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Banerjee S, Sengupta A, Ghosh SK, Banerjee R. CDH1 gene as biomarker towards breast cancer prediction. J Biomol Struct Dyn 2024:1-14. [PMID: 38373072 DOI: 10.1080/07391102.2024.2316770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/03/2024] [Indexed: 02/21/2024]
Abstract
Breast cancer is considered to be happened due to genetic aberration. Out of several genes expressed, it is found that cadherin 1, type 1 (CDH1) is responsible in several ways to control the metabolic order in human. Deregulation of the function of protein E-cadherin, expressed from CDH1 plays an important role in lobular breast cancer. In order to understand the root cause of this recent claim, we focus on CDH1 gene: whether the genetic information translated due to any deviation/alteration/modification in its sequence is related to the occurrence of the different types breast cancer. Towards this end, quantitative analysis of different biophysical and bio-chemical properties of CDH1 gene in genomic and proteomic levels from the available genomic (cDNA) sequences of CDH1 gene (obtained from the COSMIC Database for 78 patients, suffering from various types of breast cancer) clearly emphasizes that alternation/modification in the sequence of the CDH1 gene can be detrimental. Furthermore, Random forest, K-nearest neighbour and stochastic gradient descent (SGD) algorithms are applied on the derived dataset to classify the types of breast cancer, and to validate our hypothesis regarding the acute role of CDH1 as potential bio marker for breast cancer. Analysis of the mutated CDH1 gene sequences, and their related parameters using aforesaid machine learning techniques clearly establish that CDH1 gene can take the deterministic role in predicting the chances of occurrences of different types of breast cancer with an accuracy of > 90 % . Such an observation opens a new paradigm in diagnostic approach of breast cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Srijan Banerjee
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Nadia, West Bengal, India
| | - Antara Sengupta
- Department of Computer Science and Engineering, University of Calcutta, Kolkata, West Bengal, India
| | - Shankar Kumar Ghosh
- Department of Computer Science and Engineering, Shiv Nadar Institution of Eminence, Delhi, India
| | - Raja Banerjee
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Nadia, West Bengal, India
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2
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Negi SS, Sharma K, Bhargava A, Singh P. A comprehensive profile of SARS-CoV-2 variants spreading during the COVID-19 pandemic: a genomic characterization study from Chhattisgarh State, India. Arch Microbiol 2024; 206:68. [PMID: 38238530 DOI: 10.1007/s00203-023-03807-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/09/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024]
Abstract
SARS-CoV-2 has expressively changed its sequences during the COVID-19 pandemic situation by encompassing persistent evolutionary mutational changes resulting in the emergence of many clades and lineages. Evolution of these SARS-CoV-2 variants have significantly imparted fitness advantage to the virus, enhanced its transmissibility and severity of the disease. These new variants are a potential threat to the vaccine efficacy as well. It is therefore pertinent to monitor the evolution of these variants and their epidemiological and clinical impact, in a geographic setting. This study has thus looked into the geographic distribution and genetic diversity of SARS-CoV-2 variants and the evolutionary circulation of different clades in Chhattisgarh (CG) state from March 2020 to July 2023. A total of 3018 sequences were retrieved from the GISAID database, in which 558 were submitted by us. The demographic data revealed male preponderance of 56.45% versus 43.54% females, with the overall mean age of 36.5 years. SARS-CoV-2 sequences represented many variants viz., Delta (55%), Omicron (22%) and others (15%) with a small proportion of recombinant (5%), Kappa (2%), and Alpha (1%). The viral clades G was found predominant for a year from initial days of pandemic in March, 2020 to January, 2021 which then subsequently evoluted to subclade GK (Delta B.1.617.2) and remained in circulation in CG till November, 2021. From December 2021, the GRA (Omicron B.1.1.529) variant had replaced GK to become the dominant strain and continues to predominate in present time. GRA clade is however continuously encompassing new recombinant strains, having various non-synonymous mutations especially in spike protein. The non-synonymous mutation P314L in ORF1b, S84L in ORF8 and D614G in spike protein were found as the pan mutation carried over from clade G to GRA. The continuous evolution in SARS-CoV2 warrants periodical geographic genomic surveillance monitoring to timely detect any new variants having the potential of causing future outbreak.
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Affiliation(s)
- Sanjay Singh Negi
- Department of Microbiology, All India Institute of Medical Sciences, Raipur, Chhattisgarh, India
| | - Kuldeep Sharma
- Department of Microbiology, All India Institute of Medical Sciences, Raipur, Chhattisgarh, India
| | - Anudita Bhargava
- Department of Microbiology, All India Institute of Medical Sciences, Raipur, Chhattisgarh, India
| | - Pushpendra Singh
- Department of Microbiology, All India Institute of Medical Sciences, Raipur, Chhattisgarh, India.
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Karamipour S, Mojbafan M, Mazaheri Nezhad Fard R. Comparative Analysis of 198 SARS-CoV-2 Genomes from Iran and West Asia, February 2020 to December 2021. IRANIAN JOURNAL OF PATHOLOGY 2023; 18:289-298. [PMID: 37942191 PMCID: PMC10628382 DOI: 10.30699/ijp.2023.557658.2935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 06/15/2023] [Indexed: 11/10/2023]
Abstract
Background & Objective Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), resulting in a worldwide pandemic. The first case of COVID-19 was reported from Wuhan in the Hubei Province of China in December 2019; however, the disease's origin is still mysterious. Whole-genome sequence analysis is essential for monitoring the spread of infectious diseases as well as studying the pathogenesis and evolution of viruses. In this study, analysis of 198 fully sequenced genomes from Iran and West Asia was carried out to study mutations, phylogeny, amino acid changes, clades, and lineages of these genomes as well as comparison of these sequences with those of reference Wuhan genome of NC_045512.2. Methods In total, 198 completely sequenced genome data from Iran and West Asia were collected from GenBank. Mutation detection was carried out using a trial version of CLC Genomics Workbench v.21.0 (QIAGEN, Germany). Online tools such as GISAID Mutations App and Pangolin were used for further analysis of the results. Results In this study, several unique mutation sites were identified in the Iranian genomes (n = 8); positions 1397 G>A and 29742 G>T were the most frequent changes in more than 85% of the Iranian genomes. Mutation rate, mutation per sequence, and transition versus transversion for the Iranian genomes included 4.73, 14.14, and 1.6, respectively. Generally, C>T alteration was the most common substitution in all the sequences. Conclusion The ORF1ab, N, and S were the genes with the most changes. The current data can help researchers predict future epidemics and establish better strategies to control viral pandemics.
