PMID- 34067890
OWN - NLM
STAT- MEDLINE
DCOM- 20210701
LR  - 20231111
IS  - 1999-4915 (Electronic)
IS  - 1999-4915 (Linking)
VI  - 13
IP  - 5
DP  - 2021 May 17
TI  - Structural Analysis of the Novel Variants of SARS-CoV-2 and Forecasting in North 
      America.
LID - 10.3390/v13050930 [doi]
LID - 930
AB  - BACKGROUND: little is known about the forecasting of new variants of SARS-COV-2 
      in North America and the interaction of variants with vaccine-derived 
      neutralizing antibodies. METHODS: the affinity scores of the spike 
      receptor-binding domain (S-RBD) of B.1.1.7, B. 1.351, B.1.617, and P.1 variants 
      in interaction with the neutralizing antibody (CV30 isolated from a patient), and 
      human angiotensin-converting enzyme 2 (hACE2) receptor were predicted using the 
      template-based computational modeling. From the Nextstrain global database, we 
      identified prevalent mutations of S-RBD of SARS-CoV-2 from December 2019 to April 
      2021. Pre- and post-vaccination time series forecasting models were developed 
      based on the prediction of neutralizing antibody affinity scores for S-RBD of the 
      variants. RESULTS: the proportion of the B.1.1.7 variant in North America is 
      growing rapidly, but the rate will reduce due to high affinity (~90%) to the 
      neutralizing antibody once herd immunity is reached. Currently, the rates of 
      isolation of B. 1.351, B.1.617, and P.1 variants are slowly increasing in North 
      America. Herd immunity is able to relatively control these variants due to their 
      low affinity (~70%) to the neutralizing antibody. The S-RBD of B.1.617 has a 110% 
      increased affinity score to the human angiotensin-converting enzyme 2 (hACE2) in 
      comparison to the wild-type structure, making it highly infectious. CONCLUSION: 
      The newly emerged B.1.351, B.1.617, and P.1 variants escape from vaccine-induced 
      neutralizing immunity and continue circulating in North America in post- herd 
      immunity era. Our study strongly suggests that a third dose of vaccine is 
      urgently needed to cover novel variants with affinity scores (equal or less than 
      70%) to eliminate developing viral mutations and reduce transmission rates.
FAU - Quinonez, Elena
AU  - Quinonez E
AD  - Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 
      33146, USA.
FAU - Vahed, Majid
AU  - Vahed M
AD  - Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of 
      Miami Miller School of Medicine, Miami, FL 33146, USA.
FAU - Hashemi Shahraki, Abdolrazagh
AU  - Hashemi Shahraki A
AUID- ORCID: 0000-0003-1852-194X
AD  - Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of 
      Miami Miller School of Medicine, Miami, FL 33146, USA.
FAU - Mirsaeidi, Mehdi
AU  - Mirsaeidi M
AD  - Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of 
      Miami Miller School of Medicine, Miami, FL 33146, USA.
LA  - eng
PT  - Journal Article
DEP - 20210517
PL  - Switzerland
TA  - Viruses
JT  - Viruses
JID - 101509722
RN  - 0 (Antibodies, Neutralizing)
RN  - 0 (Antibodies, Viral)
RN  - 0 (Receptors, Virus)
RN  - 0 (Spike Glycoprotein, Coronavirus)
SB  - IM
MH  - Adult
MH  - Antibodies, Neutralizing/immunology
MH  - Antibodies, Viral/immunology
MH  - Binding Sites/genetics
MH  - COVID-19/*epidemiology/genetics
MH  - Female
MH  - Humans
MH  - Male
MH  - Middle Aged
MH  - Models, Theoretical
MH  - North America/epidemiology
MH  - Protein Binding/genetics
MH  - Protein Domains/genetics
MH  - Receptors, Virus/metabolism
MH  - SARS-CoV-2/*genetics/pathogenicity
MH  - Spike Glycoprotein, Coronavirus/genetics
PMC - PMC8156069
OTO - NOTNLM
OT  - COVID-19
OT  - S-RBD
OT  - SARS-CoV-2
OT  - mutation
OT  - vaccine
COIS- All authors have no conflict of interest to disclose.
EDAT- 2021/06/03 06:00
MHDA- 2021/07/02 06:00
PMCR- 2021/05/17
CRDT- 2021/06/02 01:20
PHST- 2021/04/02 00:00 [received]
PHST- 2021/05/04 00:00 [revised]
PHST- 2021/05/12 00:00 [accepted]
PHST- 2021/06/02 01:20 [entrez]
PHST- 2021/06/03 06:00 [pubmed]
PHST- 2021/07/02 06:00 [medline]
PHST- 2021/05/17 00:00 [pmc-release]
AID - v13050930 [pii]
AID - viruses-13-00930 [pii]
AID - 10.3390/v13050930 [doi]
PST - epublish
SO  - Viruses. 2021 May 17;13(5):930. doi: 10.3390/v13050930.