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Ayubov MS, Mirzakhmedov MK, Yusupov AN, Asrorov AM, Nosirov BV, Usmanov DE, Shermatov SE, Ubaydullaeva KA, Abdukarimov A, Buriev ZT, Abdurakhmonov IY. Most accurate mutations in SARS-CoV-2 genomes identified in Uzbek patients show novel amino acid changes. Front Med (Lausanne) 2024; 11:1401655. [PMID: 38882660 PMCID: PMC11176497 DOI: 10.3389/fmed.2024.1401655] [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: 03/15/2024] [Accepted: 05/14/2024] [Indexed: 06/18/2024] Open
Abstract
Purpose The rapid changes in the coronavirus genomes created new strains after the first variation was found in Wuhan in 2019. SARS-CoV-2 genotypes should periodically undergo whole genome sequencing to control it because it has been extremely helpful in combating the virus. Many diagnoses, treatments, and vaccinations have been developed against it based on genome sequencing. With its practical implications, this study aimed to determine changes in the delta variant of SARS-CoV-2 widespread in Uzbekistan during the pandemic by genome sequencing, thereby providing crucial insights for developing effective control strategies that can be directly applied in the field. Design We meticulously generated 17 high-quality whole-genome sequence data from 48 SARS-CoV-2 genotypes of COVID-19 patients who tested positive by PCR in Tashkent, Uzbekistan. Our rigorous approach, which includes stringent quality control measures and multiple rounds of verification, ensures the accuracy and reliability of our findings. Methods Our study employed a unique combination of genome sequencing and bioinformatics web tools to analyze amino acid (AA) changes in the virus genomes. This approach allowed us to understand the genetic changes in the delta variant of SARS-CoV-2 widespread in Uzbekistan during the pandemic. Results Our study revealed significant nucleotide polymorphisms, including non-synonymous (missense) and synonymous mutations in the coding regions of the sequenced sample genomes. These findings, categorized by phylogenetic analysis into the G clade (or GK sub-clade), contribute to our understanding of the delta variant of SARS-CoV-2 widespread in Uzbekistan during the pandemic. A total of 134 mutations were identified, consisting of 65 shared and 69 unique mutations. These nucleotide changes, including one frameshift mutation, one conservative and disruptive insertion-deletion, four upstream region mutations, four downstream region mutations, 39 synonymous mutations, and 84 missense mutations, are crucial in the ongoing battle against the virus. Conclusion The comprehensive whole-genome sequencing data presented in this study aids in tracing the origins and sources of circulating SARS-CoV-2 variants and analyzing emerging variations within Uzbekistan and globally. The genome sequencing of SARS-CoV-2 from samples collected in Uzbekistan in late 2021, during the peak of the pandemic's second wave nationwide, is detailed here. Following acquiring these sequences, research efforts have focused on developing DNA and plant-based edible vaccines utilizing prevalent SARS-CoV-2 strains in Uzbekistan, which are currently undergoing clinical trials.
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Affiliation(s)
- Mirzakamol S Ayubov
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Republic of Uzbekistan
| | | | - Abdurakhmon N Yusupov
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Republic of Uzbekistan
| | - Akmal M Asrorov
- Department of Chemistry for Natural Substances, National University of Uzbekistan, Tashkent, Uzbekistan
| | | | - Dilshod E Usmanov
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Republic of Uzbekistan
| | - Shukhrat E Shermatov
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Republic of Uzbekistan
| | - Khurshida A Ubaydullaeva
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Republic of Uzbekistan
| | - Abdusattor Abdukarimov
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Republic of Uzbekistan
| | - Zabardast T Buriev
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Republic of Uzbekistan
| | - Ibrokhim Y Abdurakhmonov
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Republic of Uzbekistan
