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Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York
Short title: Emergence of SARS-CoV-2 variant B.1.526
Medini K. Annavajhala
1*
, Hiroshi Mohri
2*
, Pengfei Wang
2
, Manoj Nair
2
, Jason E. Zucker
1
,
Zizhang Sheng
2
, Angela Gomez-Simmonds
1
, Anne L. Kelley
1
, Maya Tagliavia
1
, Yaoxing
Huang
2
, Trevor Bedford
3
, David D. Ho
1,2,4#
, Anne-Catrin Uhlemann
1#
1
Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos
College of Physicians and Surgeons, New York, NY, USA
2
Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians
and Surgeons, New York, NY, USA
3
Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle,
WA, USA
4
Department of Microbiology and Immunology, Columbia University Irving Medical Center,
New York, NY, USA.
* Medini K. Annavajhala and Hiroshi Mohri contributed equally to this work.
# David D. Ho and Anne-Catrin Uhlemann contributed equally to this work.
Address correspondence to au2110@cumc.columbia.edu or dh2994@cumc.columbia.edu.
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NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice.
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Recent months have seen surges of SARS-CoV-2 infection across the globe with considerable
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viral evolution
1-3
. Extensive mutations in the spike protein may threaten efficacy of vaccines
2
and therapeutic monoclonal antibodies
4
. Two signature mutations of concern are E484K,
3
which plays a crucial role in the loss of neutralizing activity of antibodies, and N501Y, a
4
driver of rapid worldwide transmission of the B.1.1.7 lineage. Here, we report the emergence
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of variant lineage B.1.526 that contains E484K and its alarming rise to dominance in New
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York City in early 2021. This variant is partially or completely resistant to two therapeutic
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monoclonal antibodies in clinical use and less susceptible to neutralization by convalescent
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plasma or vaccinee sera, posing a modest antigenic challenge. The B.1.526 lineage has now
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been reported from all 50 states in the US and numerous other countries. B.1.526 rapidly
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replaced earlier lineages in New York upon its emergence, with an estimated transmission
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advantage of 35%. Such transmission dynamics, together with the relative antibody
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resistance of its E484K sub-lineage, likely contributed to the sharp rise and rapid spread of
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B.1.526. Although SARS-CoV-2 B.1.526 initially outpaced B.1.1.7 in the region, its growth
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subsequently slowed concurrent with the rise of B.1.1.7 and ensuing variants.
15
16
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Main
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While evolution of SARS-CoV-2 was deemed to be slow at the beginning of the global pandemic
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,
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multiple major variants of concern have emerged over the past year
1-3,6
. These lineages are each
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characterized by numerous mutations in the spike protein, raising concerns that they may escape
21
from therapeutic monoclonals and vaccine-induced antibodies. The hallmark mutation of B.1.1.7,
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a SARS-CoV-2 variant of concern that emerged in the UK, is N501Y located in the receptor-
23
binding domain (RBD) of spike
1
. This variant is seemingly more transmissible and virulent
7-9
,
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perhaps due to a higher binding affinity of N501Y for ACE2
10
or a greater propensity to evade
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host innate immune responses
11
. Two other variants of concern, B.1.351
2
and P.1
12
, share the
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N501Y mutation with B.1.1.7 but also contain an E484K substitution in RBD
2,3
. P.1 emerged as
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part of a second surge in Manaus, Brazil despite a high pre-existing SARS-CoV-2 seroprevalence
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in the population
13
. Reinfections with P.1 and another related Brazilian variant P.2 harboring
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E484K, have been documented
14,15
. Our previous study on B.1.351 demonstrated that this variant
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is refractory to neutralization by a number of monoclonal antibodies directed to the top of RBD,
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including several that have received emergency use authorization
4
. B.1.351 was markedly more
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resistant to neutralization by convalescent plasma and vaccinee sera. Importantly, these effects
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were in part mediated by the E484K mutation. These finding are worrisome in light of recent
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reports that three vaccine trials showed a substantial drop in efficacy in South Africa
16,17
. Likewise,
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P.1 was also relatively resistant to antibody neutralization, although not as severely
18
. We therefore
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implemented rapid molecular screening for signature mutations implicated in the success of these
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early variants of concern.
38
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Rapid screening for SARS-CoV-2 mutations
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We first developed rapid PCR-based single-nucleotide-polymorphism (SNP) assays (Extended
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Data Fig. 1) to search for N501Y and E484K mutations in SARS-CoV-2 positive clinical samples
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stored in the Columbia University Biobank. Between November 1, 2020 and May 1, 2021, 1,602
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samples were successfully genotyped by PCR. We identified 182/1,602 (11%) samples with
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E484K and 63/1,602 (3.9%) with N501Y. Eight samples contained both mutations. The earliest
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case with E484K was collected in mid-November 2020. The proportion of E484K PCR-screened
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cases substantially increased from 2.0% at the end of 2020 to 24.3% between February 21
st
and
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March 5
th
, 2021 (Fig. 1a), when targeted PCR genotyping was replaced by whole-genome
48
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is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
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sequencing. Viruses harboring N501Y also increased over time, from the earliest detection in mid-
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January to 5.3% of screened isolates by the beginning of March.