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Affiliation(s)
- Saman Karamipour
- Department of Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Science, Tehran, Iran
| | - Marzieh Mojbafan
- Department of Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Science, Tehran, Iran
- Department of Medical Genetics, Ali-Asghar Children's Hospital, Tehran, Iran
| | - Ramin Mazaheri Nezhad Fard
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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Broni E, Miller WA. Computational Analysis Predicts Correlations among Amino Acids in SARS-CoV-2 Proteomes. Biomedicines 2023; 11:512. [PMID: 36831052 PMCID: PMC9953644 DOI: 10.3390/biomedicines11020512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/03/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a serious global challenge requiring urgent and permanent therapeutic solutions. These solutions can only be engineered if the patterns and rate of mutations of the virus can be elucidated. Predicting mutations and the structure of proteins based on these mutations have become necessary for early drug and vaccine design purposes in anticipation of future viral mutations. The amino acid composition (AAC) of proteomes and individual viral proteins provide avenues for exploitation since AACs have been previously used to predict structure, shape and evolutionary rates. Herein, the frequency of amino acid residues found in 1637 complete proteomes belonging to 11 SARS-CoV-2 variants/lineages were analyzed. Leucine is the most abundant amino acid residue in the SARS-CoV-2 with an average AAC of 9.658% while tryptophan had the least abundance of 1.11%. The AAC and ranking of lysine and glycine varied in the proteome. For some variants, glycine had higher frequency and AAC than lysine and vice versa in other variants. Tryptophan was also observed to be the most intolerant to mutation in the various proteomes for the variants used. A correlogram revealed a very strong correlation of 0.999992 between B.1.525 (Eta) and B.1.526 (Iota) variants. Furthermore, isoleucine and threonine were observed to have a very strong negative correlation of -0.912, while cysteine and isoleucine had a very strong positive correlation of 0.835 at p < 0.001. Shapiro-Wilk normality test revealed that AAC values for all the amino acid residues except methionine showed no evidence of non-normality at p < 0.05. Thus, AACs of SARS-CoV-2 variants can be predicted using probability and z-scores. AACs may be beneficial in classifying viral strains, predicting viral disease types, members of protein families, protein interactions and for diagnostic purposes. They may also be used as a feature along with other crucial factors in machine-learning based algorithms to predict viral mutations. These mutation-predicting algorithms may help in developing effective therapeutics and vaccines for SARS-CoV-2.
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Affiliation(s)
- Emmanuel Broni
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
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Abdelmalick A, Sehli S, Idrissi Azami A, Habib N, Al Idrissi N, Belyamani L, Houmeida A, Ghazal H. Genomic Evidence of Multiple Introductions of SARS-CoV-2 in Mauritania. Bioinform Biol Insights 2023; 17:11779322231167927. [PMID: 37124130 PMCID: PMC10130938 DOI: 10.1177/11779322231167927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/05/2023] [Indexed: 05/02/2023] Open
Abstract
The rapid and global spread of the novel coronavirus severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has raised serious public health concerns, including in Mauritania. We sequenced and analyzed the entire genome of 13 SARS-CoV-2 virus strains isolated from polymerase chain reaction (PCR)-positive symptomatic patients sampled from March 3 to May 31, 2021 to better understand SARS-CoV-2 introduction, propagation, and evolution in Mauritania. A phylogenetic tree using available data from the EpiCoV GISAID database and a variant network with non-Mauritanian sequences were constructed. Variant analysis of the 13 Mauritanian SARS-CoV-2 genome sequences indicated an average mutational percentage of 0.39, which is similar to that in other countries. Phylogenetic analysis revealed multiple spatiotemporal introductions, mainly from Europe (France, Belgium) and Africa (Senegal, Côte d'Ivoire), which also provided evidence of early community transmission. A total of 2 unique mutations, namely, NSP6_Q208K and NSP15_S273T, were detected in the NSP6 and NSP15 genes, respectively, confirming the aforementioned introduction of SARS-CoV-2 in Mauritania. These findings highlight the relevance of continuous genomic monitoring strategies for understanding virus transmission dynamics and acquiring knowledge to address forthcoming sources of infection in Africa.
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Affiliation(s)
| | - Sofia Sehli
- Laboratory of Genomics, Bioinformatics and Digital Health, Faculty of Medicine, Mohammed VI University of Health Sciences, Casablanca, Morocco
- Mohammed VI Center for Research and Innovation, Rabat, Morocco
| | - Abdellah Idrissi Azami
- Laboratory of Genomics, Bioinformatics and Digital Health, Faculty of Medicine, Mohammed VI University of Health Sciences, Casablanca, Morocco
- Mohammed VI Center for Research and Innovation, Rabat, Morocco
| | - Nihal Habib
- Laboratory of Genomics, Bioinformatics and Digital Health, Faculty of Medicine, Mohammed VI University of Health Sciences, Casablanca, Morocco
- Mohammed VI Center for Research and Innovation, Rabat, Morocco
| | - Najib Al Idrissi
- Laboratory of Genomics, Bioinformatics and Digital Health, Faculty of Medicine, Mohammed VI University of Health Sciences, Casablanca, Morocco
- Mohammed VI Center for Research and Innovation, Rabat, Morocco
- Cheikh Khalifa International University Hospital, Casablanca, Morocco
| | - Lahcen Belyamani
- Mohammed VI Center for Research and Innovation, Rabat, Morocco
- Mohammed VI University of Health Sciences, Casablanca, Morocco
| | - Ahmed Houmeida
- Faculty of Science and Technology, University of Nouakchott, Nouakchott, Mauritania
| | - Hassan Ghazal
- Laboratory of Genomics, Bioinformatics and Digital Health, Faculty of Medicine, Mohammed VI University of Health Sciences, Casablanca, Morocco
- Mohammed VI Center for Research and Innovation, Rabat, Morocco
- National Center for Scientific and Technical Research (CNRST), Scientific Departement, Rabat, Morocco
- Hassan Ghazal, National Center for Scientific and Technical Research (CNRST), Angle avenues des FAR et Allal El Fassi, Hay Ryad, B.P. 8027 N.U, Rabat 10102, Morocco.
