1
|
Lo Presti A, Ambrosio L, Di Martino A, Knijn A, De Sabato L, Vaccari G, Di Bartolo I, Morabito S, Palamara AT, Stefanelli P. Selective Pressure and Evolution of SARS-CoV-2 Lineages BF.7 and BQ.1.1 Circulating in Italy from July to December 2022. Microorganisms 2024; 12:908. [PMID: 38792736 PMCID: PMC11124320 DOI: 10.3390/microorganisms12050908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 05/26/2024] Open
Abstract
In this work, we studied the selective pressure and evolutionary analysis on the SARS-CoV-2 BF.7 and BQ.1.1 lineages circulating in Italy from July to December 2022. Two different datasets were constructed: the first comprised 694 SARS-CoV-2 BF.7 lineage sequences and the second comprised 734 BQ.1.1 sequences, available in the Italian COVID-19 Genomic (I-Co-Gen) platform and GISAID (last access date 15 December 2022). Alignments were performed with MAFFT v.7 under the Galaxy platform. The HYPHY software was used to study the selective pressure. Four positively selected sites (two in nsp3 and two in the spike) were identified in the BF.7 dataset, and two (one in ORF8 and one in the spike gene) were identified in the BQ.1.1 dataset. Mutation analysis revealed that R408S and N440K are very common in the spike of the BF.7 genomes, as well as L452R among BQ.1.1. N1329D and Q180H in nsp3 were found, respectively, at low and rare frequencies in BF.7, while I121L and I121T were found to be rare in ORF8 for BQ.1.1. The positively selected sites may have been driven by the selection for increased viral fitness, under circumstances of defined selective pressure, as well by host genetic factors.
Collapse
Affiliation(s)
- Alessandra Lo Presti
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.A.); (A.D.M.); (A.T.P.); (P.S.)
| | - Luigina Ambrosio
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.A.); (A.D.M.); (A.T.P.); (P.S.)
| | - Angela Di Martino
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.A.); (A.D.M.); (A.T.P.); (P.S.)
| | - Arnold Knijn
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.K.); (L.D.S.); (I.D.B.); (S.M.)
| | - Luca De Sabato
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.K.); (L.D.S.); (I.D.B.); (S.M.)
| | - Gabriele Vaccari
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.K.); (L.D.S.); (I.D.B.); (S.M.)
| | - Ilaria Di Bartolo
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.K.); (L.D.S.); (I.D.B.); (S.M.)
| | - Stefano Morabito
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.K.); (L.D.S.); (I.D.B.); (S.M.)
| | - Anna Teresa Palamara
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.A.); (A.D.M.); (A.T.P.); (P.S.)
| | - Paola Stefanelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.A.); (A.D.M.); (A.T.P.); (P.S.)
| | | |
Collapse
|
2
|
Liana DF, Novianry V, Andriani A, Mahyarudin M, Astuti P. Disappearance of Imported Cases of Omicron Lineage BA.2.40 in West Kalimantan, Indonesia. IRANIAN JOURNAL OF MEDICAL SCIENCES 2024; 49:176-185. [PMID: 38584647 PMCID: PMC10997853 DOI: 10.30476/ijms.2023.97513.2935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/23/2023] [Accepted: 03/29/2023] [Indexed: 04/09/2024]
Abstract
Background The World Health Organization has declared Omicron as the fifth variant of concern with more than 50 mutations, particularly in the spike protein. Given increased viral infectivity due to mutations, worldwide genomic surveillance and detection of severe acute respiratory syndrome 2 (SARS-CoV-2) is essential. The present study aimed to track Omicron lineage BA.2.40 in West Kalimantan, Indonesia. Methods In May-August 2022, nasopharyngeal swab samples (n=3,642) were collected from international travelers to West Kalimantan (active surveillance), and patients hospitalized due to SARS-CoV-2 infection (baseline surveillance). The samples were tested for Omicron lineages based on ORF1ab, N, and HV69-70del genes, followed by whole-genome sequencing. The sequences were then identified using two genomic databases, aligned against the reference genome (Wuhan/Hu-1/2019), and then compared with BA.2.40 lineage detected across the world. Phylogenetic analysis between the samples and other SARS-CoV-2 isolates was performed using molecular evolutionary genetics analysis software. Results Based on the genomic databases, 10 isolates were identified as BA.2.40. All samples tested positive for the ORF1ab and N genes, but negative for the HV69-70del gene, which is a marker to detect the Omicron variant. Phylogenetic analysis showed the isolates were closely related to an isolate from Malaysia, an area dominated by BA.2.40. Conclusion Omicron lineage BA.2.40 has no HV69-70 deletion in the spike protein, a marker used to screen for the Omicron variant. BA.2.40 showed a high similarity to an isolate from Malaysia and was detected only during certain periods, indicating the effect of internationally imported cases.
