Public Health England. Investigation of novel SARS-CoV-2 variant: variant of concern 202012/01, technical briefing 3. London, United Kingdom: Public Health England; 2020. https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/950823/Variant_of_Concern_VOC_202012_01_Technical_Briefing_3_-_England.pdfpdf iconexternal icon Kemp SA, Harvey WT, Datir RP, et al. Recurrent emergence and transmission of a SARS-CoV-2 spike deletion ΔH69/V70. bioRxiv [Preprint posted online January 14, 2021]. https://www.biorxiv.org/content/10.1101/2020.12.14.422555v4external icon Volz E, Mishra S, Chand M, et al. Transmission of SARS-CoV-2 lineage B.1.1.7 in England: insights from linking epidemiological and genetic data. medRxiv [Preprint posted online January 4, 2021]. https://www.medrxiv.org/content/10.1101/2020.12.30.20249034v2external icon Honein MA, Christie A, Rose DA, et al.; CDC COVID-19 Response Team. Summary of guidance for public health strategies to address high levels of community transmission of SARS-CoV-2 and related deaths, December 2020. MMWR Morb Mortal Wkly Rep 2020;69:1860–7. CrossRefexternal icon PubMedexternal icon Volz E, Hill V, McCrone JT, et al.; COG-UK Consortium. Evaluating the effects of SARS-CoV-2 spike mutation D614G on transmissibility and pathogenicity. Cell 2021;184:64–75.e11. CrossRefexternal icon PubMedexternal icon Korber B, Fischer WM, Gnanakaran S, et al.; Sheffield COVID-19 Genomics Group. Tracking changes in SARS-CoV-2 spike: evidence that D614G increases infectivity of the COVID-19 virus. Cell 2020;182:812–27. CrossRefexternal icon PubMedexternal icon McCarthy KR, Rennick LJ, Namnulli S, et al. Natural deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape. bioRxiv [Preprint posted online November 19, 2020]. https://www.biorxiv.org/content/10.1101/2020.11.19.389916v1external icon Washington NL, White S, Schiabor KM, Cirulli ET, Bolze A, Lu JT. S gene dropout patterns in SARS-CoV-2 tests suggest spread of the H69del/V70del mutation in the US. medRxiv [Preprint posted online December 30, 2020]. https://www.medrxiv.org/content/10.1101/2020.12.24.20248814v1external icon Weisblum Y, Schmidt F, Zhang F, et al. Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants. eLife 2020;9:e61312. CrossRefexternal icon PubMedexternal icon Greaney AJ, Loes AN, Crawford KHD, et al. Comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human serum antibodies. bioRxiv [Preprint posted online January 4, 2021]. https://www.biorxiv.org/content/10.1101/2020.12.31.425021v1external icon

FIGURE 2. Simulated case incidence trajectories* of current SARS-CoV-2 variants and the B.1.1.7 variant,† assuming community vaccination§ and initial Rt = 1.1 (A) or initial Rt = 0.9 (B) for current variants — United States, January–April 2021 Abbreviation: Rt = time-varying reproductive number. * For all simulations, it was assumed that the reporting rate was 25% and that persons who were seropositive or infected within the simulation became immune. The simulation was initialized with 60 reported cases of SARS-CoV-2 infection per 100,000 persons (approximately 200,000 cases per day in the U.S. population) on January 1, 2021. Bands represent simulations with 10%–30% population-level immunity as of January 1, 2021. † Initial B.1.1.7 prevalence is assumed to be 0.5% among all infections and B.1.1.7 is assumed to be 50% more transmissible than current variants. § For vaccination, it was assumed that 300 doses were administered per 100,000 persons per day (approximately 1 million doses per day in the U.S. population) beginning January 1, 2021, that 2 doses achieved 95% immunity against infection, and that there was a 14-day delay between vaccination and protection.