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Abulsoud AI, El-Husseiny HM, El-Husseiny AA, El-Mahdy HA, Ismail A, Elkhawaga SY, Khidr EG, Fathi D, Mady EA, Najda A, Algahtani M, Theyab A, Alsharif KF, Albrakati A, Bayram R, Abdel-Daim MM, Doghish AS. Mutations in SARS-CoV-2: Insights on structure, variants, vaccines, and biomedical interventions. Biomed Pharmacother 2023; 157:113977. [PMID: 36370519 PMCID: PMC9637516 DOI: 10.1016/j.biopha.2022.113977] [Citation(s) in RCA: 64] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 10/29/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
COVID-19 is a worldwide pandemic caused by SARS-coronavirus-2 (SARS-CoV-2). Less than a year after the emergence of the Covid-19 pandemic, many vaccines have arrived on the market with innovative technologies in the field of vaccinology. Based on the use of messenger RNA (mRNA) encoding the Spike SARS-Cov-2 protein or on the use of recombinant adenovirus vectors enabling the gene encoding the Spike protein to be introduced into our cells, these strategies make it possible to envisage the vaccination in a new light with tools that are more scalable than the vaccine strategies used so far. Faced with the appearance of new variants, which will gradually take precedence over the strain at the origin of the pandemic, these new strategies will allow a much faster update of vaccines to fight against these new variants, some of which may escape neutralization by vaccine antibodies. However, only a vaccination policy based on rapid and massive vaccination of the population but requiring a supply of sufficient doses could make it possible to combat the emergence of these variants. Indeed, the greater the number of infected individuals, the faster the virus multiplies, with an increased risk of the emergence of variants in these RNA viruses. This review will discuss SARS-CoV-2 pathophysiology and evolution approaches in altered transmission platforms and emphasize the different mutations and how they influence the virus characteristics. Also, this article summarizes the common vaccines and the implication of the mutations and genetic variety of SARS-CoV-2 on the COVID-19 biomedical arbitrations.
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Affiliation(s)
- Ahmed I Abulsoud
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt; Department of Biochemistry and Biotechnology, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Hussein M El-Husseiny
- Laboratory of Veterinary Surgery, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai Cho, Fuchu-shi, Tokyo 183-8509, Japan; Department of Surgery, Anesthesiology, and Radiology, Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh, Elqaliobiya 13736, Egypt.
| | - Ahmed A El-Husseiny
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt; Department of Biochemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City 11829, Cairo, Egypt
| | - Hesham A El-Mahdy
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Ahmed Ismail
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Samy Y Elkhawaga
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Emad Gamil Khidr
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Doaa Fathi
- Department of Biochemistry and Biotechnology, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Eman A Mady
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai Cho, Fuchu-shi, Tokyo 183-8509, Japan; Department of Animal Hygiene, Behavior and Management, Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh, Elqaliobiya 13736, Egypt
| | - Agnieszka Najda
- Department of Vegetable Crops and Medicinal Plants University of Life Sciences, Lublin 50A Doświadczalna Street, 20-280, Lublin, Poland.
| | - Mohammad Algahtani
- Department of Laboratory & Blood Bank, Security Forces Hospital, P.O. Box 14799, Mecca 21955, Saudi Arabia
| | - Abdulrahman Theyab
- Department of Laboratory & Blood Bank, Security Forces Hospital, P.O. Box 14799, Mecca 21955, Saudi Arabia; College of Medicine, Al-Faisal University, P.O. Box 50927, Riyadh 11533, Saudi Arabia
| | - Khalaf F Alsharif
- Department of Clinical Laboratory sciences, College of Applied medical sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Ashraf Albrakati
- Department of Human Anatomy, College of Medicine, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Roula Bayram
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia
| | - Mohamed M Abdel-Daim
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia; Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Ahmed S Doghish
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt.
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Moradi J, Moradi P, Alvandi AH, Abiri R, Moghoofei M. Variation analysis of SARS-CoV-2 complete sequences from Iran. Future Virol 2022. [PMID: 36312039 PMCID: PMC9594980 DOI: 10.2217/fvl-2021-0056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 09/30/2022] [Indexed: 11/21/2022]
Abstract
Aim: SARS-CoV-2 is an emerging coronavirus that was discovered in China and rapidly spread throughout the world. The authors looked at nucleotide and amino acid variations in SARS-CoV-2 genomes, as well as phylogenetic and evolutionary events in viral genomes, in Iran. Materials & methods: All SARS-CoV-2 sequences that were publicly released between the start of the pandemic and 15 October 2021 were included. Results: The majority of mutations were found in vaccine target proteins, Spike and Nucleocapsid proteins, and nonstructural proteins. The majority of the viruses that circulated in the early stages of the pandemic belonged to the B.4 lineage. Conclusion: We discovered the prevalence of viral populations in Iran. As a result, tracking the virus’s variation in Iran and comparing it with a variety of nearby neighborhoods may reveal a pattern for future variant introductions.
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Affiliation(s)
- Jale Moradi
- Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Parnia Moradi
- Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Amir H Alvandi
- Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ramin Abiri
- Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mohsen Moghoofei
- Infectious Diseases Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
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8
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Hassan SS, Kodakandla V, Redwan EM, Lundstrom K, Pal Choudhury P, Abd El-Aziz TM, Takayama K, Kandimalla R, Lal A, Serrano-Aroca Á, Azad GK, Aljabali AA, Palù G, Chauhan G, Adadi P, Tambuwala M, Brufsky AM, Baetas-da-Cruz W, Barh D, Azevedo V, Bazan NG, Andrade BS, Santana Silva RJ, Uversky VN. An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2. PeerJ 2022; 10:e13136. [PMID: 35341060 PMCID: PMC8944340 DOI: 10.7717/peerj.13136] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/27/2022] [Indexed: 01/12/2023] Open
Abstract
Open reading frame 8 (ORF8) shows one of the highest levels of variability among accessory proteins in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus Disease 2019 (COVID-19). It was previously reported that the ORF8 protein inhibits the presentation of viral antigens by the major histocompatibility complex class I (MHC-I), which interacts with host factors involved in pulmonary inflammation. The ORF8 protein assists SARS-CoV-2 in evading immunity and plays a role in SARS-CoV-2 replication. Among many contributing mutations, Q27STOP, a mutation in the ORF8 protein, defines the B.1.1.7 lineage of SARS-CoV-2, engendering the second wave of COVID-19. In the present study, 47 unique truncated ORF8 proteins (T-ORF8) with the Q27STOP mutations were identified among 49,055 available B.1.1.7 SARS-CoV-2 sequences. The results show that only one of the 47 T-ORF8 variants spread to over 57 geo-locations in North America, and other continents, which include Africa, Asia, Europe and South America. Based on various quantitative features, such as amino acid homology, polar/non-polar sequence homology, Shannon entropy conservation, and other physicochemical properties of all specific 47 T-ORF8 protein variants, nine possible T-ORF8 unique variants were defined. The question as to whether T-ORF8 variants function similarly to the wild type ORF8 is yet to be investigated. A positive response to the question could exacerbate future COVID-19 waves, necessitating severe containment measures.