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Sadeghi F, Halaji M, Shirafkan H, Pournajaf A, Ghorbani H, Babazadeh S, Ezami N, Fallhpour K, Fakhraie F, Gorjinejad S, Amoli SS, Amiri FH, Baghershiroodi M, Ahmadnia Z, Salehi M, Tourani M, Jafarzadeh J, Tabari FS, Ahmadian SR, Mohammadi Abandansari R, Jafarian F, Rouhi S, Zabihollahi A, Mostafanezhad S, Saeedi F, Ebrahimian A, Deldar Z, Zavareh MSH, Bayani M, Broun MB, Shirzad M, Sabbaghi S, Mohammadi M, Rahmani R, Yahyapour Y. Characteristics, outcome, duration of hospitalization, and cycle threshold of patients with COVID-19 referred to four hospitals in Babol City: a multicenter retrospective observational study on the fourth, fifth, and sixth waves. BMC Infect Dis 2024; 24:55. [PMID: 38184533 PMCID: PMC10771668 DOI: 10.1186/s12879-023-08939-w] [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: 07/04/2023] [Accepted: 12/19/2023] [Indexed: 01/08/2024] Open
Abstract
BACKGROUND The aim of the present study was to compare the epidemiological patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) infections, hospitalizations, deaths, and duration of hospitalization during the fourth, fifth and sixth epidemic waves of coronavirus disease 2019 (COVID-19) in Iran. METHODS A multicenter retrospective observational study was conducted on hospitalized patients in four hospitals in the Babol district of northern Iran. The study periods were during the fourth, fifth, and sixth waves of the epidemic in Iran, (March 2021 to March 2022). A total of 13,312 patients with suspected COVID-19 were included. Patient demographics, medical history, length of hospital stay, and clinical outcomes were obtained from the hospital information system. Data on the cycle threshold (Ct) and SARS-CoV2 variant were collected for SARS-CoV2-positive cases. RESULTS The highest number of hospitalized patients was reported during the fifth (Delta) wave (5231; 39.3%), while the lowest number of hospitalized patients was reported during the sixth (Omicron) wave (2143; 16.1%). In total, 6459 (48.5%) out of 13,312 hospitalized patients with suspected COVID-19 had a positive rRT-PCR result. The fifth (Delta) wave had the highest number of SARS-CoV2 rRT-PCR-positive hospitalized patients (3573, 55.3%), while the sixth (Omicron) wave had the lowest number (835, 12.9%). Moreover, 238 (3.7%) patients with laboratory-confirmed COVID-19 died. The hospital mortality rate was 6.8% in the fourth (Alpha) wave, which reduced to 2.7 and 3.5% in the fifth (Delta) and sixth (Omicron) waves, respectively (p < 0.001). CONCLUSIONS This is the most comprehensive study evaluating the epidemiologic characteristics of laboratory-confirmed SARS-CoV2 cases in Iran during the Alpha, Delta, and Omicron waves. The highest number of SARS-CoV2-positive hospitalized patients was in the fifth wave of COVID-19 (dominance of the Delta variant), while the sixth wave (dominance of the Omicron variant) had the lowest number. Comorbidities were similar, and cardiovascular disease, diabetes, kidney disease, and hypertension were the main risk factors in all waves.
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Affiliation(s)
- Farzin Sadeghi
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Mehrdad Halaji
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Hoda Shirafkan
- Social Determinants of Health Research Center, Health Research Institute, Babol University of Medical Science, Babol, Iran
| | - Abazar Pournajaf
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Hossein Ghorbani
- Clinical Research Development Unit of Rouhani Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Sara Babazadeh
- Clinical Research Development Unit of Rouhani Hospital, Babol University of Medical Sciences, Babol, Iran
- Department of Pathology, Ayatollah Rouhani Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Nafiseh Ezami
- Part of Medical Records, Ayatollah Rouhani Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Kobra Fallhpour
- Part of Infectious Control, Shahid Beheshti Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Fatemeh Fakhraie
- Part of Infectious Control, Shahid Yahyanejad Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Shahrbano Gorjinejad
- Part of Infectious Control, Amirkola Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Saghar Saber Amoli
- Department of Medical Microbiology and Biotechnology Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Fatemeh Hejazi Amiri
- Department of Medical Microbiology and Biotechnology Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Mahnaz Baghershiroodi
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Zahra Ahmadnia
- Clinical Research Development Unit of Rouhani Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Maryam Salehi
- Clinical Research Development Unit of Rouhani Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Mehdi Tourani
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Jalal Jafarzadeh
- Clinical Research Development Unit of Rouhani Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Farzane Shanehbandpour Tabari
