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Article ; Online: Coronavirus helicases: attractive and unique targets of antiviral drug-development and therapeutic patents.

Spratt, Austin N / Gallazzi, Fabio / Quinn, Thomas P / Lorson, Christian L / Sönnerborg, Anders / Singh, Kamal

2021 Volume 31, Issue 4, Page(s) 339–350

Abstract: ... ...

Abstract	Introduction
MeSH term(s)	Antiviral Agents/pharmacology ; COVID-19/drug therapy ; Drug Development ; Humans ; Methyltransferases/antagonists & inhibitors ; Methyltransferases/chemistry ; Methyltransferases/physiology ; Patents as Topic ; RNA Helicases/antagonists & inhibitors ; RNA Helicases/chemistry ; RNA Helicases/physiology ; SARS-CoV-2/drug effects ; Triazoles/pharmacology ; Viral Nonstructural Proteins/antagonists & inhibitors ; Viral Nonstructural Proteins/chemistry ; Viral Nonstructural Proteins/physiology
Chemical Substances	Antiviral Agents ; SSYA10-001 ; Triazoles ; Viral Nonstructural Proteins ; Methyltransferases (EC 2.1.1.-) ; Nsp13 protein, SARS-CoV (EC 2.1.1.-) ; RNA Helicases (EC 3.6.4.13)
Language	English
Publishing date	2021-04-21
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1186201-4
ISSN	1744-7674 ; 0962-2594 ; 1354-3776
ISSN (online)	1744-7674
ISSN	0962-2594 ; 1354-3776
DOI	10.1080/13543776.2021.1884224
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Article ; Online: Omicron SARS-CoV-2 variant: Unique features and their impact on pre-existing antibodies.

Kannan, Saathvik R / Spratt, Austin N / Sharma, Kalicharan / Chand, Hitendra S / Byrareddy, Siddappa N / Singh, Kamal

Journal of autoimmunity

2021 Volume 126, Page(s) 102779

Abstract: ... N). Phylogenetic analysis showed that the Omicron is closely related to the Gamma (P.1) variant ...

Abstract	Severe Acute Respiratory Coronavirus (SARS-CoV-2) has been emerging in the form of different variants since its first emergence in early December 2019. A new Variant of Concern (VOC) named the Omicron variant (B.1.1.529) was reported recently. This variant has a large number of mutations in the S protein. To date, there exists a limited information on the Omicron variant. Here we present the analyses of mutation distribution, the evolutionary relationship of Omicron with previous variants, and probable structural impact of mutations on antibody binding. Our analyses show the presence of 46 high prevalence mutations specific to Omicron. Twenty-three of these are localized within the spike (S) protein and the rest localized to the other 3 structural proteins of the virus, the envelope (E), membrane (M), and nucleocapsid (N). Phylogenetic analysis showed that the Omicron is closely related to the Gamma (P.1) variant. The structural analyses showed that several mutations are localized to the region of the S protein that is the major target of antibodies, suggesting that the mutations in the Omicron variant may affect the binding affinities of antibodies to the S protein.
MeSH term(s)	Antibodies, Viral/immunology ; Binding Sites ; COVID-19/immunology ; COVID-19/virology ; Humans ; Mutation ; Phylogeny ; Protein Structure, Tertiary ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/genetics
Chemical Substances	Antibodies, Viral ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2021-12-13
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	639452-8
ISSN	1095-9157 ; 0896-8411
ISSN (online)	1095-9157
ISSN	0896-8411
DOI	10.1016/j.jaut.2021.102779
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Article: Continued Complexity of Mutations in Omicron Sublineages.

Spratt, Austin N / Kannan, Saathvik R / Sharma, Kalicharan / Sachdev, Shrikesh / Kandasamy, Shree L / Sönnerborg, Anders / Lorson, Christian L / Singh, Kamal

Biomedicines

2022 Volume 10, Issue 10

Abstract: The latest SARS-CoV-2 variant of concern (VOC), Omicron (B.1.1.529), has diversified into more than 300 sublineages. With an expanding number of newly emerging sublineages, the mutation profile is also becoming complicated. There exist mutually exclusive ...

