Acquisition of the L452R mutation in the ACE2-binding interface of Spike protein triggers recent massive expansion of SARS-Cov-2 variants

Abstract

The recent rise in mutational variants of SARS-CoV-2, especially with changes in the Spike protein, is of significant concern due to the potential ability for these mutations to increase viral infectivity, virulence and/or ability to escape protective antibodies. Here, we investigated genetic variations in a 414-583 amino acid region of the Spike protein, partially encompassing the ACE2 receptor-binding domain (RBD), across a subset of 570 nasopharyngeal samples isolated between April 2020 and February 2021, from Washington, California, Arizona, Colorado, Minnesota and Illinois. We found that samples isolated since November have an increased number of amino acid mutations in the region, with L452R being the dominant mutation. This mutation is associated with a recently discovered CAL.20C viral variant from clade 20C, lineage B.1.429, that since November-December 2020 is associated with multiple outbreaks and is undergoing massive expansion across California. In some samples, however, we found a distinct L452R-carrying variant of the virus that, upon detailed analysis of the GISAID database genomes, is also circulating primarily in California, but emerged even more recently. The newly identified variant derives from the clade 20A (lineage B.1.232) and is named CAL.20A. We also found that the SARS-CoV-2 strain that caused the only recorded case of infection in an ape - gorillas in the San Diego Zoo, reported in January 2021 - is CAL.20A. In contrast to CAL.20C that carries two additional to L452R mutations in the Spike protein, L452R is the only mutation found in CAL.20A. According to the phylogenetic analysis, however, emergence of CAL.20C was also specifically triggered by acquisition of the L452R mutation. Further analysis of GISAID-deposited genomes revealed that several independent L452R-carrying lineages have recently emerged across the globe, with over 90% of the isolates reported between December 2020 -February 2021. Taken together, these results indicate that the L452R mutation alone is of significant adaptive value to SARS-CoV-2 and, apparently, the positive selection for this mutation became particularly strong only recently, possibly reflecting viral adaptation to the containment measures or increasing population immunity. While the functional impact of L452R has not yet been extensively evaluated, leucine-452 is positioned in the receptor-binding motif of RBD, in the interface of direct contact with the ACE2 receptor. Its replacement with arginine is predicted to result in both a much stronger binding to the receptor and escape from neutralizing antibodies. If true, this in turn might lead to significantly increased infectivity of the L452R variants, warranting their close surveillance and in-depth functional studies.

The localized rise of a B.1.526 SARS-CoV-2 variant containing an E484K mutation in New York State

“…For example, B.1.429 – defined by an L452R mutation in spike – was responsible for 24% of all COVID-19 cases in Southern California by November after its first detection in July (Zhang et al 2021). L452R might increase infectivity by stabilizing the spike-ACE2 receptor interaction and has evolved independently in multiple lineages (such as B.1.427; Tchesnokova et al 2021). While surveillance efforts have increased in the US, the country has not yet met the recommended sequencing of 5% of all COVID-19 cases in order to detect variants before they reach high prevalence in the population (Vavrek et al 2021).…”

Emergence of a recurrent insertion in the N-terminal domain of the SARS-CoV-2 spike glycoprotein

“…9, Figure 6, detailed in Table 1) is only second to the VOCs B.1.1.7, B.1.351 and P.1, and slightly lower than the emerging lineage P.3. Curiously, this rate of molecular evolution appears to be much higher than the VOCs B.1.427 and B.1.429 [44], and superior to that of other recently described emerging lineage A variants, such as A.23.1 and A.27 [12]. The total number of substitutions/insertions/deletions found in B.1.214.2, albeit slightly inferior to A.2.5 (i.e.…”

A tale of three SARS-CoV-2 variants with independently acquired P681H mutations in New York State

“…The proportion of SARS-CoV-2 genomes containing P681H and S494P mutations in New York also increased by over 4% since December 2020 (Table 1 and Figure 4). This is less than the increase demonstrated by B.1.1.7 and both B.1.526 variants but greater than B.1.427 and B.1.429 (Table 1 and Figure 4), which carry the L452R mutation and were identified as rapidly spreading in California (Zhang et al 2021; Tchesnokova et al 2021). In fact, if we count the B.1 variants separately from the B.1 lineage, they ranked 12 th in abundance in January 2021 compared to other lineages detected and 5 th in February 2021, surpassed only by B.1 and B.1.2, which have been circulating in New York since the early days of the pandemic (Lasek-Nesselquist, Singh, et al 2021; Maurano et al 2020; Gonzalez-Reiche et al 2020), and the B.1.1.7 and B.1.526 variants.…”

“…While neither the B.1.1.222 nor the B.1 variant appears to be rising as dramatically as B.1.526 or B.1.1.7 within New York State, they have increased faster than the B.1.427 and B.1.429, which showed a rapid expansion in California (Zhang et al 2021; Tchesnokova et al 2021). However, we cannot rule out the effects of sampling biases, particularly for February 2021, when almost all specimens sequenced derived from the NYC metropolitan area - the location where the majority of B.1.1.222 and B.1 variants were circulating (Figure 5).…”

“…The change in frequency of select SARS CoV-2 variants in New York as a function of time. B.1, variant with P681H and S494P mutations; B.1.1.222, variant with T478K and P681H mutations; B.1.1.7 the highly transmissible variant first identified in the United Kingdom (Rambaut et al 2020); B.1.243, variants with a P681H mutation; B.1.427 and B.1.428 variants with an L452R mutation that are rapidly spreading in California (Zhang et al 2021; Tchesnokova et al 2021); B.1.526K and B.1.526N, B.1.526 variants with an E484K or S477N mutation rapidly spreading in New York (Lasek-Nesselquist, Lapierre, et al 2021; Annavajhala et al 2021; West et al 2021); Other, all other lineages detected in New York.…”