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Seyed Raheleh Ahmadian
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | | | - Farzaneh Jafarian
- Clinical Research Development Unit of Rouhani Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Samaneh Rouhi
- Clinical Research Development Unit of Rouhani Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Arezoo Zabihollahi
- Clinical Research Development Unit of Rouhani Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Sarina Mostafanezhad
- Clinical Research Development Unit of Rouhani Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Fatemeh Saeedi
- Department of Pathology, Ayatollah Rouhani Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Arefeh Ebrahimian
- Department of Medical Microbiology and Biotechnology Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Zeinab Deldar
- Department of Medical Microbiology and Biotechnology Faculty of Medicine Guilan, University of Medical Sciences, City, Ondo, Nigeria
| | - Mahmoud Sadeghi Haddad Zavareh
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Masoumeh Bayani
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Mana Bazi Broun
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Moein Shirzad
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Siamak Sabbaghi
- Clinical Research Development Unit of Rouhani Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Mohsen Mohammadi
- Non-Communicable Pediatric Diseases Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Rabeae Rahmani
- MSc. in Cellular and Molecular Biology, Education of Amol Teacher, Amol, Iran
| | - Yousef Yahyapour
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
- Biomedical and Microbial Advanced Technologies Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
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Shirafkan H, Sadeghi F, Halaji M, Rahmani R, Yahyapour Y. Demographics, clinical characteristics, and outcomes in hospitalized patients during six waves of COVID‑19 in Northern Iran: a large cohort study. Sci Rep 2023; 13:22527. [PMID: 38110656 PMCID: PMC10728067 DOI: 10.1038/s41598-023-50139-8] [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: 07/09/2023] [Accepted: 12/15/2023] [Indexed: 12/20/2023] Open
Abstract
Since the first report of coronavirus disease 2019 (COVID-19) in Iran, our country has experienced several waves of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Northern Iran was one of the most affected regions of the country by COVID-19. In the current study, the demographic and clinical characteristics and outcomes of hospitalized patients were determined over a 2-year period (during six waves of SARS-CoV-2). This is a large cohort study investigating hospitalized patients with suspected and probable, and confirmed SARS-CoV-2 infection in Babol district, northern Iran, during the two years of COVID-19. The study population included patients admitted to four hospitals affiliated with Babol University of Medical Sciences between March 7, 2020 (start of the first wave) and March 20, 2022 (end of the sixth wave). Epidemiological and demographic characteristics, real-time PCR, cycle thresholds, clinical data and outcomes of COVID-19 were analyzed in 24,287 hospitalized patients. A total of 24,287 hospitalized patients were included in the study: 13,250 (46.6%) patients were suspected of having COVID-19, 11037(45.4%) were confirmed COVID-19 cases. The mean age of confirmed COVID-19 patients was 54.5 ± 18.9 years and 5961 (54%) were female. The median length of hospitalization for COVID-19 survivors and non-survivors was 5 (interquartile range [IQR] 4-8) and 7 (IQR 3-15) days, respectively. Of the patients with confirmed COVID-19, 714 (6.5%) died during hospitalization. In addition, the mortality rate from the first to the sixth wave was 22.9%, 8.1%, 9.9%, 6.8%, 2.7% and 3.5% in confirmed COVID-19 patients. The patients in the fifth wave were significantly younger than the others (mean age and SD of 51.1 ± 17.4 versus 59.2 ± 16.9, 54.7 ± 19.9, 58.4 ± 17.9, 53.5 ± 16.8 and 58.5 ± 25.1 years; p<0.001). The highest in-hospital mortality rate was 22.9% (126/551) in the first wave and the lowest in the fifth wave was 2.7% (96/3573) of cases. In conclusion, in the present study, the in-hospital mortality rate was 6.5% and more than half of the deceased patients were ≥65 years old. Male gender, advanced age and comorbidities significantly increased the mortality rate. The patients in the fifth wave were significantly younger than those in the other waves, and the lowest mortality rate and intensive care unit admission were also observed in the fifth wave.