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Affiliation(s)
- Sk. Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, India
| | - Vaishnavi Kodakandla
- Department of Life sciences, Sophia College For Women, University of Mumbai, Mumbai, India
| | - Elrashdy M. Redwan
- Faculty of Science, Department of Biological Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | | | - Tarek Mohamed Abd El-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Ramesh Kandimalla
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
| | - Amos Lal
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic Rochester, Rochester, NY, United States
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigacion Traslacional San Alberto Magno, Universidad Catolica de Valencia San Vicente Martir, Valencia, Spain
| | | | - Alaa A.A. Aljabali
- Department of Pharmaceutics and Pharmaceutical, Yarmouk University, Irbid, Jordan
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, Mexico
| | - Parise Adadi
- Department of Food Science, University of Otago, University of Otago, Dunedin, New Zealand
| | - Murtaza Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine, UK
| | - Adam M. Brufsky
- Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and 46 Applied Biotechnology (IIOAB), Nonakuri, India
| | - Vasco Azevedo
- Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Nikolas G. Bazan
- Neuroscience Center of Excellence, School of Medicine, LSU Health New Orleans, New Orleans, LA, United States
| | - Bruno Silva Andrade
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié, Brazil
| | - Raner José Santana Silva
- Departamento de Ciencias Biologicas (DCB), Programa de Pos-Graduacao em Genetica e Biologia Molecular (PPGGBM), Universidade Estadual de Santa Cruz (UESC), Ilheus, Brazil
| | - Vladimir N. Uversky
- Department of Molecular Medicine, University of South Florida, Tampa, FL, United States
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9
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Zainulabid UA, Mat Yassim AS, Hussain M, Aslam A, Soffian SN, Mohd Ibrahim MS, Kamarudin N, Kamarulzaman MN, Hin HS, Ahmad HF. Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. PLoS One 2022; 17:e0263678. [PMID: 35213571 PMCID: PMC8880882 DOI: 10.1371/journal.pone.0263678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 01/25/2022] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 has spread throughout the world since its discovery in China, and Malaysia is no exception. WGS has been a crucial approach in studying the evolution and genetic diversity of SARS-CoV-2 in the ongoing pandemic. Despite considerable number of SARS-CoV-2 genome sequences have been submitted to GISAID and NCBI databases, there is still scarcity of data from Malaysia. This study aims to report new Malaysian lineages of the virus, responsible for the sustained spikes in COVID-19 cases during the third wave of the pandemic. Patients with nasopharyngeal and/or oropharyngeal swabs confirmed COVID-19 positive by real-time RT-PCR with CT value < 25 were chosen for WGS. The selected SARS-CoV-2 isolates were then sequenced, characterized and analyzed along with 986 sequences of the dominant lineages of D614G variants currently circulating throughout Malaysia. The prevalence of clade GH and G formed strong ground for the presence of two Malaysian lineages of AU.2 and B.1.524 that has caused sustained spikes of cases in the country. Statistical analysis on the association of gender and age group with Malaysian lineages revealed a significant association (p <0.05). Phylogenetic analysis revealed dispersion of 41 lineages, of these, 22 lineages are still active. Mutational analysis showed presence of unique G1223C missense mutation in transmembrane domain of the spike protein. For better understanding of the SARS-CoV-2 evolution in Malaysia especially with reference to the reported lineages, large scale studies based on WGS are warranted.
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Affiliation(s)
- Ummu Afeera Zainulabid
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Gambang, Pahang, Malaysia
- Department of Internal Medicine, Kulliyyah of Medicine, International Islamic University of Malaysia, Kuantan, Pahang, Malaysia
| | | | - Mushtaq Hussain
- Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan
| | - Ayesha Aslam
- Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan
| | - Sharmeen Nellisa Soffian
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Gambang, Pahang, Malaysia
| | - Mohamad Shafiq Mohd Ibrahim
- Department of Paediatric and Dental Public Health, Kulliyyah of Dentistry, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Norhidayah Kamarudin
- Department of Pathology and Laboratory Medicine, Kulliyyah of Medicine, International Islamic University of Malaysia, Kuantan, Pahang, Malaysia
| | - Mohd Nazli Kamarulzaman
- Department of Surgery, Kulliyyah of Medicine, International Islamic University of Malaysia, Kuantan, Pahang, Malaysia
| | - How Soon Hin
- Department of Internal Medicine, Kulliyyah of Medicine, International Islamic University of Malaysia, Kuantan, Pahang, Malaysia
| | - Hajar Fauzan Ahmad
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Gambang, Pahang, Malaysia
- Centre for Research in Advanced Tropical Bioscience (Biotropic Centre), Universiti Malaysia Pahang, Gambang, Pahang, Malaysia
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10
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Hassan SS, Kodakandla V, Redwan EM, Lundstrom K, Pal Choudhury P, Abd El-Aziz TM, Takayama K, Kandimalla R, Lal A, Serrano-Aroca Á, Azad GK, Aljabali AAA, Palù G, Chauhan G, Adadi P, Tambuwala M, Brufsky AM, Baetas-da-Cruz W, Barh D, Azevedo V, Bazan NG, Andrade BS, Santana Silva RJ, Uversky VN. An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2. PeerJ 2022. [PMID: 35341060 DOI: 10.1101/2021.05.25.445557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023] Open
Abstract
Open reading frame 8 (ORF8) shows one of the highest levels of variability among accessory proteins in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus Disease 2019 (COVID-19). It was previously reported that the ORF8 protein inhibits the presentation of viral antigens by the major histocompatibility complex class I (MHC-I), which interacts with host factors involved in pulmonary inflammation. The ORF8 protein assists SARS-CoV-2 in evading immunity and plays a role in SARS-CoV-2 replication. Among many contributing mutations, Q27STOP, a mutation in the ORF8 protein, defines the B.1.1.7 lineage of SARS-CoV-2, engendering the second wave of COVID-19. In the present study, 47 unique truncated ORF8 proteins (T-ORF8) with the Q27STOP mutations were identified among 49,055 available B.1.1.7 SARS-CoV-2 sequences. The results show that only one of the 47 T-ORF8 variants spread to over 57 geo-locations in North America, and other continents, which include Africa, Asia, Europe and South America. Based on various quantitative features, such as amino acid homology, polar/non-polar sequence homology, Shannon entropy conservation, and other physicochemical properties of all specific 47 T-ORF8 protein variants, nine possible T-ORF8 unique variants were defined. The question as to whether T-ORF8 variants function similarly to the wild type ORF8 is yet to be investigated. A positive response to the question could exacerbate future COVID-19 waves, necessitating severe containment measures.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, India
| | - Vaishnavi Kodakandla
- Department of Life sciences, Sophia College For Women, University of Mumbai, Mumbai, India
| | - Elrashdy M Redwan
- Faculty of Science, Department of Biological Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | | | - Tarek Mohamed Abd El-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Ramesh Kandimalla
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
| | - Amos Lal
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic Rochester, Rochester, NY, United States
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigacion Traslacional San Alberto Magno, Universidad Catolica de Valencia San Vicente Martir, Valencia, Spain
| | | | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical, Yarmouk University, Irbid, Jordan
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, Mexico
| | - Parise Adadi