Collapse
Affiliation(s)
- Delima Fajar Liana
- Department of Microbiology, School of Medicine, Universitas Tanjungpura, Pontianak, Indonesia
| | - Virhan Novianry
- Department of Biochemistry and Biomolecular, School of Medicine, Universitas Tanjungpura, Pontianak, Indonesia
| | - Andriani Andriani
- Department of Biochemistry and Biomolecular, School of Medicine, Universitas Tanjungpura, Pontianak, Indonesia
| | - Mahyarudin Mahyarudin
- Department of Microbiology, School of Medicine, Universitas Tanjungpura, Pontianak, Indonesia
| | - Puji Astuti
- Department of Biochemistry and Biomolecular, School of Medicine, Universitas Tanjungpura, Pontianak, Indonesia
| |
Collapse
|
3
|
Moharana M, Pattanayak SK, Khan F. Bioactive compounds from Pandanous fascicularis as potential therapeutic candidate to tackle hepatitis a inhibition: Docking and molecular dynamics simulation study. J Biomol Struct Dyn 2023; 41:10478-10494. [PMID: 36541128 DOI: 10.1080/07391102.2022.2158940] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 12/10/2022] [Indexed: 12/24/2022]
Abstract
Due to extensive pharmacological research, medicinal plants the underpinning of indigenous herbal serve as a possible source of key compounds for the development of new drugs. Hepatitis A, one of the most widespread infectious diseases associated with global public health issues. The transmission of hepatitis A virus (HAV) occurs, through personal contact, as well as contaminated food/water. The HAV 3C cysteine protease is a non-structural protein, plays pivotal role in proliferation and viral replication. Significant phytochemicals of Pandanous fascicularis include phytosterol, kobusin, epipinoresinol, and ceroptene, which have a wide variety of biological functions. Through ADMET investigation, we have screened fifteen phytochemicals for this study. Additionally, using molecular docking, these phytochemicals were docked with the HAV 3C protease which signifies the phytochemicals phytosterol, kobusin, epipinoresinol, and ceroptene have a significant capability to bind with hepatitis A virus protein.The docking study was further accompanied by analyzes RMSD, RMSF, Rg, SASA, H-bond number, and principal component analysis through 100 ns MD simulations. The molecular dynamics study reveals that, all four phytochemicals possess considerable binding efficacy with hepatitis A virus protein. Based on our computational study and MMGBSA calculations, phytosterol, kobusin and epipinoresinol phytochemicals may be a potential drug candidate for inhibition of hepatitis A. The potential therapeutic characteristics of the phytochemicals against hepatitis A inhibition offer additional support for the in vitro and in vivo studies in future.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Maheswata Moharana
- Department of Chemistry, National Institute of Technology, Raipur, India
| | | | - Fahmida Khan
- Department of Chemistry, National Institute of Technology, Raipur, India
| |
Collapse
|
4
|
Peka M, Balatsky V. The impact of mutation sets in receptor-binding domain of SARS-CoV-2 variants on the stability of RBD–ACE2 complex. Future Virol 2023. [PMID: 37064325 PMCID: PMC10089296 DOI: 10.2217/fvl-2022-0152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 02/01/2023] [Indexed: 04/08/2023]
Abstract
Aim: Bioinformatic analysis of mutation sets in receptor-binding domain (RBD) of currently and previously circulating SARS-CoV-2 variants of concern (VOCs) and interest (VOIs) to assess their ability to bind the ACE2 receptor. Methods: In silico sequence and structure-oriented approaches were used to evaluate the impact of single and multiple mutations. Results: Mutations detected in VOCs and VOIs led to the reduction of binding free energy of the RBD–ACE2 complex, forming additional chemical bonds with ACE2, and to an increase of RBD–ACE2 complex stability. Conclusion: Mutation sets characteristic of SARS-CoV-2 variants have complex effects on the ACE2 receptor-binding affinity associated with amino acid interactions at mutation sites, as well as on the acquisition of other viral adaptive advantages.