FIGURE 1. Simulated case incidence trajectories* of current SARS-CoV-2 variants and the B.1.1.7 variant,† assuming no community vaccination and either initial Rt = 1.1 (A) or initial Rt = 0.9 (B) for current variants — United States, January–April 2021 Abbreviation: Rt = time-varying reproductive number. * For all simulations, it was assumed that the reporting rate was 25% and that persons who were seropositive or infected within the simulation became immune. The simulation was initialized with 60 reported cases of SARS-CoV-2 infection per 100,000 persons (approximately 200,000 cases per day in the U.S. population) on January 1, 2021. Bands represent simulations with 10%–30% population-level immunity as of January 1, 2021. † Initial B.1.1.7 prevalence is assumed to be 0.5% among all infections and B.1.1.7 is assumed to be 50% more transmissible than current variants.

TABLE. Characteristics of SARS-CoV-2 variants of concern — worldwide, September 2020–January 2021 Variant designation First identification Characteristic mutations (protein: mutation) No. of current sequence-confirmed cases No. of countries with sequences Location Date United States Worldwide B.1.1.7 (20I/501Y.V1) United Kingdom Sep 2020 ORF1ab: T1001I, A1708D, I2230T, del3675–3677 SGF 76 15,369 36 S: del69–70 HV, del144 Y, N501Y, A570D, D614G, P681H, T761I, S982A, D1118H ORF8: Q27stop, R52I, Y73C N: D3L, S235F B.1.351 (20H/501Y.V2) South Africa Oct 2020 ORF1ab: K1655N 0 415 13 E: P71L N: T205I S:K417N, E484K, N501Y, D614G, A701V P.1 (20J/501Y.V3) Brazil and Japan Jan 2021 ORF1ab: F681L, I760T, S1188L, K1795Q, del3675–3677 SGF, E5662D 0 35 2 S: L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, H655Y, T1027I ORF3a: C174G ORF8: E92K ORF9: Q77E ORF14: V49L N: P80R Abbreviations: del = deletion; E = envelope protein; N = nucleocapsid protein; ORF = open reading frame; S = spike protein.

Discussion Currently, there is no known difference in clinical outcomes associated with the described SARS-CoV-2 variants; however, a higher rate of transmission will lead to more cases, increasing the number of persons overall who need clinical care, exacerbating the burden on an already strained health care system, and resulting in more deaths. Continued genomic surveillance to identify B.1.1.7 cases, as well as the emergence of other variants of concern in the United States, is important for the COVID-19 public health response. Whereas the SGTF results can help identify potential B.1.1.7 cases that can be confirmed by sequencing, identifying priority variants that do not exhibit SGTF relies exclusively on sequence-based surveillance. The experience in the United Kingdom and the B.1.1.7 models presented in this report illustrate the impact a more contagious variant can have on the number of cases in a population. The increased transmissibility of this variant requires an even more rigorous combined implementation of vaccination and mitigation measures (e.g., distancing, masking, and hand hygiene) to control the spread of SARS-CoV-2. These measures will be more effective if they are instituted sooner rather than later to slow the initial spread of the B.1.1.7 variant. Efforts to prepare the health care system for further surges in cases are warranted. Increased transmissibility also means that higher than anticipated vaccination coverage must be attained to achieve the same level of disease control to protect the public compared with less transmissible variants. In collaboration with academic, industry, state, territorial, tribal, and local partners, CDC and other federal agencies are coordinating and enhancing genomic surveillance and virus characterization efforts across the United States. CDC coordinates U.S. sequencing efforts through the SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology, and Surveillance (SPHERES)§§ consortium, which includes approximately 170 