- Department of Food Science, University of Otago, University of Otago, Dunedin, New Zealand
| | - Murtaza Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine, UK
| | - Adam M Brufsky
- Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and 46 Applied Biotechnology (IIOAB), Nonakuri, India
| | - Vasco Azevedo
- Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Nikolas G Bazan
- Neuroscience Center of Excellence, School of Medicine, LSU Health New Orleans, New Orleans, LA, United States
| | - Bruno Silva Andrade
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié, Brazil
| | - Raner José Santana Silva
- Departamento de Ciencias Biologicas (DCB), Programa de Pos-Graduacao em Genetica e Biologia Molecular (PPGGBM), Universidade Estadual de Santa Cruz (UESC), Ilheus, Brazil
| | - Vladimir N Uversky
- Department of Molecular Medicine, University of South Florida, Tampa, FL, United States
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11
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Spurbeck RR, Minard-Smith A, Catlin L. Feasibility of neighborhood and building scale wastewater-based genomic epidemiology for pathogen surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 789:147829. [PMID: 34051492 PMCID: PMC8542657 DOI: 10.1016/j.scitotenv.2021.147829] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 05/09/2021] [Accepted: 05/12/2021] [Indexed: 05/02/2023]
Abstract
The benefits of wastewater-based epidemiology (WBE) for tracking the viral load of SARS-CoV-2, the causative agent of COVID-19, have become apparent since the start of the pandemic. However, most sampling occurs at the wastewater treatment plant influent and therefore monitors the entire catchment, encompassing multiple municipalities, and is conducted using quantitative polymerase chain reaction (qPCR), which only quantifies one target. Sequencing methods provide additional strain information and also can identify other pathogens, broadening the applicability of WBE to beyond the COVID-19 pandemic. Here we demonstrate feasibility of sampling at the neighborhood or building complex level using qPCR, targeted sequencing, and untargeted metatranscriptomics (total RNA sequencing) to provide a refined understanding of the local dynamics of SARS-CoV-2 strains and identify other pathogens circulating in the community. We demonstrate feasibility of tracking SARS-CoV-2 at the neighborhood, hospital, and nursing home level with the ability to detect one COVID-19 positive out of 60 nursing home residents. The viral load obtained was correlative with the number of COVID-19 patients being treated in the hospital. Targeted wastewater-based sequencing over time demonstrated that nonsynonymous mutations fluctuate in the viral population. Clades and shifts in mutation profiles within the community were monitored and could be used to determine if vaccine or diagnostics need to be adapted to ensure continued efficacy. Furthermore, untargeted RNA sequencing identified several other pathogens in the samples. Therefore, untargeted RNA sequencing could be used to identify new outbreaks or emerging pathogens beyond the COVID-19 pandemic.
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Affiliation(s)
- Rachel R Spurbeck
- Health Outcomes and Biotechnology Solutions, Battelle Memorial Institute, 505 King Ave, Columbus, OH 43201, United States of America.
| | - Angela Minard-Smith
- Health Outcomes and Biotechnology Solutions, Battelle Memorial Institute, 505 King Ave, Columbus, OH 43201, United States of America
| | - Lindsay Catlin
- National Security Bioscience Center, Battelle Memorial Institute, 505 King Ave, Columbus, OH 43201, United States of America
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12
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Spurbeck RR, Minard-Smith A, Catlin L. Feasibility of neighborhood and building scale wastewater-based genomic epidemiology for pathogen surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 789:147829. [PMID: 34051492 DOI: 10.1101/2021.02.18.21251939] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 05/09/2021] [Accepted: 05/12/2021] [Indexed: 05/27/2023]
Abstract
The benefits of wastewater-based epidemiology (WBE) for tracking the viral load of SARS-CoV-2, the causative agent of COVID-19, have become apparent since the start of the pandemic. However, most sampling occurs at the wastewater treatment plant influent and therefore monitors the entire catchment, encompassing multiple municipalities, and is conducted using quantitative polymerase chain reaction (qPCR), which only quantifies one target. Sequencing methods provide additional strain information and also can identify other pathogens, broadening the applicability of WBE to beyond the COVID-19 pandemic. Here we demonstrate feasibility of sampling at the neighborhood or building complex level using qPCR, targeted sequencing, and untargeted metatranscriptomics (total RNA sequencing) to provide a refined understanding of the local dynamics of SARS-CoV-2 strains and identify other pathogens circulating in the community. We demonstrate feasibility of tracking SARS-CoV-2 at the neighborhood, hospital, and nursing home level with the ability to detect one COVID-19 positive out of 60 nursing home residents. The viral load obtained was correlative with the number of COVID-19 patients being treated in the hospital. Targeted wastewater-based sequencing over time demonstrated that nonsynonymous mutations fluctuate in the viral population. Clades and shifts in mutation profiles within the community were monitored and could be used to determine if vaccine or diagnostics need to be adapted to ensure continued efficacy. Furthermore, untargeted RNA sequencing identified several other pathogens in the samples. Therefore, untargeted RNA sequencing could be used to identify new outbreaks or emerging pathogens beyond the COVID-19 pandemic.
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Affiliation(s)
- Rachel R Spurbeck
- Health Outcomes and Biotechnology Solutions, Battelle Memorial Institute, 505 King Ave, Columbus, OH 43201, United States of America.
| | - Angela Minard-Smith
- Health Outcomes and Biotechnology Solutions, Battelle Memorial Institute, 505 King Ave, Columbus, OH 43201, United States of America
| | - Lindsay Catlin
- National Security Bioscience Center, Battelle Memorial Institute, 505 King Ave, Columbus, OH 43201, United States of America
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13
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Kaffashi A, Huang J, Bairami A, Fallah Mehrabadi MH, Yaslianifard S, Bashashati M, Banihashemi SR, Soleimanifar F, Lotfi M, Taghizadeh M, Soleimani A, Khorasani A, Moshiri F, Mozhgani SH. Complete genome sequencing and molecular characterization of SARS-COV-2 from COVID-19 cases in Alborz province in Iran. Heliyon 2021; 7:e08027. [PMID: 34549097 PMCID: PMC8447724 DOI: 10.1016/j.heliyon.2021.e08027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/05/2021] [Accepted: 09/15/2021] [Indexed: 12/03/2022] Open
Abstract
Iran was among countries which was hard hit at the early stage of the coronavirus disease 2019 (COVID-19) pandemic and dealt with the second wave of the pandemic in May and June 2020; however, there are a very limited number of complete genome sequences of acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from Iran. In this study, complete genome sequences of the virus in the samples obtained from three patients in Alborz province in May and June 2020 were generated and analyzed using bioinformatic methods. The sequenced genomes were positioned in a cluster with B.4 lineage along with the sequences from other countries namely, United Arab Emirates and Oman. There were seven single nucleotide variations (SNVs) in common in all samples and only one of the sequenced genomes showed the D614G amino acid substitution. Three SNVs, 1397 G > A, 28688T > C, 29742 G > T, which had already been reported in February, were found with high frequency in all the sequenced genomes in this study, implying that viral diversity reflected in the early stages of viral transmission in Iran were established in the second wave. Considering the importance of molecular epidemiology in response to ongoing pandemic, there is an urgent need for more complete genome sequencing and comprehensive analyses to gain insight into the transmission, adaptation and evolution of the virus in Iran.