Collapse
Affiliation(s)
- Mykyta Peka
- V. N. Karazin Kharkiv National University, Kharkiv, 61022, Ukraine
- Institute of Pig Breeding & Agroindustrial Production, National Academy of Agrarian Sciences of Ukraine, Poltava, 36013, Ukraine
| | - Viktor Balatsky
- V. N. Karazin Kharkiv National University, Kharkiv, 61022, Ukraine
- Institute of Pig Breeding & Agroindustrial Production, National Academy of Agrarian Sciences of Ukraine, Poltava, 36013, Ukraine
| |
Collapse
|
5
|
Navas MC, Cerón JD, Aguilar-Jiménez W, Rugeles MT, Díaz FJ. Outbreak report of SARS-CoV-2 infection by airborne transmission: Epidemiologic and molecular evidence. BIOMEDICA : REVISTA DEL INSTITUTO NACIONAL DE SALUD 2023; 43:121-130. [PMID: 37167462 PMCID: PMC10501502 DOI: 10.7705/biomedica.6695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 03/04/2023] [Indexed: 05/13/2023]
Abstract
INTRODUCTION It has been shown that the transmission of SARS-CoV-2 occurs mainly by air, and the risk of infection is greater in closed spaces. OBJECTIVE To describe the epidemiology, virology and molecular characterization of a COVID-19 outbreak at a closed vaccination point during the third wave of SARS-CoV-2 in Colombia. MATERIALS AND METHODS Diagnostic tests, interviews, sampling, cell cultures and viral sequencing were carried out, the latter being molecular characterization and lineage identification. RESULTS Seven workers were positive for SARS-CoV-2; among these, 3 samples were analyzed, plus an additional sample belonging to the mother of the presumed index case; all samples were identified with lineage B.1.625, with a maximum of 2 nucleotides difference between them. CONCLUSIONS Variant B.1.625 was identified as the cause of the COVID-19 outbreak, and a co-worker was also identified as the index case. Unexpectedly, attending a vaccination day became a risk factor for acquiring the infection.
Collapse
Affiliation(s)
- María-Cristina Navas
- Grupo Gastrohepatología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.
| | - Juan D Cerón
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.
| | | | - María T Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.
| | - Francisco J Díaz
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.
| |
Collapse
|
6
|
Zareei S, Pourmand S, Amanlou M. Design of novel disturbing peptides against ACE2 SARS-CoV-2 spike-binding region by computational approaches. Front Pharmacol 2022; 13:996005. [PMID: 36438825 PMCID: PMC9692113 DOI: 10.3389/fphar.2022.996005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 10/24/2022] [Indexed: 10/12/2023] Open
Abstract
The SARS-CoV-2, the virus which is responsible for COVID-19 disease, employs its spike protein to recognize its receptor, angiotensin-converting enzyme 2 (ACE2), and subsequently enters the host cell. In this process, the receptor-binding domain (RBD) of the spike has an interface with the α1-helix of the peptidase domain (PD) of ACE2. This study focuses on the disruption of the protein-protein interaction (PPI) of RBD-ACE2. Among the residues in the template (which was extracted from the ACE2), those with unfavorable energies were selected for substitution by mutagenesis. As a result, a library of 140 peptide candidates was constructed and the binding affinity of each candidate was evaluated by molecular docking and molecular dynamics simulations against the α1-helix of ACE2. Finally, the most potent peptides P23 (GFNNYFPHQSYGFMPTNGVGY), P28 (GFNQYFPHQSYGFPPTNGVGY), and P31 (GFNRYFPHQSYGFCPTNGVGY) were selected and their dynamic behaviors were studied. The results showed peptide inhibitors increased the radius, surface accessible area, and overall mobility of residues of the protein. However, no significant alteration was seen in the key residues in the active site. Meanwhile, they can be proposed as promising agents against COVID-19 by suppressing the viral attachment and curbing the infection at its early stage. The designed peptides showed potency against beta, gamma, delta, and omicron variants of SARS-CoV-2.
