key: cord-0973946-cj6x3h6l
authors: Plante, Jessica A.; Mitchell, Brooke M.; Plante, Kenneth S.; Debbink, Kari; Weaver, Scott C.; Menachery, Vineet D.
title: The Variant Gambit: COVID’s Next Move
date: 2021-03-01
journal: Cell Host Microbe
DOI: 10.1016/j.chom.2021.02.020
sha: d6e09f9a014cad78e5860aee3f5c5d9be8422d4c
doc_id: 973946
cord_uid: cj6x3h6l

Over a year after its emergence, COVID-19, the disease caused by SARS-CoV-2, continues to plague the world and dominate our daily lives. Even with the development of effective vaccines, this coronavirus pandemic continues to cause a fervor with the identification of major new variants hailing from the United Kingdom, South Africa, Brazil, and California. Coupled with worries over a distinct mink strain that has caused human infections and potential for further mutations, SARS-CoV-2 variants bring concerns for increased spread and escape from both vaccine and natural infection immunity. Here, we outline factors driving SARS-CoV-2 variant evolution, explore the potential impact of specific mutations, examine the risk of further mutations, and consider the experimental studies needed to understand the threat these variants pose.

However, with a naïve initial population, SARS-CoV-2 encountered minimal adaptive immunity sufficient to generate variants driven primarily by escape from antibodies. Even in areas like et al., 2021), identified variant mutations are similar to those that evolved in independent 70 lineages in regions with lower exposure. These results suggest that many of the current 71 mutations confer a fitness advantage based on infection, replication, and/or transmission 72 efficiency, although potential escape from antibodies may be a byproduct of these mutations.

However, as herd immunity is achieved through natural infection and vaccination, the increased 74 selective pressure for escape variants may become much more prominent, further challenging 75 vaccine development.

Finally, variant mutations may result in no significant advantage or disadvantage for 77 infection or transmission. Such mutations may result from genetic drift including genetic that facilitate virus replication. Further studies with individual mutations are required to confirm their effects on for fitness and to determine their specific impacts.

substitutions in the SARS-CoV-2 spike protein (Table 1) . However, the location within different 119 domains of the spike protein ultimately impacts the degree and mechanism by which each 120 substitution affects viral characteristics. The spike protein of coronaviruses is traditionally 121 divided into the S1 and S2 portions, but here we further divide them into a head and stalk 122 portion (Fig. 1B) . The NTD (orange) and the RBD (red) make up the globular head of the spike 123 trimer, the most diverse region of the spike protein (Fig. 1A) . While most attention is paid to the 124 RBD due to its interaction with the host receptor ACE2, the NTD is heavily glycosylated and 125 may play a role in attachment, as seen with related coronaviruses MERS-CoV and Human CoV 126 OC43 (Tortorici et al., 2019) . In contrast to the globular head, the stalk portion comprising the C-127 terminal domain of S1 (CTS1, pink) and the S2 domain (grey) are more conserved across the 128 SARS-like strains found in group 2B CoVs ( Fig. 1A-B) . The CTS1 contains the S1 cleavage site 129 that is typically processed by a host protease and is required in the first step of virus activation 130 and entry. The S2 portion maintains a second cleavage site and the highly conserved fusion 131 machinery. Together, each of the domains plays a key role in CoV infection and variant 132 substitutions within these domains may have a major impact on infectivity and immunity.

Examining the most conserved domains, it is difficult to predict how substitutions in the 135 CTS1 and S2 will alter infection. The D614G substitution that was first detected during early 136 2020 is found in all of the discussed variants, but initially its potential impact was not easily 137 predicted based on its location. Examination of the structure suggests that D614G increases the 138 ability to shift the RBD into the up position required for ACE2 receptor interaction (Yurkovetskiy et al., 2020) . This structural prediction is consistent with augmented infection and transmission the spike protein (T1027I, D1118H). Two changes (A570D, S982A), while internal to the spike 146 protein, are adjacent to the RBD and are more exposed when the RBD is the up conformation 147 ( Fig. 1C-D) . In terms of functional consequences, V1176F is located in the second heptad 148 repeat of the S2 domain, part of the fusion core necessary for entry (Huang et al., 2020) .

Similarly, P681H is adjacent to the SARS-CoV-2 furin cleavage site; absent in other group 2B 150 viruses, substitutions at this site may impact infection and pathogenesis (Johnson et al., 2021) .

Together, these CTS1 and S2 variant substitutions do not imply a clear mechanism of action, 152 but require further examination to reveal their potential roles in of SARS-CoV-2 spread and 153 escape from immunity.

In contrast to the S2 and CTS1, the NTD of the SARS-CoV-2 spike protein is the least 156 conserved domain, likely due to its prominent location on the globular head of the spike (Fig. more likely targets for antibody recognition (Fig. 1E ) (Watanabe et al., 2020, McCarthy et al., In exploring the variants, several of the NTD substitutions appear in independent NTD surface residue adjacent to a glycosylation site ( Fig. 1E-F 

The other NTD substitutions are lineage-specific within these variants of concern (Fig. 

In addition to N501Y, substitutions at K417N/T and E484K have been identified as key been observed in a virulent mouse-adapted strain of SARS-CoV-2, suggesting an improvement the same position described by a pseudotyping study, and would likely also disrupt interaction 222 with D30 (Starr et al., 2021) . As with 417N/T, E484K has been observed in both the RSA and 223 the Brazilian variants (Fig. 2E) . Located in the RBD binding cleft, this substitution extends the 224 amino acid side chain and changes the charge from negative to positive (Fig. 2D ). This change 225 may correspond with improved binding to ACE2, but has also been associated with immune Fig. 2A-B) . This change is within the RBD, but may not have a robust impact on the 237 binding interface with human ACE2. For N439K and S477N, these residues are found on the 238 far edges of the binding domain making them exposed and relatively pliable for substitutions.

Both positions have been associated with predicted escape mutations and human sequence 240 data have revealed sporadic occurrence of these substitutions in deposited sequences on 241 GSIAD (Liu et al., 2021 , McCallum et al., 2021 . Finally, Q493K has been implicated in a 242 number of escape mutants and in mouse-adaptation studies (Weisblum et al., 2020 , Starr et al., populations (Leist et al., 2020 . Overall, these other RBD substitutions have not yet emerged in 246 the variants of concern, but with increased herd immunity due to vaccine deployment and 247 further natural infections, these changes may be selected by increasing immune pressure.

Analysis, testing, and interpretations.

As the COVID19 pandemic continues, research examining SARS-CoV-2 variants will 

Overall, the neutralization data will need to be evaluated across several platforms to confirm the 287 impact of mutations on immune protection.

Beyond the impact on immunity, basic science studies should also explore changes in 

However, for each variant, the mutations may work individually or in parallel to drive the 317 phenotypic outcome, requiring significant efforts and time to decipher.

As SARS-CoV-2 circulates around the globe, variants will continue to emerge due to new variants will impact the spread of the SARS-CoV-2 and the efficacy of vaccines. In 

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SARS-CoV-2 spike D614G 612 variant confers enhanced replication and transmissibility