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Genomic surveillance of SARS-CoV-2
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We next performed untargeted whole genome nanopore sequencing of nasopharyngeal samples
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collected throughout the study period with cycle threshold (Ct)≤35. We successfully obtained
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1,507 SARS-CoV-2 whole genomes (59% of samples with Ct≤35; Extended Data Fig. 2).
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Sequencing results verified the E484K and N501Y substitutions in all samples identified by PCR
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screening. Of sequenced N501Y isolates, 31/41 (76%) were consistent with the B.1.1.7 lineage.
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Samples which harbored both N501Y and E484K were genotyped as P.1 (n=6), B.1.351 (n=1),
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and B.1.623 (n=1). However, quite unexpectedly, the large majority of PCR-screened cases with
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E484K (n=98/128, 77%) fell within a single lineage, B.1.526,
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recently labeled the Iota variant
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by the WHO
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.
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Analysis of the entire collection of CUIMC genomic sequences (Fig. 1b) showed that by May
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2021, SARS-CoV-2 variants (including B.1.526, B.1.1.7, and more recently P.1) comprised two-
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thirds of all sequenced isolates, replacing the vast majority of earlier lineages (Fig. 1b). The
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proportion of cases caused by B.1.526 rose rapidly from late 2020 through February 2021, and
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remained at approximately 40-50% of all sequenced cases from March to May 2021, despite a
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concurrent increase in B.1.1.7. In fact, during the months of December and January when the
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prevalence of B.1.1.7 was still negligible (Fig. 1b, marking under horizontal axis), the frequency
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of all viruses in the B.1.526 lineage rose from <5% to 50% while the frequency of other lineages
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declined from >95% to 50% (Fig. 1b, where white blank space represents other lineages).
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Calculations using these numbers in a head-to-head comparison and an established mathematical
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method
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indicate that B.1.526 has a growth advantage of ~5% per day. Likewise, fitting a logistic
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regression model to 478 individual observations from the extended timeframe of November 2020
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through January 2021 shows that B.1.526 had a similar growth advantage of 4.6% per day (95%
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CI 2.8–6.5% per day). Given that the serial interval for SARS-CoV-2 transmission is about 7
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days
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in the absence of any intervention, these results suggest that B.1.526 is ~35% more
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transmissible than non-variant viruses.
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Demographic and clinical features, including clinical outcomes, were largely comparable in
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patients with E484K versus those without the signature E484K or N501Y mutations, and between
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patients with B.1.526-E484K versus those with non-variant lineages
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(Extended Data Table 1).
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However, significantly lower Ct values were associated with both E484K (29.49 vs 30.71,
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p=0.013) and B.1.526-E484K (27.65 vs 28.81 in non-variant lineages, p=0.015), indicating a
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modestly higher viral load in these variant samples. A significantly higher proportion of patients
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B.1.526-E484K were also admitted to the hospital or presented to the emergency department
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(p=0.037).
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Signature B.1.526 lineage mutations
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We identified signature spike-protein mutations in the B.1.526 lineage by comparing all genomes
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generated in this study (Fig. 1c). Phylogenetic examination showed that the B.1.526 lineage is
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comprised of two closely related sub-lineages harboring either E484K (B.1.526-E484K; defined
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as Pangolin lineage B.1.526) or S477N (B.1.526-S477N; Pangolin lineage B.1.526.2), and the
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additional sub-lineage B.1.526.1, harboring the L452R substitution (B.1.526-L452R). Both
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B.1.526-E484K and B.1.526-S477N share characteristic spike-protein mutations L5F, T95I,
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D253G, D614G, and either A701V or Q957R along with either E484K or S477N. Non-spike
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mutations widely shared by B.1.526-E484K and B.1.526-S477N isolates include: T85I in ORF1a-
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nsp2; L438P in ORF1a-nsp4, a 9bp deletion Δ106-108 in ORF1a-nsp6; P323L in ORF1b-nsp12;
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Q88H in ORF1b-nsp13; Q57H in ORF3a; and P199L and M234I in the N gene. While B.1.526-
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L452R isolates shared a number of mutations across the genome in ORF-1ab, ORF-3ab, ORF-8,
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and N, it does not share characteristic spike mutations with B.1.526-E484K and B.1.526-S477N.
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To further investigate the evolutionary history of B.1.526, we performed phylogenetic analyses on
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genomes in this collection and in GISAID harboring the ORF1a-nsp6 deletion Δ106-108, along
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with mutation A20262G that uniquely defines the parent clade containing B.1.526 and related
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viruses (Fig. 2a). We observed a stepwise emergence of the key lineage-defining mutations, with
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T95I, D253G, and L5F appearing in the earliest phylogenetic nodes. Isolates subsequently
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branched into four sub-lineages, with two major groups B.1.526-E484K and B.1.526-S477N
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containing A701V, with a smaller sub-lineage B.1.526-S477N containing Q957R. The B.1.526-
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