participating institutions and promotes open data-sharing to facilitate the use of SARS-CoV-2 sequence data. To track SARS-CoV-2 viral evolution, CDC is implementing multifaceted genomic surveillance to understand the epidemiologic, immunologic, and evolutionary processes that shape viral phylogenies (phylodynamics); guide outbreak investigations; and facilitate the detection and characterization of possible reinfections, vaccine breakthrough cases, and emerging viral variants. In November 2020, CDC established the National SARS-CoV-2 Strain Surveillance (NS3) program to improve the representativeness of domestic SARS-CoV-2 sequences. The program collaborates with 64 U.S. public health laboratories to support a genomic surveillance system; NS3 is also building a collection of SARS-CoV-2 specimens and sequences to support public health response and scientific research to evaluate the impact of concerning mutations on existing recommended medical countermeasures. CDC has also contracted with several large commercial clinical laboratories to rapidly sequence tens of thousands of SARS-CoV-2–positive specimens each month and has funded seven academic institutions to conduct genomic surveillance in partnership with public health agencies, thereby adding substantially to the availability of timely genomic surveillance data from across the United States. In addition to these national initiatives, many state and local public health agencies are sequencing SARS-CoV-2 to better understand local epidemiology and support public health response to the pandemic. The findings in this report are subject to at least three limitations. First, the magnitude of the increase in transmissibility in the United States compared with that observed in the United Kingdom remains unclear. Second, the prevalence of B.1.1.7 in the United States is also unknown at this time, but detection of variants and estimation of prevalence will improve with enhanced U.S. surveillance efforts. Finally, local mitigation measures are also highly variable, leading to variation in Rt. The specific outcomes presented here are based on simulations and assumed no change in mitigations beyond January 1. The increased transmissibility of the B.1.1.7 variant warrants rigorous implementation of public health strategies to reduce transmission and lessen the potential impact of B.1.1.7, buying critical time to increase vaccination coverage. CDC’s modeling data show that universal use of and increased compliance with mitigation measures and vaccination are crucial to reduce the number of new cases and deaths substantially in the coming months. Further, strategic testing of persons without symptoms of COVID-19, but who are at increased risk for infection with SARS-CoV-2, provides another opportunity to limit ongoing spread. Collectively, enhanced genomic surveillance combined with increased compliance with public health mitigation strategies, including vaccination, physical distancing, use of masks, hand hygiene, and isolation and quarantine, will be essential to limiting the spread of SARS-CoV-2 and protecting public health. * https://www.gov.uk/government/news/phe-investigating-a-novel-variant-of-covid-19external icon. † https://www.cdc.gov/coronavirus/2019-ncov/transmission/variant-cases.html. § https://www.japantimes.co.jp/news/2021/01/11/national/science-health/new-coronavirus-variant-japan/external icon. ¶ https://www.fda.gov/news-events/press-announcements/fda-issues-alert-regarding-sars-cov-2-viral-mutation-health-care-providers-and-clinical-laboratory?utm_mediumexternal icon. ** https://virological.org/t/spike-e484k-mutation-in-the-first-sars-cov-2-reinfection-case-confirmed-in-brazil-2020/584external icon. †† https://www.cdc.gov/coronavirus/2019-ncov/more/science-and-research/scientific-brief-emerging-variants.html. §§ https://www.cdc.gov/coronavirus/2019-ncov/covid-data/spheres.html.