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Affiliation(s)
- Amir Kaffashi
- Agricultural Research Education and Extension Organization (AREEO), Razi Vaccine and Serum Research Institute, Karaj, Iran
| | - Jiabin Huang
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Amir Bairami
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | | | - Somayeh Yaslianifard
- The Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Mohsen Bashashati
- Agricultural Research Education and Extension Organization (AREEO), Razi Vaccine and Serum Research Institute, Karaj, Iran
| | - S Reza Banihashemi
- Agricultural Research Education and Extension Organization (AREEO), Razi Vaccine and Serum Research Institute, Karaj, Iran
| | - Fatemeh Soleimanifar
- Department of Medical Biotechnology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Mohsen Lotfi
- Agricultural Research Education and Extension Organization (AREEO), Razi Vaccine and Serum Research Institute, Karaj, Iran
| | - Morteza Taghizadeh
- Agricultural Research Education and Extension Organization (AREEO), Razi Vaccine and Serum Research Institute, Karaj, Iran
| | - Alireza Soleimani
- Department of Infectious Disease, Imam Ali Hospital, Alborz University of Medical Sciences, Karaj, Iran
| | - Akbar Khorasani
- Agricultural Research Education and Extension Organization (AREEO), Razi Vaccine and Serum Research Institute, Karaj, Iran
| | - Farzaneh Moshiri
- Department of Medical Biotechnology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Sayed-Hamidreza Mozhgani
- The Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
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14
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Characterisation of SARS-CoV-2 clades based on signature SNPs unveils continuous evolution. Methods 2021; 203:282-296. [PMID: 34547443 PMCID: PMC8450220 DOI: 10.1016/j.ymeth.2021.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 09/03/2021] [Accepted: 09/15/2021] [Indexed: 12/23/2022] Open
Abstract
Since the emergence of SARS-CoV-2 in Wuhan, China more than a year ago, it has spread across the world in a very short span of time. Although, different forms of vaccines are being rolled out for vaccination programs around the globe, the mutation of the virus is still a cause of concern among the research communities. Hence, it is important to study the constantly evolving virus and its strains in order to provide a much more stable form of cure. This fact motivated us to conduct this research where we have initially carried out multiple sequence alignment of 15359 and 3033 global dataset without Indian and the dataset of exclusive Indian SARS-CoV-2 genomes respectively, using MAFFT. Subsequently, phylogenetic analyses are performed using Nextstrain to identify virus clades. Consequently, the virus strains are found to be distributed among 5 major clades or clusters viz. 19A, 19B, 20A, 20B and 20C. Thereafter, mutation points as SNPs are identified in each clade. Henceforth, from each clade top 10 signature SNPs are identified based on their frequency i.e. number of occurrences in the virus genome. As a result, 50 such signature SNPs are individually identified for global dataset without Indian and dataset of exclusive Indian SARS-CoV-2 genomes respectively. Out of each 50 signature SNPs, 39 and 41 unique SNPs are identified among which 25 non-synonymous signature SNPs (out of 39) resulted in 30 amino acid changes in protein while 27 changes in amino acid are identified from 22 non-synonymous signature SNPs (out of 41). These 30 and 27 amino acid changes for the non-synonymous signature SNPs are visualised in their respective protein structure as well. Finally, in order to judge the characteristics of the identified clades, the non-synonymous signature SNPs are considered to evaluate the changes in proteins as biological functions with the sequences using PROVEAN and PolyPhen-2 while I-Mutant 2.0 is used to evaluate their structural stability. As a consequence, for global dataset without Indian sequences, G251V in ORF3a in clade 19A, F308Y and G196V in NSP4 and ORF3a in 19B are the unique amino acid changes which are responsible for defining each clade as they are all deleterious and unstable. Such changes which are common for both global dataset without Indian and dataset of exclusive Indian sequences are R203M in Nucleocapsid for 20B, T85I and Q57H in NSP2 and ORF3a respectively for 20C while for exclusive Indian sequences such unique changes are A97V in RdRp, G339S and G339C in NSP2 in 19A and Q57H in ORF3a in 20A.
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15
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Soh SM, Kim Y, Kim C, Jang US, Lee HR. The rapid adaptation of SARS-CoV-2-rise of the variants: transmission and resistance. J Microbiol 2021; 59:807-818. [PMID: 34449057 PMCID: PMC8390340 DOI: 10.1007/s12275-021-1348-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/09/2021] [Accepted: 08/09/2021] [Indexed: 01/18/2023]
Abstract
The causative factor of COVID-19, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is continuously mutating. Interestingly, identified mutations mainly occur in the spike (S) protein which interacts with the ACE2 receptor and is cleaved via serine protease TMPRSS2. Some mutated strains are becoming dominant in various parts of the globe because of increased transmissibility as well as cell entry efficacy. Remarkably, the neutralizing activity of monoclonal antibodies, convalescent sera, and vaccines against the variants has been reported to be significantly reduced. Therefore, the efficacy of various monoclonal antibodies therapy and vaccines against these variants is becoming a great global concern. We herein summarize the current status of SARS-CoV-2 with gears shifted towards the recent and most common genetic variants in relation to transmission, neutralizing activity, and vaccine efficacy.
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Affiliation(s)
- Sandrine M Soh
- Department of Biotechnology and Bioinformatics, College of Science and Technology, Korea University, Sejong, 30019, Republic of Korea
| | - Yeongjun Kim
- Department of Biotechnology and Bioinformatics, College of Science and Technology, Korea University, Sejong, 30019, Republic of Korea
| | - Chanwoo Kim
- Department of Biotechnology and Bioinformatics, College of Science and Technology, Korea University, Sejong, 30019, Republic of Korea
| | - Ui Soon Jang
- Department of Biotechnology and Bioinformatics, College of Science and Technology, Korea University, Sejong, 30019, Republic of Korea
| | - Hye-Ra Lee
- Department of Biotechnology and Bioinformatics, College of Science and Technology, Korea University, Sejong, 30019, Republic of Korea.