Abstract	The latest SARS-CoV-2 variant of concern (VOC), Omicron (B.1.1.529), has diversified into more than 300 sublineages. With an expanding number of newly emerging sublineages, the mutation profile is also becoming complicated. There exist mutually exclusive and revertant mutations in different sublineages. Omicron sublineages share some common mutations with previous VOCs (Alpha, Beta, Gamma, and Delta), indicating an evolutionary relationship between these VOCs. A diverse mutation profile at the spike-antibody interface, flexibility of the regions harboring mutations, mutation types, and coexisting mutations suggest that SARS-CoV-2's evolution is far from over.
Language	English
Publishing date	2022-10-16
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720867-9
ISSN	2227-9059
ISSN	2227-9059
DOI	10.3390/biomedicines10102593
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Article ; Online: Complex Mutation Pattern of Omicron BA.2: Evading Antibodies without Losing Receptor Interactions.

Kannan, Saathvik R / Spratt, Austin N / Sharma, Kalicharan / Goyal, Ramesh / Sönnerborg, Anders / Apparsundaram, Subbu / Lorson, Christian L / Byrareddy, Siddappa N / Singh, Kamal

International journal of molecular sciences

2022 Volume 23, Issue 10

Abstract: BA.2, a sublineage of Omicron BA.1, is now prominent in many parts of the world. Early reports have indicated that BA.2 is more infectious than BA.1. To gain insight into BA.2 mutation profile and the resulting impact of mutations on interactions with ... ...

Abstract	BA.2, a sublineage of Omicron BA.1, is now prominent in many parts of the world. Early reports have indicated that BA.2 is more infectious than BA.1. To gain insight into BA.2 mutation profile and the resulting impact of mutations on interactions with receptor and/or monoclonal antibodies, we analyzed available sequences, structures of Spike/receptor and Spike/antibody complexes, and conducted molecular dynamics simulations. The results showed that BA.2 had 50 high-prevalent mutations, compared to 48 in BA.1. Additionally, 17 BA.1 mutations were not present in BA.2. Instead, BA.2 had 19 unique mutations and a signature Delta variant mutation (G142D). The BA.2 had 28 signature mutations in Spike, compared to 30 in BA.1. This was due to two revertant mutations, S446G and S496G, in the receptor-binding domain (RBD), making BA.2 somewhat similar to Wuhan-Hu-1 (WT), which had G446 and G496. The molecular dynamics simulations showed that the RBD consisting of G446/G496 was more stable than S446/S496 containing RBD. Thus, our analyses suggested that BA.2 evolved with novel mutations (i) to maintain receptor binding similar to WT, (ii) evade the antibody binding greater than BA.1, and (iii) acquire mutation of the Delta variant that may be associated with the high infectivity.
MeSH term(s)	Antibodies, Monoclonal ; Molecular Dynamics Simulation ; Mutation
Chemical Substances	Antibodies, Monoclonal
Language	English
Publishing date	2022-05-16
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23105534
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Article ; Online: Infectivity of SARS-CoV-2: there Is Something More than D614G?

Kannan, Saathvik R / Spratt, Austin N / Quinn, Thomas P / Heng, Xiao / Lorson, Christian L / Sönnerborg, Anders / Byrareddy, Siddappa N / Singh, Kamal

Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology

2020 Volume 15, Issue 4, Page(s) 574–577

MeSH term(s)	5' Untranslated Regions ; Base Sequence ; Humans ; Models, Molecular ; Mutation/genetics ; SARS-CoV-2/genetics ; SARS-CoV-2/pathogenicity ; Viral Proteins/chemistry
Chemical Substances	5' Untranslated Regions ; Viral Proteins
Keywords	covid19
Language	English
Publishing date	2020-09-15
Publishing country	United States
Document type	Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	2227405-4
ISSN	1557-1904 ; 1557-1890
ISSN (online)	1557-1904
ISSN	1557-1890
DOI	10.1007/s11481-020-09954-3
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Article: Evolution, correlation, structural impact and dynamics of emerging SARS-CoV-2 variants

Spratt, Austin N. / Kannan, Saathvik R. / Woods, Lucas T. / Weisman, Gary A. / Quinn, Thomas P. / Lorson, Christian L. / Sönnerborg, Anders / Byrareddy, Siddappa N. / Singh, Kamal

Computational and Structural Biotechnology Journal. 2021, v. 19

2021

Abstract: Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infections remain unmanageable in some parts of the world. As with other RNA viruses, mutations in the SARS-CoV-2 gene have been continuously evolving. Recently, four variants have been ... ...