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Affiliation(s)
- Hoda Shirafkan
- Social Determinants of Health Research Center, Health Research Institute, Babol University of Medical Science, Babol, Iran
| | - Farzin Sadeghi
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Mehrdad Halaji
- Biomedical and Microbial Advanced Technologies Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
- Department of Medical Microbiology and Biotechnology, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Rabeae Rahmani
- Cellular and Molecular Biology, Education of Amol Teacher, Amol, Iran
| | - Yousef Yahyapour
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
- Biomedical and Microbial Advanced Technologies Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
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4
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Ahmadi AS, Shafiei-Jandaghi NZ, Sadeghi K, Nejati A, Zadheidar S, Mokhtari-Azad T, Yavarian J. Comparison of Circulating Variants during the Beginning, Middle and the End of the 4th Wave of COVID-19 in Tehran Province, Iran in 2021. IRANIAN JOURNAL OF PUBLIC HEALTH 2023; 52:2621-2629. [PMID: 38435775 PMCID: PMC10903313 DOI: 10.18502/ijph.v52i12.14323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 08/11/2023] [Indexed: 03/05/2024]
Abstract
Background Whole viral genome sequencing with next generation sequencing (NGS) technique is useful tool for determining the diversity of variants and mutations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this study we have attempted to characterize the mutations and circulating variants of the SARSCoV-2 genome during the 4th wave of COVID-19 pandemic in Tehran, Iran in 2021. Methods We performed complete genome sequencing of 15 SARS-CoV-2 detected from 15 COVID-19 patients during the 4th wave of COVID-19 pandemic with NGS. Three groups of the patients at the beginning, middle and the end of the 4th wave were compared together. Results We detected alpha and delta variants during the 4th wave of the pandemic. The results illustrated a dominance of amino acid substitution D614G in spike, and the most frequent mutants were N-R203K, G204R, S235F, nsp12-P323L, nsp6-G106del, G107del and F108del. Conclusion The detection of the virus mutations is a useful procedure for identifying the virus behavior and its genetic evolution in order to improve the efficacy of the monitoring strategies and therapeutic measures.
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Affiliation(s)
- Akram Sadat Ahmadi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Kaveh Sadeghi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad Nejati
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Sevrin Zadheidar
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Talat Mokhtari-Azad
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Jila Yavarian
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Antibiotic Stewardship and Antimicrobial Resistance, Tehran University of Medical Sciences, Tehran, Iran
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Islam MA, Marzan AA, Arman MS, Shahi S, Sakif TI, Hossain M, Islam T, Hoque MN. Some common deleterious mutations are shared in SARS-CoV-2 genomes from deceased COVID-19 patients across continents. Sci Rep 2023; 13:18644. [PMID: 37903828 PMCID: PMC10616235 DOI: 10.1038/s41598-023-45517-1] [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: 06/19/2023] [Accepted: 10/20/2023] [Indexed: 11/01/2023] Open
Abstract
The identification of deleterious mutations in different variants of SARS-CoV-2 and their roles in the morbidity of COVID-19 patients has yet to be thoroughly investigated. To unravel the spectrum of mutations and their effects within SARS-CoV-2 genomes, we analyzed 5,724 complete genomes from deceased COVID-19 patients sourced from the GISAID database. This analysis was conducted using the Nextstrain platform, applying a generalized time-reversible model for evolutionary phylogeny. These genomes were compared to the reference strain (hCoV-19/Wuhan/WIV04/2019) using MAFFT v7.470. Our findings revealed that SARS-CoV-2 genomes from deceased individuals belonged to 21 Nextstrain clades, with clade 20I (Alpha variant) being the most predominant, followed by clade 20H (Beta variant) and clade 20J (Gamma variant). The majority of SARS-CoV-2 genomes from deceased patients (33.4%) were sequenced in North America, while the lowest percentage (0.98%) came from Africa. The 'G' clade was dominant in the SARS-CoV-2 genomes of Asian, African, and North American regions, while the 'GRY' clade prevailed in Europe. In our analysis, we identified 35,799 nucleotide (NT) mutations throughout the genome, with the highest frequency (11,402 occurrences) found in the spike protein. Notably, we observed 4150 point-specific amino acid (AA) mutations in SARS-CoV-2 genomes, with D614G (20%) and N501Y (14%) identified as the top two deleterious mutations in the spike protein on a global scale. Furthermore, we detected five common deleterious AA mutations, including G18V, W45S, I33T, P30L, and Q418H, which play a key role in defining each clade of SARS-CoV-2. Our novel findings hold potential value for genomic surveillance, enabling the monitoring of the evolving pattern of SARS-CoV-2 infection, its emerging variants, and their impact on the development of effective vaccination and control strategies.
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Affiliation(s)
- Md Aminul Islam
- Advanced Molecular Lab, Department of Microbiology, President Abdul Hamid Medical College, Karimganj, Kishoreganj, 2310, Bangladesh.
