Attenuated SARS-CoV-2 variants with deletions at the S1/S2 junction

Abstract

The emergence of SARS-CoV-2 has led to the current global coronavirus pandemic and more than one million infections since December 2019. The exact origin of SARS-CoV-2 remains elusive, but the presence of a distinct motif in the S1/S2 junction region suggests the possible acquisition of cleavage site(s) in the spike protein that promoted cross-species transmission. Through plaque purification of Vero-E6 cultured SARS-CoV-2, we found a series of variants which contain 15-30-bp deletions (Del-mut) or point mutations respectively at the S1/S2 junction. Examination of the original clinical specimen from which the isolate was derived, and 26 additional SARS-CoV-2 positive clinical specimens, failed to detect these variants. Infection of hamsters shows that one of the variants (Del-mut-1) which carries deletion of 10 amino acids (30bp) does not cause the body weight loss or more severe pathological changes in the lungs that is associated with wild type virus infection. We suggest that the unique cleavage motif promoting SARS-CoV-2 infection in humans may be under strong selective pressure, given that replication in permissive Vero-E6 cells leads to the loss of this adaptive function. It would be important to screen the prevalence of these variants in asymptomatic infected cases. The potential of the Del-mut variants as an attenuated vaccine or laboratory tool should be evaluated.

SARS-CoV-2 growth, furin-cleavage-site adaptation and neutralization using serum from acutely infected, hospitalized COVID-19 patients

“…However, there was no trace of the deletion in the chromatograms for the received P4 virus or a P5 stock, indicating that once a deletion occurs it is rapidly selected in Vero cells and enriched in the virus population. Other groups have reported similar perturbations of this region (36, [42][43][44], and the deletions have been linked to the development of a large plaque phenotype (36). We observed variations in plaque phenotype, although in our experience, plaque size and morphology is governed by the concentration of agarose or Avicell in the semi-solid overlay medium and varies significantly depending on the protocol used.…”

Neuropilin-1 is a host factor for SARS-CoV-2 infection

“…A SARS-CoV-2 virus with a natural deletion of the S1/S2 furin cleavage site demonstrated attenuated pathogenicity in hamster models, causing less alveolar damage 17 . NRP1 binding to the CendR-motif in S1 is thus likely to play a role in the increased pathogenicity of SARS-CoV-2 compared with SARS-CoV.…”

An Update on the Origin of SARS-CoV-2: Though Closest Identity, Bat (RaTG13) and Pangolin Derived Coronaviruses Varied in the Critical Binding Site and O-Linked Glycan Residues

“…A study data support the natural origin of SARS-CoV-2, likely derived from bats, possibly transferred to pangolins, before spreading to man and it not arti cial CoV, including the chimeric SL-SHC014-MA15 [38]. The study proposes a unique cleavage motif promoting SARS-CoV-2 infection in humans may be under strong selective pressure, given that replication in permissive Vero-E6 cells leads to the loss of this adaptive function [39]. Overall, we demonstrate the key residues of RBD (455, 486, 493, 494, 501 and 505) and polybasic cleavage sites varies signi cantly; need to be studied in detail for a better understanding of cross-species transmission.…”