Abstract	Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infections remain unmanageable in some parts of the world. As with other RNA viruses, mutations in the SARS-CoV-2 gene have been continuously evolving. Recently, four variants have been identified, B.1.1.7, B.1.351, P.1 and CAL.20C. These variants appear to be more infectious and transmissible than the original Wuhan-Hu-1 virus. Using a combination of bioinformatics and structural analyses, we show that the new SARS-CoV-2 variants emerged in the background of an already known Spike protein mutation D614G together with another mutation P323L in the RNA polymerase of SARS-CoV-2. The phylogenetic analysis showed that the CAL.20C and B.1.351 shared one common ancestor, whereas the B.1.1.7 and P.1 shared a different ancestor. Structural comparisons did not show any significant difference between the wild-type and mutant ACE2/Spike complexes. Structural analysis indicated that the N501Y mutation may increase hydrophobic interactions at the ACE2/Spike interface. However, reported greater binding affinity of N501Y Spike with ACE2 does not seem to be entirely due to increased hydrophobic interactions, given that Spike mutation R417T in P.1 or K417N in B.1.351 results in the loss of a salt-bridge interaction between ACE2 and S-RBD. The calculated change in free energy did not provide a clear trend of S protein stability of mutations in the variants. As expected, we show that the CAL.20C generally migrated from the west coast to the east coast of the USA. Taken together, the analyses suggest that the evolution of variants and their infectivity is complex and may depend upon many factors.
Keywords	DNA-directed RNA polymerase ; Gibbs free energy ; RNA ; Severe acute respiratory syndrome coronavirus 2 ; ancestry ; bioinformatics ; biotechnology ; coasts ; genes ; hydrophobicity ; mutants ; mutation ; pathogenicity ; phylogeny ; viruses
Language	English
Size	p. 3799-3809.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	2694435-2
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2021.06.037
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Complex Mutation Pattern of Omicron BA.2

Saathvik R. Kannan / Austin N. Spratt / Kalicharan Sharma / Ramesh Goyal / Anders Sönnerborg / Subbu Apparsundaram / Christian L. Lorson / Siddappa N. Byrareddy / Kamal Singh

International Journal of Molecular Sciences, Vol 23, Iss 5534, p

Evading Antibodies without Losing Receptor Interactions

2022 Volume 5534

Abstract	BA.2, a sublineage of Omicron BA.1, is now prominent in many parts of the world. Early reports have indicated that BA.2 is more infectious than BA.1. To gain insight into BA.2 mutation profile and the resulting impact of mutations on interactions with receptor and/or monoclonal antibodies, we analyzed available sequences, structures of Spike/receptor and Spike/antibody complexes, and conducted molecular dynamics simulations. The results showed that BA.2 had 50 high-prevalent mutations, compared to 48 in BA.1. Additionally, 17 BA.1 mutations were not present in BA.2. Instead, BA.2 had 19 unique mutations and a signature Delta variant mutation (G142D). The BA.2 had 28 signature mutations in Spike, compared to 30 in BA.1. This was due to two revertant mutations, S446G and S496G, in the receptor-binding domain (RBD), making BA.2 somewhat similar to Wuhan-Hu-1 (WT), which had G446 and G496. The molecular dynamics simulations showed that the RBD consisting of G446/G496 was more stable than S446/S496 containing RBD. Thus, our analyses suggested that BA.2 evolved with novel mutations (i) to maintain receptor binding similar to WT, (ii) evade the antibody binding greater than BA.1, and (iii) acquire mutation of the Delta variant that may be associated with the high infectivity.
Keywords	COVID-19 ; SARS-CoV-2 ; viruses ; Omicron BA.1 ; BA.2 ; Delta ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	616
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Infectivity of SARS-CoV-2: there Is Something More than D614G?

