The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types

Daniloski, Zharko; Jordan, Tristan X.; Ilmain, Juliana K; Guo, Xinyi; Bhabha, Gira; tenOever, Benjamin R.; Sanjana, Neville E.

doi:10.1101/2020.06.14.151357

Cited by 166 publications

(215 citation statements)

References 23 publications

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“…Although virions produced from Calu-3 cells had more complete S1/S2 cleavage than those produced form Vero E6 cells, no substantial differences in spike cleavage were detectable between the D614 and G614 virions produced from either cell type, suggesting that the enhanced virion infectivity is not likely due to the D614G-mediated spike cleavage difference. Our results from authentic SARS-CoV-2 are in contrast with previous studies reporting that the D614G mutation changes the cleavage and shedding of spike protein when expressed alone or in the context of pseudotyped virions 24,25 . Mechanistically, two recent studies showed that the D614G mutation abolishes a hydrogen-bond interaction with T859 from a neighboring protomer of the spike trimer 6 , which allosterically promotes the RDB domain to an "up" conformation for receptor ACE2 binding and fusion 7 , leading to an enhanced virion infectivity.…”

Section: Discussioncontrasting

confidence: 99%

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

Shi

Plante

Liu

et al. 2020

Preprint

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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.

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Section: Discussioncontrasting

confidence: 99%

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

Shi

Plante

Liu

et al. 2020

Preprint

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“…The subunit S2 has a fusion peptide (788 to 806), a heptad repeat 1 (912-984), a heptad repeat 2 (1163-1213), a transmembrane domain (1213-1237) and a cytoplasmic tail (1238-1273) 47 . As reported in the earlier studies [48][49][50][51] D614G (present in the S1 subunit flanked by the receptor binding site) (Figure 4) mutation is found to be highly significant and present at 75% rate in the second phase. Together in both the phases, 68 countries (except 16 countries, namely, Brunei, Sweden, Panama, Cambodia, Tunisia, Malaysia, Nepal, South Korea, Philippines, Iran, Pakistan, Ghana, Uruguay, Qatar, Bangladesh and Guam) have this mutation (Figure 2(B)).…”

Section: D614g and D936y Are The Prominent Mutations In The Spike Prosupporting

confidence: 83%

Global variation in the SARS-CoV-2 proteome reveals the mutational hotspots in the drug and vaccine candidates

Patro

Sathyaseelan

Uttamrao

et al. 2020

Preprint

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To accelerate the drug and vaccine development against the severe acute respiratory syndrome virus 2 (SARS-CoV-2), a comparative analysis of SARS-CoV-2 proteome has been performed in two phases by considering manually curated 31389 whole genome sequences from 84 countries. Among the 9 mutations that occur at a high significance (T85I-NPS2, L37F-NSP6, P323L-NSP12, D614G-spike, Q57H-ORF3a, G251V-ORF3a, L84S-ORF8, R203K-nucleocapsid and G204R-nucleocapsid), R203K-nucleocapsid and G204R-nucleocapsid are co-occurring mutations and P323L-NSP12 and D614G-spike often appear simultaneously. Other notable variations that appear with a moderate to low significance are, M85-NSP1 deletion, D268-NSP2 deletion, 112 amino acids deletion in ORF8, a phenylalanine insertion amidst F34-F36 (NSP6) and several co-existing substitution/deletion (I559V & P585S in NSP2, P504L & Y541C in NSP13, G82 & H83 deletions in NSP1 and K141, S142 & F143 deletions in NSP2) mutations. P323L-NSP12, D614G-spike, L37F-NSP6, L84S-ORF8 and the sequences deficient of the high significant mutations has led to 4 major SARS-CoV-2 clades. The top 5 countries bearing all the high significant and majority of the moderate significant mutations are: USA, England, Wales, Australia and Scotland. Further, the majority of the significant mutations has evolved in the first phase and has already transmitted around the globe indicating the positive selection pressure. Among the 26 SARS-CoV-2 proteins, nucleocapsid protein, ORF3a, ORF8, RNA dependent RNA polymerase and spike exhibit a higher heterogeneity compared with the rest of the proteins. However, NSP9, NSP10, NSP8, the envelope protein and NSP4 are highly resistant to mutations and can be exploited for drug/vaccine development.