Collapse
Affiliation(s)
- Sara Zareei
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Saeed Pourmand
- Department of Chemical Engineering, Faculty of Chemical and Petroleum Engineering, University of Tabriz, Tabriz, Iran
| | - Massoud Amanlou
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Experimental Medicine Research Center, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
7
|
Gangadharan S, Ambrose JM, Rajajagadeesan A, Kullappan M, Patil S, Gandhamaneni SH, Veeraraghavan VP, Nakkella AK, Agarwal A, Jayaraman S, Surapaneni KM. Repurposing of potential antiviral drugs against RNA-dependent RNA polymerase of SARS-CoV-2 by computational approach. J Infect Public Health 2022; 15:1180-1191. [PMID: 36240528 PMCID: PMC9514006 DOI: 10.1016/j.jiph.2022.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/16/2022] [Accepted: 09/20/2022] [Indexed: 01/18/2023] Open
Abstract
The high incidences of COVID-19 cases are believed to be associated with high transmissibility rates, which emphasizes the need for the discovery of evidence-based antiviral therapies for curing the disease. The rationale of repurposing existing classes of antiviral small molecule therapeutics against SARS-CoV-2 infection has been expected to accelerate the tedious and expensive drug development process. While Remdesivir has been recently approved to be the first treatment option for specific groups of COVID-19 patients, combinatory therapy with potential antiviral drugs may be necessary to enhance the efficacy in different populations. Hence, a comprehensive list of investigational antimicrobial drug compounds such as Favipiravir, Fidaxomicin, Galidesivir, GC376, Ribavirin, Rifabutin, and Umifenovir were computationally evaluated in this study. We performed in silico docking and molecular dynamics simulation on the selected small molecules against RNA-dependent RNA polymerase, which is one of the key target proteins of SARS-CoV-2, using AutoDock and GROMACS. Interestingly, our results revealed that the macrocyclic antibiotic, Fidaxomicin, possesses the highest binding affinity with the lowest energy value of -8.97 kcal/mol binding to the same active sites of RdRp. GC376, Rifabutin, Umifenovir and Remdesivir were identified as the next best compounds. Therefore, the above-mentioned compounds could be considered good leads for further preclinical and clinical experimentations as potentially efficient antiviral inhibitors for combination therapies against SARS-CoV-2.
Collapse
Affiliation(s)
- Sivakumar Gangadharan
- Department of Chemistry, Panimalar Engineering College, Varadharajapuram, Poonamallee, Chennai 600123, Tamil Nadu, India.
| | - Jenifer Mallavarpu Ambrose
- Department of Research, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Chennai 600123, Tamil Nadu, India.
| | - Anusha Rajajagadeesan
- Department of Biochemistry, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Chennai 600123, Tamil Nadu, India.
| | - Malathi Kullappan
- Department of Research, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Chennai 600123, Tamil Nadu, India.
| | - Shankargouda Patil
- College of Dental Medicine, Roseman University of Health Sciences, South Jordan, UTAH-84095, USA; Centre of Molecular Medicine and Diagnostics ( COMManD), Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, India.
| | - Sri Harshini Gandhamaneni
- Department of General Medicine, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Chennai 600123, Tamil Nadu, India.
| | - Vishnu Priya Veeraraghavan
- Centre of Molecular Medicine and Diagnostics ( COMManD), Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, India.
| | - Aruna Kumari Nakkella
- Department of Engineering Chemistry, Dr B R Ambedkar University, Etcherla, Srikakulam 532410, Andhra Pradesh, India.
| | - Alok Agarwal
- Department of Chemistry, Chinmaya Degree College, BHEL, Haridwar 249403, Uttarakhand, India.
| | - Selvaraj Jayaraman
- Centre of Molecular Medicine and Diagnostics ( COMManD), Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, India.
| | - Krishna Mohan Surapaneni
- Departments of Biochemistry, Molecular Virology, Research, Clinical Skills & Simulation, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai 600123, Tamil Nadu, India.
| |
Collapse
|
8
|
Saifi S, Ravi V, Sharma S, Swaminathan A, Chauhan NS, Pandey R. SARS-CoV-2 VOCs, Mutational diversity and clinical outcome: Are they modulating drug efficacy by altered binding strength? Genomics 2022; 114:110466. [PMID: 36041637 PMCID: PMC9419439 DOI: 10.1016/j.ygeno.2022.110466] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/12/2022] [Accepted: 08/26/2022] [Indexed: 11/29/2022]
Abstract
The global COVID-19 pandemic continues due to emerging Severe Acute Respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC). Here, we performed comprehensive analysis of in-house sequenced SARS-CoV-2 genome mutations dynamics in the patients infected with the VOCs - Delta and Omicron, within Recovered and Mortality patients. Statistical analysis highlighted significant mutations - T4685A, N4992N, and G5063S in RdRp; T19R in NTD spike; K444N and N532H in RBD spike, associated with Delta mortality. Mutations, T19I in NTD spike, Q493R and N440K in the RBD spike were significantly associated with Omicron mortality. We performed molecular docking for possible effect of significant mutations on the binding of Remdesivir. We found that Remdesivir showed less binding efficacy with the mutant Spike protein of both Delta and Omicron mortality compared to recovered patients. This indicates that mortality associated mutations could have a modulatory effect on drug binding which could be associated with disease outcome.
