Rapid Emergence and Epidemiologic Characteristics of the SARS-CoV-2 B.1.526 Variant

New York City, New York, January 1-April 5, 2021

Corinne N. Thompson, PhD; Scott Hughes, PhD; Stephanie Ngai, MPH; Jennifer Baumgartner, MSPH; Jade C. Wang, MS; Emily McGibbon, MPH; Katelynn Devinney, MPH; Elizabeth Luoma, MPH; Daniel Bertolino, MPH; Christina Hwang, MPH; Kelsey Kepler, MPH; Cybill Del Castillo; Melissa Hopkins; Henry Lee, PhD; Andrea K. DeVito, MPH; Jennifer L. Rakeman, PhD; Anne D. Fine, MD

Disclosures

Morbidity and Mortality Weekly Report. 2021;70(19):712-716. 

In This Article

Abstract and Introduction

Introduction

Recent studies have documented the emergence and rapid growth of B.1.526, a novel variant of interest (VOI) of SARS-CoV-2, the virus that causes COVID-19, in the New York City (NYC) area after its identification in NYC in November 2020.[1–3] Two predominant subclades within the B.1.526 lineage have been identified, one containing the E484K mutation in the receptor-binding domain,[1,2] which attenuates in vitro neutralization by multiple SARS-CoV-2 antibodies and is present in variants of concern (VOCs) first identified in South Africa (B.1.351)[4] and Brazil (P.1).* The NYC Department of Health and Mental Hygiene (DOHMH) analyzed laboratory and epidemiologic data to characterize cases of B.1.526 infection, including illness severity, transmission to close contacts, rates of possible reinfection, and laboratory-diagnosed breakthrough infections among vaccinated persons. Preliminary data suggest that the B.1.526 variant does not lead to more severe disease and is not associated with increased risk for infection after vaccination (breakthrough infection) or reinfection. Because relatively few specimens were sequenced over the study period, the statistical power might have been insufficient to detect modest differences in rates of uncommon outcomes such as breakthrough infection or reinfection. Collection of timely viral genomic data for a larger proportion of citywide cases and rapid integration with population-based surveillance data would enable improved understanding of the impact of emerging SARS-CoV-2 variants and specific mutations to help guide public health intervention efforts.

SARS-CoV-2 specimens were sequenced at the Public Health Laboratory (PHL) or the Pandemic Response Laboratory (PRL). During January 1–April 5, 2021, PHL received specimens primarily from NYC residents at nine COVID Express laboratories. All nucleic acid amplification test (NAAT)-positive SARS-CoV-2 specimens with a cycle threshold (Ct) value <32 underwent whole genome sequencing (WGS) (Scott Hughes, PhD, NYC PHL, personal communication, April 2021). At PRL, specimens collected at approximately 190 outpatient facilities were randomly selected, and those with a Ct value ≤30 were sequenced.[5,6] Characteristics of persons with sequenced viruses were compared with those of NYC residents with COVID-19 diagnoses during the same period to evaluate representativeness. Records of persons with sequenced viruses were matched to the DOHMH COVID-19 surveillance Citywide Immunization and Vital Registry databases.

Persons infected with B.1.526 were compared with persons infected with variants that were not classified as VOIs or VOCs (i.e., non-VOI/VOC infections). Persons infected with B.1.526 were also compared with those infected with B.1.1.7 because of the recent increase in B.1.1.7 cases in NYC and the documented increased transmissibility[7] and illness severity associated with this variant.[8] To evaluate trends in socioeconomic status, neighborhood-level poverty was calculated as the percentage of residents in a ZIP code with household incomes <100% of the federal poverty level, per the American Community Survey 2014–2018. A case of possible reinfection was defined as an infection in a person with a sequenced specimen collected ≥90 days after a positive SARS-CoV-2 antigen or NAAT result. Breakthrough infections among partially vaccinated persons were defined as infections in persons with a sequenced specimen collected ≥14 days after the first vaccine dose and <14 days after the second dose (for mRNA vaccines). Breakthrough infections among fully vaccinated persons were defined as infections in persons with a sequenced specimen collected ≥14 days after either a second mRNA vaccine dose or a single dose viral vector vaccine. Comparisons across categorical characteristics were made using the chi-square or Fisher's exact test; continuous variables were compared using the Kruskal-Wallis test (SAS Enterprise Guide, version 7.1).