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“…Recently, several groups also reported that S-G614 enhances viral infectivity based on pseudovirus assays [23][24][25][26] , but due to the small sample size, they found no effect on the neutralization sensitivity of the virus 23,24,26 . Given the evolving nature of the SARS-CoV-2 RNA genome, antibody treatment and vaccine design require further considerations to accommodate D614G and other mutations that may affect the immunogenicity of the virus.…”

Section: Discussionmentioning

confidence: 99%

D614G mutation of SARS-CoV-2 spike protein enhances viral infectivity

Gao

et al. 2020

Preprint

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22Coronavirus disease 2019 is caused by severe acute respiratory 23 syndrome coronavirus 2 (SARS-CoV-2). The spike protein that mediates 24 SARS-CoV-2 entry into host cells, is one of the major targets for vaccines and 25 therapeutics. Thus, insights into the sequence variations of S protein are key to 26 understanding the infection and antigenicity of SARS-CoV-2. Here, we observed a 27 dominant mutational variant at the 614 position of S protein (aspartate to glycine, 28 D614G mutation). Using pseudovirus-based assay, we found that S-D614 and 29 S-G614 protein pseudotyped viruses share a common receptor, human 30 angiotensin-converting enzyme 2 (ACE2), which could be blocked by recombinant 31 ACE2 with the fused Fc region of human IgG1. However, S-D614 and S-G614 32 protein demonstrated functional differences. First, S-G614 protein could be cleaved 33 by serine protease elastase-2 more efficiently. Second, S-G614 pseudovirus 34 infected 293T-ACE2 cells significantly more efficiently than the S-D614 pseudovirus, 35 Moreover, 93% (38/41) sera from convalescent COVID-19 patients could neutralize 36 both S-D614 and S-G614 pseudotyped viruses with comparable efficiencies, but 37 about 7% (3/41) convalescent sera showed decreased neutralizing activity against 38 S-G614 pseudovirus. These findings have important implications for SARS-CoV-2 39 transmission and immune interventions.40 42 43 44 SARS-CoV-2 is a novel coronavirus reported in 2019 that caused the recent 45 outbreak of coronavirus disease-2019 (COVID-19) 1 . By June 17, 2020, the World 46 Health Organization (WHO) reported that 8.06 million people worldwide had been 47 infected with SARS-CoV-2, and 440,290 individuals died of COVID-19. This 48 pandemic had a significant adverse impact on international social and economic 49 activities. The RNA genome of SARS-CoV-2 was rapidly sequenced to facilitate 50 diagnostic testing, molecular epidemiologic source tracking, and development of 51 vaccines and therapeutic strategies 2 . Coronaviruses are enveloped, 52 positive-stranded RNA viruses that contain the largest known RNA genomes to 53 date. The mutation rate for RNA viruses is extremely high, which may contribute to 54 its transmission and virulence. The only significant variation in the SARS-CoV-2 55 spike (S) protein is a non-synonymous D614G (Aspartate (D) to Glycine (G)) 56 mutation 3 . Primary data showed that S-G614 is a more pathogenic strain of 57 SARS-CoV-2 with high transmission efficiency 3 , however whether D614G 58 conversion in S protein affect the viral entry and infectivity in cell model is still 59 unclear. 60 61The S protein of coronavirus, the major determinant of host and tissue tropism, is a 62 major target for vaccines, neutralizing antibodies, and viral entry inhibitors 4,5 . 63Similar to SARS-CoV, the cellular receptor of SARS-CoV-2 is 64 angiotensin-converting enzyme 2 (ACE2); however, the SARS-CoV-2 S protein has 65 a 10-to 20-fold higher affinity for ACE2 than the corresponding S protein of 66 SARS-CoV 6,7 . Coronaviruses use two d...

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The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types

Cited by 166 publications

References 23 publications

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

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

Global variation in the SARS-CoV-2 proteome reveals the mutational hotspots in the drug and vaccine candidates

D614G mutation of SARS-CoV-2 spike protein enhances viral infectivity

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