Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility

Abstract

A spike protein mutation D614G became dominant in SARS-CoV-2 during the COVID-19 pandemic. However, the mutational impact on viral spread and vaccine efficacy remains to be defined. Here we engineer the D614G mutation in the SARS-CoV-2 USA-WA1/2020 strain and characterize its effect on viral replication, pathogenesis, and antibody neutralization. The D614G mutation significantly enhances SARS-CoV-2 replication on human lung epithelial cells and primary human airway tissues, through an improved infectivity of virions with the spike receptor-binding domain in an “up” conformation for binding to ACE2 receptor. Hamsters infected with D614 or G614 variants developed similar levels of weight loss. However, the G614 virus produced higher infectious titers in the nasal washes and trachea, but not lungs, than the D614 virus. The hamster results confirm clinical evidence that the D614G mutation enhances viral loads in the upper respiratory tract of COVID-19 patients and may increases transmission. For antibody neutralization, sera from D614 virus-infected hamsters consistently exhibit higher neutralization titers against G614 virus than those against D614 virus, indicating that (i) the mutation may not reduce the ability of vaccines in clinical trials to protect against COVID-19 and (ii) therapeutic antibodies should be tested against the circulating G614 virus before clinical development.ImportanceUnderstanding the evolution of SARS-CoV-2 during the COVID-19 pandemic is essential for disease control and prevention. A spike protein mutation D614G emerged and became dominant soon after the pandemic started. By engineering the D614G mutation into an authentic wild-type SARS-CoV-2 strain, we demonstrate the importance of this mutation to (i) enhanced viral replication on human lung epithelial cells and primary human airway tissues, (ii) improved viral fitness in the upper airway of infected hamsters, and (iii) increased susceptibility to neutralization. Together with clinical findings, our work underscores the importance of this mutation in viral spread, vaccine efficacy, and antibody therapy.

Paired heavy and light chain signatures contribute to potent SARS-CoV-2 neutralization in public antibody responses

“…Conversely, a sustained RBD 'up' also could make the virus more sensitive to neutralization, as the exposed 'up' RBD enhances exposure of vulnerable epitopes (Mansbach et al, 2020;Zhou et al, 2020c). We outlined differences in RBD display caused by the D614G mutation that enhance antibody class recognition of spike across a broad pH range, and we show that D614G had no detrimental impact on IGHV3-53/3-66 antibody class neutralization, which agrees with prior reports (Plante et al, 2020;Weisblum et al, 2020;Weissman et al, 2020). Interestingly, only the most potent antibodies could bind to the D614 variant at endosomal pH which demonstrated that high-affinity antibody recognition can prevent D614 RBD from rotating down at pH 5.5-4.5.…”

Functional importance of the D614G mutation in the SARS-CoV-2 spike protein

“…This effect was also demonstrated in primary human airway cultures. Further, a competition experiment produced similar results to those seen in a PV system; G614 virus predominated in primary human airway cells even when co-inoculated with a 9-fold excess of D614 virus [ 47 ]. Infection of Syrian hamsters with the G614 virus also resulted in significantly increased replication in nasal tissues, as well as relatively more infectious (by PFU to RNA ratio) virus in nasal, tracheal, and lung tissues, although only a handful of conditions and timepoints attained statistical significance [ 47 ].…”

“…However, one must consider that the viruses used in the study are not isogenic and thus other genetic differences may have contributed to the observed infectivity. Addressing this limitation, Plante et al utilized an infectious cDNA clone to produce isogenic SARS-CoV-2 bearing either S(D614) or S(G614) [ 47 ]. The investigators observed increased replication of G614 virus upon infection of Calu-3 human lung epithelial cells [ 47 ].…”

“…Addressing this limitation, Plante et al utilized an infectious cDNA clone to produce isogenic SARS-CoV-2 bearing either S(D614) or S(G614) [ 47 ]. The investigators observed increased replication of G614 virus upon infection of Calu-3 human lung epithelial cells [ 47 ]. This effect was also demonstrated in primary human airway cultures.…”

“…We also observed higher incorporation of S(G614) compared to S(D614) into MLV PVs. On the contrary, several studies observed no effect of the D614G mutation on spike density, using lentiviral PV or live SARS-CoV-2 [ 44 , 47 , 48 ]. Cytotoxicity can explain, at least partially, this apparent discrepancy.…”