- Department of Lab Medicine, College of Medicine, Korea University, Seoul, 02841, Republic of Korea.
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16
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Ghanchi NK, Nasir A, Masood KI, Abidi SH, Mahmood SF, Kanji A, Razzak S, Khan W, Shahid S, Yameen M, Raza A, Ashraf J, Ansar Z, Dharejo MB, Islam N, Hasan Z, Hasan R. Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. PLoS One 2021; 16:e0256451. [PMID: 34464419 PMCID: PMC8407562 DOI: 10.1371/journal.pone.0256451] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 08/09/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND We investigated the genome diversity of SARS-CoV-2 associated with the early COVID-19 period to investigate evolution of the virus in Pakistan. MATERIALS AND METHODS We studied ninety SARS-CoV-2 strains isolated between March and October 2020. Whole genome sequences from our laboratory and available genomes were used to investigate phylogeny, genetic variantion and mutation rates of SARS-CoV-2 strains in Pakistan. Site specific entropy analysis compared mutation rates between strains isolated before and after June 2020. RESULTS In March, strains belonging to L, S, V and GH clades were observed but by October, only L and GH strains were present. The highest diversity of clades was present in Sindh and Islamabad Capital Territory and the least in Punjab province. Initial introductions of SARS-CoV-2 GH (B.1.255, B.1) and S (A) clades were associated with overseas travelers. Additionally, GH (B.1.255, B.1, B.1.160, B.1.36), L (B, B.6, B.4), V (B.4) and S (A) clades were transmitted locally. SARS-CoV-2 genomes clustered with global strains except for ten which matched Pakistani isolates. RNA substitution rates were estimated at 5.86 x10-4. The most frequent mutations were 5' UTR 241C > T, Spike glycoprotein D614G, RNA dependent RNA polymerase (RdRp) P4715L and Orf3a Q57H. Strains up until June 2020 exhibited an overall higher mean and site-specific entropy as compared with sequences after June. Relative entropy was higher across GH as compared with GR and L clades. More sites were under selection pressure in GH strains but this was not significant for any particular site. CONCLUSIONS The higher entropy and diversity observed in early pandemic as compared with later strains suggests increasing stability of the genomes in subsequent COVID-19 waves. This would likely lead to the selection of site-specific changes that are advantageous to the virus, as has been currently observed through the pandemic.
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Affiliation(s)
- Najia Karim Ghanchi
- Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan
| | - Asghar Nasir
- Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan
| | - Kiran Iqbal Masood
- Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan
| | - Syed Hani Abidi
- Department of Biological and Biomedical Sciences, AKU, Karachi, Pakistan
| | | | - Akbar Kanji
- Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan
| | - Safina Razzak
- Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan
| | - Waqasuddin Khan
- Department of Pediatrics and Child Health, AKU, Karachi, Pakistan
| | - Saba Shahid
- Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan
| | - Maliha Yameen
- Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan
| | - Ali Raza
- Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan
| | - Javaria Ashraf
- Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan
| | - Zeeshan Ansar
- Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan
| | | | - Nazneen Islam
- Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan
| | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan
- Faculty of Infectious and Tropical Disease, London School of Hygiene and Tropical Medicine, London, United Kingdom
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17
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Fayad N, Abi Habib W, Kandeil A, El-Shesheny R, Kamel MN, Mourad Y, Mokhbat J, Kayali G, Goldstein J, Abdallah J. SARS-CoV-2 Variants in Lebanon: Evolution and Current Situation. BIOLOGY 2021; 10:531. [PMID: 34198622 PMCID: PMC8232177 DOI: 10.3390/biology10060531] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 05/30/2021] [Accepted: 06/08/2021] [Indexed: 12/18/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has seen a worldwide spread since its emergence in 2019, including to Lebanon, where 534,968 confirmed cases (8% of the population) and 7569 deaths have been reported as of 14 May 2021. With the genome sequencing of strains from various countries, several classification systems were established via genome comparison. For instance, the GISAID clades classification highlights key mutations in the encoded proteins that could potentially affect the virus' infectivity and transmission rates. In this study, 58 genomes of Lebanese SARS-CoV-2 strains were analyzed, 28 of which were sequenced for this study, and 30 retrieved from the GISAID and GenBank databases. We aimed to classify these strains, establish their phylogenetic relationships, and extract the mutations causing amino acid substitutions within, particularly, the structural proteins. The sequenced Lebanese SARS-COV-2 strains were classified into four GISAID clades and 11 Pango lineages. Moreover, 21 uncommon mutations in the structural proteins were found in the newly sequenced strains, underlining interesting combinations of mutations in the spike proteins. Hence, this study constitutes an observation and description of the current SARS-CoV-2 genetic and clade situation in Lebanon according to the available sequenced strains.
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Affiliation(s)
- Nancy Fayad
- School of Pharmacy, Lebanese American University, P.O. Box 36, Byblos, Lebanon; (N.F.); (W.A.H.)
| | - Walid Abi Habib
- School of Pharmacy, Lebanese American University, P.O. Box 36, Byblos, Lebanon; (N.F.); (W.A.H.)
| | - Ahmed Kandeil
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt; (A.K.); (R.E.-S.); (M.N.K.)
| | - Rabeh El-Shesheny
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt; (A.K.); (R.E.-S.); (M.N.K.)
- St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Mina Nabil Kamel
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt; (A.K.); (R.E.-S.); (M.N.K.)
| | - Youmna Mourad
- Al Hadi Laboratory and IVF Center, P.O. Box 44, Beirut, Lebanon;
| | - Jacques Mokhbat
- School of Medicine, Lebanese American University, P.O. Box 36, Byblos, Lebanon;
| | - Ghazi Kayali
- Human Link, Dubai 971, United Arab Emirates;
- Department of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas, Houston, TX 77030, USA
| | - Jimi Goldstein
- Human Link, Dubai 971, United Arab Emirates;
- School of Engineering and Technology, University of Hertfordshire, Hatfield, Hertfordshire AL10 9AB, UK
| | - Jad Abdallah
- School of Pharmacy, Lebanese American University, P.O. Box 36, Byblos, Lebanon; (N.F.); (W.A.H.)