- COVID-19 Diagnostic Lab, Department of Microbiology, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh.
| | - Abdullah Al Marzan
- Advanced Molecular Lab, Department of Microbiology, President Abdul Hamid Medical College, Karimganj, Kishoreganj, 2310, Bangladesh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Md Sakil Arman
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Shatila Shahi
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Tahsin Islam Sakif
- Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV, 26506-6109, USA
| | - Maqsud Hossain
- University of Nottingham, Sutton Bonington Campus, LE12 5RD, Loughborough, NG7 2RD, Leicestershire, UK
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh.
| | - M Nazmul Hoque
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh.
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Ahmadi AS, Shafiei‐Jandaghi NZ, Sadeghi K, Salimi V, Nejati A, Azad TM, Yavarian J. SARS-CoV-2 in patient with protein C deficiency: A case report. Clin Case Rep 2023; 11:e8030. [PMID: 37850062 PMCID: PMC10577157 DOI: 10.1002/ccr3.8030] [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: 06/13/2023] [Revised: 09/18/2023] [Accepted: 09/27/2023] [Indexed: 10/19/2023] Open
Abstract
In SARS-CoV-2 pandemic different disorders in coagulation pathways in COVID-19 patients were reported. We described a 44-year-old female with COVID-19 and protein C deficiency history. She did not show any coagulation disorder during her disease course. Complete genome sequencing of SARS-CoV-2 was performed and some mutations identified and compared with Wuhan strain. Besides hospitalized patients, in COVID-19 outpatients with low concentration of protein C, early prescription of an anticoagulant such as heparin could be helpful in prevention of venous thromboembolism or pulmonary embolism.
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Affiliation(s)
- Akram Sadat Ahmadi
- Department of Virology, School of Public HealthTehran University of Medical SciencesTehranIran
| | | | - Kaveh Sadeghi
- Department of Virology, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Vahid Salimi
- Department of Virology, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Ahmad Nejati
- Department of Virology, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Talat Mokhtari Azad
- Department of Virology, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Jila Yavarian
- Department of Virology, School of Public HealthTehran University of Medical SciencesTehranIran
- Research Center for Antibiotic Stewardship and Antimicrobial ResistanceTehran University of Medical SciencesTehranIran
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Klein A, Bastard M, Hemat H, Singh S, Muniz B, Manangama G, Alayyan A, Tamanna AH, Barakzaie B, Popal N, Kakar MAZ, Poulet E, Finger F. Factors associated with adverse outcomes among patients hospitalized at a COVID-19 treatment center in Herat, Afghanistan. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0001687. [PMID: 37619213 PMCID: PMC10449473 DOI: 10.1371/journal.pgph.0001687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 06/30/2023] [Indexed: 08/26/2023]
Abstract
Though many studies on COVID have been published to date, data on COVID-19 epidemiology, symptoms, risk factors and severity in low- and middle-income countries (LMICS), such as Afghanistan are sparse. To describe clinical characteristics, severity, and outcomes of patients hospitalized in the MSF COVID-19 treatment center (CTC) in Herat, Afghanistan and to assess risk factors associated with severe outcomes. 1113 patients were included in this observational study between June 2020 and April 2022. Descriptive analysis was performed on clinical characteristics, complications, and outcomes of patients. Univariate description by Cox regression to identify risk factors for an adverse outcome was performed. Adverse outcome was defined as death or transfer to a level 3 intensive care located at another health facility. Finally, factors identified were included in a multivariate Cox survival analysis. A total of 165 patients (14.8%) suffered from a severe disease course, with a median time of 6 days (interquartile range: 2-11 days) from admission to adverse outcome. In our multivariate model, we identified male gender, age over 50, high O2 flow administered during admission, lymphopenia, anemia and O2 saturation < = 93% during the first three days of admission as predictors for a severe disease course (p<0.05). Our analysis concluded in a relatively low rate of adverse outcomes of 14.8%. This is possibly related to the fact that the resources at an MSF-led facility are higher, in terms of human resources as well as supply of drugs and biomedical equipment, including oxygen therapy devices, compared to local hospitals. Predictors for severe disease outcomes were found to be comparable to other settings.