Kannan, Saathvik R / Spratt, Austin N / Quinn, Thomas P / Heng, Xiao / Lorson, Christian L / Sönnerborg, Anders / Byrareddy, Siddappa N / Singh, Kamal

J. neuroimmune pharmacol

Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #758177
Database	COVID19

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Article: Factors Associated with Emerging and Re-emerging of SARS-CoV-2 Variants.

Spratt, Austin N / Kannan, Saathvik R / Woods, Lucas T / Weisman, Gary A / Quinn, Thomas P / Lorson, Christian L / Sönnerborg, Anders / Byrareddy, Siddappa N / Singh, Kamal

bioRxiv : the preprint server for biology

2021

Abstract: Global spread of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has triggered unprecedented scientific efforts, as well as containment and treatment measures. Despite these efforts, SARS-CoV-2 infections remain unmanageable in some parts of ...

Abstract	Global spread of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has triggered unprecedented scientific efforts, as well as containment and treatment measures. Despite these efforts, SARS-CoV-2 infections remain unmanageable in some parts of the world. Due to inherent mutability of RNA viruses, it is not surprising that the SARS-CoV-2 genome has been continuously evolving since its emergence. Recently, four functionally distinct variants, B.1.1.7, B.1.351, P.1 and CAL.20C, have been identified, and they appear to more infectious and transmissible than the original (Wuhan-Hu-1) virus. Here we provide evidence based upon a combination of bioinformatics and structural approaches that can explain the higher infectivity of the new variants. Our results show that the greater infectivity of SARS-CoV-2 than SARS-CoV can be attributed to a combination of several factors, including alternate receptors. Additionally, we show that new SARS-CoV-2 variants emerged in the background of D614G in Spike protein and P323L in RNA polymerase. The correlation analyses showed that all mutations in specific variants did not evolve simultaneously. Instead, some mutations evolved most likely to compensate for the viral fitness.
Language	English
Publishing date	2021-03-24
Publishing country	United States
Document type	Preprint
DOI	10.1101/2021.03.24.436850
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Article: Evolution, correlation, structural impact and dynamics of emerging SARS-CoV-2 variants.

Spratt, Austin N / Kannan, Saathvik R / Woods, Lucas T / Weisman, Gary A / Quinn, Thomas P / Lorson, Christian L / Sönnerborg, Anders / Byrareddy, Siddappa N / Singh, Kamal

Computational and structural biotechnology journal

2021 Volume 19, Page(s) 3799–3809

Abstract	Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infections remain unmanageable in some parts of the world. As with other RNA viruses, mutations in the SARS-CoV-2 gene have been continuously evolving. Recently, four variants have been identified, B.1.1.7, B.1.351, P.1 and CAL.20C. These variants appear to be more infectious and transmissible than the original Wuhan-Hu-1 virus. Using a combination of bioinformatics and structural analyses, we show that the new SARS-CoV-2 variants emerged in the background of an already known Spike protein mutation D614G together with another mutation P323L in the RNA polymerase of SARS-CoV-2. The phylogenetic analysis showed that the CAL.20C and B.1.351 shared one common ancestor, whereas the B.1.1.7 and P.1 shared a different ancestor. Structural comparisons did not show any significant difference between the wild-type and mutant ACE2/Spike complexes. Structural analysis indicated that the N501Y mutation may increase hydrophobic interactions at the ACE2/Spike interface. However, reported greater binding affinity of N501Y Spike with ACE2 does not seem to be entirely due to increased hydrophobic interactions, given that Spike mutation R417T in P.1 or K417N in B.1.351 results in the loss of a salt-bridge interaction between ACE2 and S-RBD. The calculated change in free energy did not provide a clear trend of S protein stability of mutations in the variants. As expected, we show that the CAL.20C generally migrated from the west coast to the east coast of the USA. Taken together, the analyses suggest that the evolution of variants and their infectivity is complex and may depend upon many factors.
Language	English
Publishing date	2021-06-24
Publishing country	Netherlands
Document type	Journal Article
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2021.06.037
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