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18
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Luo R, Delaunay‐Moisan A, Timmis K, Danchin A. SARS-CoV-2 biology and variants: anticipation of viral evolution and what needs to be done. Environ Microbiol 2021; 23:2339-2363. [PMID: 33769683 PMCID: PMC8251359 DOI: 10.1111/1462-2920.15487] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 03/24/2021] [Indexed: 12/14/2022]
Abstract
The global propagation of SARS-CoV-2 and the detection of a large number of variants, some of which have replaced the original clade to become dominant, underscores the fact that the virus is actively exploring its evolutionary space. The longer high levels of viral multiplication occur - permitted by high levels of transmission -, the more the virus can adapt to the human host and find ways to success. The third wave of the COVID-19 pandemic is starting in different parts of the world, emphasizing that transmission containment measures that are being imposed are not adequate. Part of the consideration in determining containment measures is the rationale that vaccination will soon stop transmission and allow a return to normality. However, vaccines themselves represent a selection pressure for evolution of vaccine-resistant variants, so the coupling of a policy of permitting high levels of transmission/virus multiplication during vaccine roll-out with the expectation that vaccines will deal with the pandemic, is unrealistic. In the absence of effective antivirals, it is not improbable that SARS-CoV-2 infection prophylaxis will involve an annual vaccination campaign against 'dominant' viral variants, similar to influenza prophylaxis. Living with COVID-19 will be an issue of SARS-CoV-2 variants and evolution. It is therefore crucial to understand how SARS-CoV-2 evolves and what constrains its evolution, in order to anticipate the variants that will emerge. Thus far, the focus has been on the receptor-binding spike protein, but the virus is complex, encoding 26 proteins which interact with a large number of host factors, so the possibilities for evolution are manifold and not predictable a priori. However, if we are to mount the best defence against COVID-19, we must mount it against the variants, and to do this, we must have knowledge about the evolutionary possibilities of the virus. In addition to the generic cellular interactions of the virus, there are extensive polymorphisms in humans (e.g. Lewis, HLA, etc.), some distributed within most or all populations, some restricted to specific ethnic populations and these variations pose additional opportunities for/constraints on viral evolution. We now have the wherewithal - viral genome sequencing, protein structure determination/modelling, protein interaction analysis - to functionally characterize viral variants, but access to comprehensive genome data is extremely uneven. Yet, to develop an understanding of the impacts of such evolution on transmission and disease, we must link it to transmission (viral epidemiology) and disease data (patient clinical data), and the population granularities of these. In this editorial, we explore key facets of viral biology and the influence of relevant aspects of human polymorphisms, human behaviour, geography and climate and, based on this, derive a series of recommendations to monitor viral evolution and predict the types of variants that are likely to arise.
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Affiliation(s)
- Ruibang Luo
- Department of Computer ScienceThe University of Hong KongBonham RoadPokfulamHong Kong
| | - Agnès Delaunay‐Moisan
- Université Paris‐Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC)Gif‐sur‐Yvette91198France
| | - Kenneth Timmis
- Institute of MicrobiologyTechnical University of BraunschweigBraunschweigGermany
| | - Antoine Danchin
- Kodikos Labs, Institut Cochin, 24 rue du Faubourg Saint‐JacquesParis75014France
- School of Biomedical Sciences, Li Kashing Faculty of MedicineUniversity of Hong Kong21 Sassoon RoadHong Kong
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Nidom RV, Indrasari S, Normalina I, Nidom AN, Afifah B, Dewi L, Putra AK, Ansori ANM, Kusala MKJ, Alamudi MY, Nidom CA. Phylogenetic and full-length genome mutation analysis of SARS-CoV-2 in Indonesia prior to COVID-19 vaccination program in 2021. BULLETIN OF THE NATIONAL RESEARCH CENTRE 2021; 45:200. [PMID: 34840498 PMCID: PMC8606223 DOI: 10.1186/s42269-021-00657-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 11/07/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND Indonesia has started the big project of COVID-19 vaccination program since 13 January 2021 by employing the first shot of vaccine to the President of Indonesia as the outbreak and rapid transmission of COVID-19 have endangered not only Indonesian but the global health and economy. This study aimed to investigate the full-length genome mutation analysis of 166 Indonesian SARS-CoV-2 isolates as of 12 January 2021. RESULTS All data of the isolates were extracted from the Global Initiative on Sharing All Influenza Data (GISAID) EpiCoV database. CoVsurver platform was employed to investigate the full-length genome mutation analysis of all isolates. This study also focused on the phylogeny analysis in unlocking the mutation of S protein in Indonesian SARS-CoV-2 isolates. WIV04 isolate that was originated from Wuhan, China was used as the virus reference according to the CoVsurver default. The result showed that a full-length genome mutation analysis of 166 Indonesian SARS-CoV-2 isolates was successfully generated. Every single mutation in S protein was described and then visualized by utilizing BioRender platform. Furthermore, it also found that D614G mutation appeared in 103 Indonesian SARS-CoV-2 isolates. CONCLUSIONS To sum up, this study helped to observe the spread of COVID-19 transmission. However, it also proposed that the epidemiological surveillance and genomics studies might be improved on COVID-19 pandemic in Indonesia. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1186/s42269-021-00657-0.
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Affiliation(s)
- Reviany V. Nidom
- Coronavirus and Vaccine Formulation Research Group, Professor Nidom Foundation, Surabaya, Indonesia
- Riset AIRC Indonesia, Surabaya, Indonesia
| | - Setyarina Indrasari
- Coronavirus and Vaccine Formulation Research Group, Professor Nidom Foundation, Surabaya, Indonesia
- Riset AIRC Indonesia, Surabaya, Indonesia
| | - Irine Normalina
- Coronavirus and Vaccine Formulation Research Group, Professor Nidom Foundation, Surabaya, Indonesia
- Riset AIRC Indonesia, Surabaya, Indonesia
| | - Astria N. Nidom
- Coronavirus and Vaccine Formulation Research Group, Professor Nidom Foundation, Surabaya, Indonesia
| | - Balqis Afifah
- Coronavirus and Vaccine Formulation Research Group, Professor Nidom Foundation, Surabaya, Indonesia
| | - Lestari Dewi
- Faculty of Medicine, Universitas Hang Tuah, Surabaya, Indonesia
| | | | - Arif N. M. Ansori
- Coronavirus and Vaccine Formulation Research Group, Professor Nidom Foundation, Surabaya, Indonesia
- Program Pendidikan Magister Menuju Doktor Untuk Sarjana Unggul (PMDSU) Program - Batch III, Ministry of Education, Culture, Research, and Technology, Jakarta, Indonesia
| | - Muhammad K. J. Kusala
- Coronavirus and Vaccine Formulation Research Group, Professor Nidom Foundation, Surabaya, Indonesia
- Program Pendidikan Magister Menuju Doktor Untuk Sarjana Unggul (PMDSU) Program - Batch III, Ministry of Education, Culture, Research, and Technology, Jakarta, Indonesia
| | - Mohammad Y. Alamudi
- Coronavirus and Vaccine Formulation Research Group, Professor Nidom Foundation, Surabaya, Indonesia
| | - Chairul A. Nidom
- Coronavirus and Vaccine Formulation Research Group, Professor Nidom Foundation, Surabaya, Indonesia
- Riset AIRC Indonesia, Surabaya, Indonesia
- Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, Indonesia
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