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heydarifard Z, Shafiei‐Jandaghi N, Safaei M, Tavakoli F, Shatizadeh Malekshahi S. Comparison of clinical outcomes, demographic, and laboratory characteristics of hospitalized COVID-19 patients during major three waves driven by Alpha, Delta, and Omicron variants in Tehran, Iran. Influenza Other Respir Viruses 2023; 17:e13184. [PMID: 37565071 PMCID: PMC10410233 DOI: 10.1111/irv.13184] [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: 03/22/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/12/2023] Open
Abstract
Introduction This study is the first study in which demographic, laboratory data, and outcomes of coronavirus disease-2019 (COVID-19) patients due to the circulating SARS-CoV-2 infections caused by different variants (Alpha, Delta, and Omicron) are compared in Iran. Methods We conducted a retrospective study of confirmed hospitalized COVID-19 cases from April 9, 2021, to May 22, 2022. Demographic data and laboratory findings were extracted from patients' electronic medical records on the first day of admission to the hospital. All patients were followed up for outcomes related to COVID-19 including intensive care unit (ICU) admission and mortality rate. Results Of 760 confirmed hospitalized COVID-19 cases, 362, 298, and 100 represented patients during waves 4-6, respectively. During the Omicron wave, hospitalized patients were older than the other two waves and had a lower median level of C-reactive protein (CRP), alanine transaminase (ALT), aspartate transaminase (AST), and erythrocyte sedimentation rate (ESR). The median length of hospital stay during waves 4-6 was 5 days (interquartile range [IQR]: 4.0-8.0), 7 days (IQR: 6.0-11), and 6 days (IQR: 5.0-9.0), respectively (p < 0.001). The rate of ICU admission during waves 4-6 significantly increased. Conclusions Although the Omicron variant caused less severe disease, in older patients who were hospitalized due to Omicron infection, longer hospital and ICU stays were reported, which could be attributed to their old age. In particular, elderly patients are more vulnerable to severe COVID-19; otherwise, as expected, other laboratory parameters and clinical outcomes were in accordance with differences in pathogenicity and infectivity of these variants.
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Affiliation(s)
- Zahra heydarifard
- Hepatitis Research Center, Department of Virology, Faculty of MedicineLorestan University of Medical SciencesKhorramabadIran
| | | | - Moslem Safaei
- Department of Pharmacy, School of PharmacyShahid Sadoughi University of Medical ScienceYazdIran
| | - Forough Tavakoli
- Department of Bacteriology and Virology, School of MedicineIsfahan University of Medical SciencesIsfahanIran
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De La Cruz-Montoya AH, Díaz Velásquez CE, Martínez-Gregorio H, Ruiz-De La Cruz M, Bustos-Arriaga J, Castro-Jiménez TK, Olguín-Hernández JE, Rodríguez-Sosa M, Terrazas-Valdes LI, Jiménez-Alvarez LA, Regino-Zamarripa NE, Ramírez-Martínez G, Cruz-Lagunas A, Peralta-Arrieta I, Armas-López L, Contreras-Garza BM, Palma-Cortés G, Cabello-Gutierrez C, Báez-Saldaña R, Zúñiga J, Ávila-Moreno F, Vaca-Paniagua F. Molecular transition of SARS-CoV-2 from critical patients during the first year of the COVID-19 pandemic in Mexico City. Front Cell Infect Microbiol 2023; 13:1155938. [PMID: 37260697 PMCID: PMC10227454 DOI: 10.3389/fcimb.2023.1155938] [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: 02/01/2023] [Accepted: 05/02/2023] [Indexed: 06/02/2023] Open
Abstract
Background The SARS-CoV-2 virus has caused unprecedented mortality since its emergence in late 2019. The continuous evolution of the viral genome through the concerted action of mutational forces has produced distinct variants that became dominant, challenging human immunity and vaccine development. Aim and methods In this work, through an integrative genomic approach, we describe the molecular transition of SARS-CoV-2 by analyzing the viral whole genome sequences from 50 critical COVID-19 patients recruited during the first year of the pandemic in Mexico City. Results Our results revealed differential levels of the evolutionary forces across the genome and specific mutational processes that have shaped the first two epidemiological waves of the pandemic in Mexico. Through phylogenetic analyses, we observed a genomic transition in the circulating SARS-CoV-2 genomes from several lineages prevalent in the first wave to a dominance of the B.1.1.519 variant (defined by T478K, P681H, and T732A mutations in the spike protein) in the second wave. Conclusion This work contributes to a better understanding of the evolutionary dynamics and selective pressures that act at the genomic level, the prediction of more accurate variants of clinical significance, and a better comprehension of the molecular mechanisms driving the evolution of SARS-CoV-2 to improve vaccine and drug development.