WGS was completed on 9,765 SARS-CoV-2 specimens, including 1,186 (12%) sequenced at PHL and 8,579 (88%) at PRL, representing 3.1% of NAAT-positive cases identified citywide during January 1–April 5, 2021. The number of specimens undergoing WGS at these laboratories increased over time (Figure), representing 7.7% of all NAAT-positive specimens by the week ending April 5. The B.1.1.7 variant was identified in 1,815 (19%) specimens. Among 3,679 (38%) B.1.526 variant viruses identified, 2,050 (56%) carried the E484K mutation. The proportion of B.1.526 viruses identified increased from 3% in mid-January to 34% by February 22 (Figure) and stabilized at 35%–45% weekly beginning March 8. The proportion of B.1.526 variants with the E484K mutation increased more quickly and as of April 5 represented 25% of all sequenced SARS-CoV-2 viruses, compared with 16% of B.1.526 variants without the E484K mutation. The proportion of B.1.1.7 viruses increased recently, reaching 36% by April 5. Other VOIs/VOCs were found among 253 specimens and were removed from additional analyses (B.1.427/B.1.429 variant in 166 specimens [viruses of B.1.427 or B.1.429 lineage, including those reported as B.1.427/B.1.429, without further differentiation]; P.1 variant in 50; B.1.525 variant in 20; B.1.351 variant in 12; and P.2 variant in 5).

Figure.

Number of specimens undergoing whole genome sequencing* (A) and percentage of specimens with B1.526 variant with or without E484K mutation, B.1.1.7 variant, and other variants of concern or interest (B), by week of specimen collection — New York City, New York, January 1–April 5, 2021
Abbreviations: VOC = variant of concern; VOI = variant of interest.
*Whole genome sequencing of specimens (collection date during January 1–April 5, 2021) from New York City residents was performed at the Public Health Laboratory or the Pandemic Response Laboratory.

The geographic distribution of persons with viruses sequenced at PHL or PRL was similar to that of persons with positive SARS-CoV-2 NAAT tests citywide; however, these persons were more frequently aged <45 years (67% versus 60% citywide), residents of neighborhoods with high poverty or very high poverty (45% versus 40%), or Black/African American (19% versus 16%) or Hispanic/Latino (35% versus 28%). A lower percentage of these persons were hospitalized (4% versus 9%) and died (0.5% versus 1.5%).

Among 3,679 persons infected with the B.1.526 variant, the median age was 35 years (Table 1). Compared with persons with non-VOI/VOC infections, those with B.1.526 infections were significantly more likely to live in the Bronx or in neighborhoods with high or very high poverty or to identify as Black/African American. Among persons with B.1.526 infections, 2,618 (71%) were symptomatic, 104 (4.3%) were hospitalized, and 11 (0.5%) died; these proportions are similar to or lower than those in persons with non-VOI/VOC infections (71%, 4.1%, and 0.7%, respectively). However, persons infected with the B.1.1.7 variant were more likely to be hospitalized (5.8%) than were persons with non-VOI/VOC infections (4.1%) (p = 0.04) (Table 2).

Possible reinfections were rare overall (0.5%), and the prevalence was similar among all persons with sequenced specimens (Table 1). No difference in rates of possible reinfection was found between persons infected with B.1.1.7 variants and those infected with B.1.526 variants with or without the E484K mutation (Supplementary Figure, https://stacks.cdc.gov/view/cdc/105634). The proportion of persons with a previous positive serology test result was 0.9% overall and similar among patients infected with all lineages (Table 1). Among persons infected with the B.1.526 variant carrying the E484K mutation, previous seropositivity was slightly more common (1.3%) than that among persons infected with the B.1.526 variant without the E484K mutation (0.7%), with the B.1.1.7 variant (0.7%), and with other non-VOI/VOC infections (0.9%); however, the difference was not significant (p = 0.23).

Among 32 fully vaccinated persons with sequenced viruses, eight (25%) were identified who were infected with the B.1.526 variant carrying the E484K mutation, three (9%) with the B.1.526 variant without the E484K mutation, seven (22%) with the B.1.1.7 variant, and 14 (44%) with non-VOI/VOC infections. No major differences between persons with B.1.526 and non-VOI/VOC infections were found in the secondary COVID-19 attack rate among household or community members identified as close contacts (Table 2).

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