B.1.1.7 lineage (20I/501Y.V1) The B.1.1.7 variant carries a mutation in the S protein (N501Y) that affects the conformation of receptor-binding domain. This variant has 13 other B.1.1.7 lineage-defining mutations (Table), several of which are in the S protein, including a deletion at positions 69 and 70 (del69–70) that evolved spontaneously in other SARS-CoV-2 variants and is hypothesized to increase transmissibility (2,7). The deletion at positions 69 and 70 causes S-gene target failure (SGTF) in at least one RT-PCR–based diagnostic assay (i.e., with the ThermoFisher TaqPath COVID-19 assay, the B.1.1.7 variant and other variants with the del69–70 produce a negative result for S-gene target and a positive result for the other two targets); SGTF has served as a proxy in the United Kingdom for identifying B.1.1.7 cases (1). Multiple lines of evidence indicate that B.1.1.7 is more efficiently transmitted compared with other SARS-CoV-2 variants circulating in the United Kingdom. U.K. regions with a higher proportion of B.1.1.7 sequences had faster epidemic growth than did other areas, diagnoses with SGTF increased faster than did non-SGTF diagnoses in the same areas, and a higher proportion of contacts were infected by index patients with B.1.1.7 infections than by index patients infected with other variants (1,3). Variant B.1.1.7 has the potential to increase the U.S. pandemic trajectory in the coming months. To illustrate this effect, a simple, two-variant compartmental model was developed. The current U.S. prevalence of B.1.1.7 among all circulating viruses is unknown but is thought to be <0.5% based on the limited number of cases detected and SGTF data (8). For the model, initial assumptions included a B.1.1.7 prevalence of 0.5% among all infections, SARS-CoV-2 immunity from previous infection of 10%–30%, a time-varying reproductive number (Rt) of 1.1 (mitigated but increasing transmission) or 0.9 (decreasing transmission) for current variants, and a reported incidence of 60 cases per 100,000 persons per day on January 1, 2021. These assumptions do not precisely represent any single U.S. location, but rather, indicate a generalization of conditions common across the country. The change in Rt over time resulting from acquired immunity and increasing prevalence of B.1.1.7, was modeled, with the B.1.1.7 Rt assumed to be a constant 1.5 times the Rt of current variants, based on initial estimates from the United Kingdom (1,3). Next, the potential impact of vaccination was modeled assuming that 1 million vaccine doses were administered per day beginning January 1, 2021, and that 95% immunity was achieved 14 days after receipt of 2 doses. Specifically, immunity against infection with either current variants or the B.1.1.7 variant was assumed, although the effectiveness and duration of protection against infection remains uncertain, because these were not the primary endpoint of clinical trials for initial vaccines. In this model, B.1.1.7 prevalence is initially low, yet because it is more transmissible than are current variants, it exhibits rapid growth in early 2021, becoming the predominant variant in March (Figure 1). Whether transmission of current variants is increasing (initial Rt = 1.1) or slowly decreasing (initial Rt = 0.9) in January, B.1.1.7 drives a substantial change in the transmission trajectory and a new phase of exponential growth. With vaccination that protects against infection, the early epidemic trajectories do not change and B.1.1.7 spread still occurs (Figure 2). However, after B.1.1.7 becomes the dominant variant, its transmission was substantially reduced. The effect of vaccination on reducing transmission in the near term was greatest in the scenario in which transmission was already decreasing (initial Rt = 0.9) (Figure 2). Early efforts that can limit the spread of the B.1.1.7 variant, such as universal and increased compliance with public health mitigation strategies, will allow more time for ongoing vaccination to achieve higher population-level immunity.

On December 14, 2020, the United Kingdom reported a SARS-CoV-2 variant of concern (VOC), lineage B.1.1.7, also referred to as VOC 202012/01 or 20I/501Y.V1.* The B.1.1.7 variant is estimated to have emerged in September 2020 and has quickly become the dominant circulating SARS-CoV-2 variant in England (1). B.1.1.7 has been detected in over 30 countries, including the United States. As of January 13, 2021, approximately 76 cases of B.1.1.7 have been detected in 10 U.S. states.