Collapse
Affiliation(s)
- Sheeba Saifi
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Varsha Ravi
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Sparsh Sharma
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Aparna Swaminathan
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | | | - Rajesh Pandey
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| |
Collapse
|
9
|
Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
Collapse
Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
| |
Collapse
|
10
|
Ao D, Lan T, He X, Liu J, Chen L, Baptista‐Hon DT, Zhang K, Wei X. SARS-CoV-2 Omicron variant: Immune escape and vaccine development. MedComm (Beijing) 2022; 3:e126. [PMID: 35317190 PMCID: PMC8925644 DOI: 10.1002/mco2.126] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/02/2022] [Accepted: 03/02/2022] [Indexed: 02/05/2023] Open
Abstract
New genetic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) constantly emerge through unmitigated spread of the virus in the ongoing Coronavirus disease 2019 pandemic. Omicron (B.1.1.529), the latest variant of concern (VOC), has so far shown exceptional spread and infectivity and has established itself as the dominant variant in recent months. The SARS-CoV-2 spike glycoprotein is a key component for the recognition and binding to host cell angiotensin-converting enzyme 2 receptors. The Omicron variant harbors a cluster of substitutions/deletions/insertions, and more than 30 mutations are located in spike. Some noticeable mutations, including K417N, T478K, N501Y, and P681H, are shared with the previous VOCs Alpha, Beta, Gamma, or Delta variants and have been proven to be associated with higher transmissibility, viral infectivity, and immune evasion potential. Studies have revealed that the Omicron variant is partially resistant to the neutralizing activity of therapeutic antibodies and convalescent sera, which poses significant challenges for the clinical effectiveness of the current vaccines and therapeutic antibodies. We provide a comprehensive analysis and summary of the epidemiology and immune escape mechanisms of the Omicron variant. We also suggest some therapeutic strategies against the Omicron variant. This review, therefore, aims to provide information for further research efforts to prevent and contain the impact of new VOCs during the ongoing pandemic.
Collapse
Affiliation(s)
- Danyi Ao
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of Biotherapy and Cancer CenterNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduSichuanChina
| | - Tianxia Lan
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of Biotherapy and Cancer CenterNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduSichuanChina
| | - Xuemei He
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of Biotherapy and Cancer CenterNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduSichuanChina
| | - Jian Liu
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of Biotherapy and Cancer CenterNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduSichuanChina
| | - Li Chen
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of Biotherapy and Cancer CenterNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduSichuanChina
| | - Daniel T. Baptista‐Hon
- Center for Biomedicine and InnovationsFaculty of MedicineMacau University of Science and TechnologyMacauChina
| | - Kang Zhang
- Center for Biomedicine and InnovationsFaculty of MedicineMacau University of Science and TechnologyMacauChina
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of Biotherapy and Cancer CenterNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduSichuanChina
| |
Collapse
|
11
|
Isolation and Genomic Characterization of SARS-CoV-2 Omicron Variant Obtained from Human Clinical Specimens. Viruses 2022; 14:v14030461. [PMID: 35336868 PMCID: PMC8951364 DOI: 10.3390/v14030461] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/17/2022] [Accepted: 02/22/2022] [Indexed: 02/04/2023] Open
Abstract
Due to the failure of virus isolation of the Omicron variant in Vero CCL-81 from the clinical specimens of COVID-19 cases, an initial in vivo and subsequent in vitro approach was utilized for the isolation of the virus. A total of 74 oropharyngeal/nasopharyngeal specimens were collected from SARS-CoV-2 positive international travellers and a contact case at Delhi and Mumbai, India. All the specimens were sequenced using next-generation sequencing and simultaneously inoculated onto Vero CCL-81 cells for virus isolation. Subsequently, two omicron positive specimens were inoculated into Syrian hamsters for two passages. The initial passage of the positive hamster specimens was inoculated onto Vero CCL-81 cells. The clinical specimens, hamster specimens, and Vero CCL-81 passages were sequenced to assess the mutational changes in different host species. The replication of the Omicron variant in hamsters was confirmed with the presence of a high viral load in nasal turbinate and lung specimens of both passages. The successful isolation of the virus from hamster specimens with Vero CCL-81 was observed with cytopathic effect in infected cells and high viral load in the cell suspension. The genome analysis revealed the presence of L212C mutation, Tyrosine 69 deletion, and C25000T nucleotide change in spike gene of hamster passage sequences and an absence of V17I mutation in E gene in hamster passage sequences, unlike human clinical specimen and Vero CCL-81 passages. No change was observed in the furin cleavage site in any of the specimen sequences, suggesting intact pathogenicity of the virus isolate. Our data demonstrated successful isolation of the Omicron variant with the in vivo method first followed by in vitro method. The virus isolate could be used in the future to explore different aspects of the Omicron variant.
Collapse
|