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Affiliation(s)
- Aldo Hugo De La Cruz-Montoya
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Mexico
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Clara Estela Díaz Velásquez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Mexico
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Héctor Martínez-Gregorio
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Mexico
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Miguel Ruiz-De La Cruz
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Mexico
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Avenida Instituto Politécnico Nacional, Colonia San Pedro Zacatenco, Delegación Gustavo A. Madero, Ciudad de México, Mexico
| | - José Bustos-Arriaga
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Tannya Karen Castro-Jiménez
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Jonadab Efraín Olguín-Hernández
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Mexico
| | - Miriam Rodríguez-Sosa
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Luis Ignacio Terrazas-Valdes
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Mexico
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Luis Armando Jiménez-Alvarez
- Laboratorio de Inmunobiología y Genética y Departamento de Virología, Instituto Nacional de Enfermedades Respiratorias (INER) Ismael Cosio Villegas, Ciudad de México, Mexico
| | - Nora Elemi Regino-Zamarripa
- Laboratorio de Inmunobiología y Genética y Departamento de Virología, Instituto Nacional de Enfermedades Respiratorias (INER) Ismael Cosio Villegas, Ciudad de México, Mexico
- Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Ciudad de México, Mexico
| | - Gustavo Ramírez-Martínez
- Laboratorio de Inmunobiología y Genética y Departamento de Virología, Instituto Nacional de Enfermedades Respiratorias (INER) Ismael Cosio Villegas, Ciudad de México, Mexico
| | - Alfredo Cruz-Lagunas
- Laboratorio de Inmunobiología y Genética y Departamento de Virología, Instituto Nacional de Enfermedades Respiratorias (INER) Ismael Cosio Villegas, Ciudad de México, Mexico
| | - Irlanda Peralta-Arrieta
- Instituto Nacional de Enfermedades Respiratorias (INER) Ismael Cosio Villegas, Ciudad de México, Mexico
| | - Leonel Armas-López
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | | | - Gabriel Palma-Cortés
- Department of Research in Virology and Mycology, Instituto Nacional de Enfermedades Respiratorias (INER) Ismael Cosio Villegas, Ciudad de México, Mexico
| | - Carlos Cabello-Gutierrez
- Department of Research in Virology and Mycology, Instituto Nacional de Enfermedades Respiratorias (INER) Ismael Cosio Villegas, Ciudad de México, Mexico
| | - Renata Báez-Saldaña
- Instituto Nacional de Enfermedades Respiratorias (INER) Ismael Cosio Villegas, Ciudad de México, Mexico
| | - Joaquín Zúñiga
- Laboratorio de Inmunobiología y Genética y Departamento de Virología, Instituto Nacional de Enfermedades Respiratorias (INER) Ismael Cosio Villegas, Ciudad de México, Mexico
- Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Ciudad de México, Mexico
- Instituto Nacional de Enfermedades Respiratorias (INER) Ismael Cosio Villegas, Ciudad de México, Mexico
| | - Federico Ávila-Moreno
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
- Instituto Nacional de Enfermedades Respiratorias (INER) Ismael Cosio Villegas, Ciudad de México, Mexico
- Laboratorio 12 de Enfermedades Pulmonares y Epigenómica del Cáncer, Unidad de Investigación en Biomedicina (UBIMED), Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Felipe Vaca-Paniagua
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Mexico
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, Ciudad de México, Mexico
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10
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Alsuwairi FA, Alsaleh AN, Alsanea MS, Al-Qahtani AA, Obeid D, Almaghrabi RS, Alahideb BM, AlAbdulkareem MA, Mutabagani MS, Althawadi SI, Altamimi SA, Alshukairi AN, Alhamlan FS. Association of SARS-CoV-2 Nucleocapsid Protein Mutations with Patient Demographic and Clinical Characteristics during the Delta and Omicron Waves. Microorganisms 2023; 11:1288. [PMID: 37317262 PMCID: PMC10224071 DOI: 10.3390/microorganisms11051288] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/22/2023] [Accepted: 04/28/2023] [Indexed: 06/16/2023] Open
Abstract
SARS-CoV-2 genomic mutations outside the spike protein that may increase transmissibility and disease severity have not been well characterized. This study identified mutations in the nucleocapsid protein and their possible association with patient characteristics. We analyzed 695 samples from patients with confirmed COVID-19 in Saudi Arabia between 1 April 2021, and 30 April 2022. Nucleocapsid protein mutations were identified through whole genome sequencing. 𝜒2 tests and t tests assessed associations between mutations and patient characteristics. Logistic regression estimated the risk of intensive care unit (ICU) admission or death. Of the 60 mutations identified, R203K was the most common, followed by G204R, P13L, E31del, R32del, and S33del. These mutations were associated with reduced risk of ICU admission. P13L, E31del, R32del, and S33del were also associated with reduced risk of death. By contrast, D63G, R203M, and D377Y were associated with increased risk of ICU admission. Most mutations were detected in the SR-rich region, which was associated with low risk of death. The C-tail and central linker regions were associated with increased risk of ICU admission, whereas the N-arm region was associated with reduced ICU admission risk. Consequently, mutations in the N protein must be observed, as they may exacerbate viral infection and disease severity. Additional research is needed to validate the mutations' associations with clinical outcomes.