† Multiple lines of evidence indicate that B.1.1.7 is more efficiently transmitted than are other SARS-CoV-2 variants (1–3). The modeled trajectory of this variant in the U.S. exhibits rapid growth in early 2021, becoming the predominant variant in March. Increased SARS-CoV-2 transmission might threaten strained health care resources, require extended and more rigorous implementation of public health strategies (4), and increase the percentage of population immunity required for pandemic control. Taking measures to reduce transmission now can lessen the potential impact of B.1.1.7 and allow critical time to increase vaccination coverage. Collectively, enhanced genomic surveillance combined with continued compliance with effective public health measures, including vaccination, physical distancing, use of masks, hand hygiene, and isolation and quarantine, will be essential to limiting the spread of SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19). Strategic testing of persons without symptoms but at higher risk of infection, such as those exposed to SARS-CoV-2 or who have frequent unavoidable contact with the public, provides another opportunity to limit ongoing spread. Global genomic surveillance and rapid open-source sharing of viral genome sequences have facilitated near real-time detection, comparison, and tracking of evolving SARS-CoV-2 variants that can inform public health efforts to control the pandemic. Whereas some mutations in the viral genome emerge and then recede, others might confer a selective advantage to the variant, including enhanced transmissibility, so that such a variant can rapidly dominate other circulating variants. Early in the pandemic, variants of SARS-CoV-2 containing the D614G mutation in the spike (S) protein that increases receptor binding avidity rapidly became dominant in many geographic regions (5,6). In late fall 2020, multiple countries reported detecting SARS-CoV-2 variants that spread more efficiently. In addition to the B.1.1.7 variant, notable variants include the B.1.351 lineage first detected in South Africa and the recently identified B.1.1.28 subclade (renamed “P.1”) detected in four travelers from Brazil during routine screening at the Haneda (Tokyo) airport.§ These variants carry a constellation of genetic mutations, including in the S protein receptor-binding domain, which is essential for binding to the host cell angiotensin-converting enzyme-2 (ACE-2) receptor to facilitate virus entry. Evidence suggests that other mutations found in these variants might confer not only increased transmissibility but might also affect the performance of some diagnostic real-time reverse transcription–polymerase chain reaction (RT-PCR) assays¶ and reduce susceptibility to neutralizing antibodies (2,3,5–10). A recent case report documented the first case of SARS-CoV-2 reinfection in Brazil with a SARS-CoV-2 variant that contained the E484K mutation,** which has been shown to reduce neutralization by convalescent sera and monoclonal antibodies (9,10). This report focuses on the emergence of the B.1.1.7 variant in the United States. As of January 12, 2021, neither the B.1.351 nor the P.1 variants have been detected in the United States. For information about emerging SARS-CoV-2 variants of concern, CDC maintains a webpage dedicated to providing information on emerging SARS-CoV-2 variants.††

Summary What is already known about this topic? A more highly transmissible variant of SARS-CoV-2, B.1.1.7, has been detected in 10 U.S. states. What is added by this report? Modeling data indicate that B.1.1.7 has the potential to increase the U.S. pandemic trajectory in the coming months. CDC’s system for genomic surveillance and the effort to expand sequencing will increase the availability of timely U.S. genomic surveillance data. What are the implications for public health practice? The increased transmissibility of the B.1.1.7 variant warrants universal and increased compliance with mitigation strategies, including distancing and masking. Higher vaccination coverage might need to be achieved to protect the public. Genomic sequence analysis through the National SARS-CoV-2 Strain Surveillance program will enable a targeted approach to identifying variants of concern in the United States.

Emergence of SARS-CoV-2 B.1.1.7 Lineage — United States, December 29, 2020–January 12, 2021 Early Release / January 15, 2021 / 70 Summer E. Galloway, PhD1; Prabasaj Paul, PhD1; Duncan R. MacCannell, PhD2; Michael A. Johansson, PhD1; John T. Brooks, MD1; Adam MacNeil, PhD1; Rachel B. Slayton, PhD1; Suxiang Tong, PhD1; Benjamin J. Silk, PhD1; Gregory L. Armstrong, MD2; Matthew Biggerstaff, ScD1; Vivien G. Dugan, PhD1 1CDC COVID-19 Response Team; 2Office of Advanced Molecular Detection, National Center for Emerging and Zoonotic Infectious Diseases, CDC. Members of the Sequencing for Public Health Emergency Response, Epidemiology and Surveillance consortium; state and local public health laboratories; Association of Public Health Laboratories; CDC COVID-19 Response Team; Respiratory Viruses Branch, Division of Viral Diseases, CDC. Top Corresponding author: Summer E. Galloway, [email protected].