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Affiliation(s)
- Feda A. Alsuwairi
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Asma N. Alsaleh
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Madain S. Alsanea
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Ahmed A. Al-Qahtani
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Dalia Obeid
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
- Public Health Laboratories, Public Health Authority, Riyadh 13351, Saudi Arabia
| | - Reem S. Almaghrabi
- Organ Transplant Center of Excellence, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Basma M. Alahideb
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Maha A. AlAbdulkareem
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Maysoon S. Mutabagani
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Sahar I. Althawadi
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Sara A. Altamimi
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Abeer N. Alshukairi
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah 23433, Saudi Arabia
| | - Fatimah S. Alhamlan
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
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11
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Sadeghi K, Zadheidar S, Zebardast A, Nejati A, Faraji M, Ghavami N, Kalantari S, Salimi V, Yavarian J, Abedi A, Jandaghi NZS, Mokhtari‐Azad T. Genomic surveillance of SARS-CoV-2 strains circulating in Iran during six waves of the pandemic. Influenza Other Respir Viruses 2023; 17:e13135. [PMID: 37078070 PMCID: PMC10106497 DOI: 10.1111/irv.13135] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/25/2023] [Accepted: 04/03/2023] [Indexed: 04/21/2023] Open
Abstract
Background SARS-CoV-2 genomic surveillance is necessary for the detection, monitoring, and evaluation of virus variants, which can have increased transmissibility, disease severity, or other adverse effects. We sequenced 330 SARS-CoV-2 genomes during the sixth wave of the COVID pandemic in Iran and compared them with five previous waves, for identifying SARS-CoV-2 variants, the genomic behavior of the virus, and understanding its characteristics. Methods After viral RNA extraction from clinical samples collected during the COVID-19 pandemic, next generation sequencing was performed using the Nextseq and Nanopore platforms. The sequencing data were analyzed and compared with reference sequences. Results In Iran during the first wave, V and L clades were detected. The second wave was recognized by G, GH, and GR clades. Circulating clades during the third wave were GH and GR. In the fourth wave, GRY (alpha variant), GK (delta variant), and one GH clade (beta variant) were detected. All viruses in the fifth wave were in GK clade (delta variant). In the sixth wave, Omicron variant (GRA clade) was circulating. Conclusions Genome sequencing, a key strategy in genomic surveillance systems, helps to detect and monitor the prevalence of SARS-CoV-2 variants, monitor the viral evolution of SARS-CoV-2, identify new variants for disease prevention, control, and treatment, and also provide information for and conduct public health measures in this area. With this system, Iran could be ready for surveillance of other respiratory virus diseases besides influenza and SARS-CoV-2.
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Affiliation(s)
- Kaveh Sadeghi
- Virology Department, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Sevrin Zadheidar
- Virology Department, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Arghavan Zebardast
- Virology Department, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Ahmad Nejati
- Virology Department, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Marziyeh Faraji
- Virology Department, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Nastaran Ghavami
- Virology Department, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Shirin Kalantari
- Virology Department, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Vahid Salimi
- Virology Department, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Jila Yavarian
- Virology Department, School of Public HealthTehran University of Medical SciencesTehranIran
- Research Center for Antibiotic Stewardship & Antimicrobial ResistanceTehran University of Medical SciencesTehranIran
| | - Adel Abedi
- Mathematics DepartmentShahid Beheshti UniversityTehranIran
| | | | - Talat Mokhtari‐Azad
- Virology Department, School of Public HealthTehran University of Medical SciencesTehranIran
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12
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Filippi M, Ribeiro Amorim M, Soares da Silva M, Schons Gularte J, Demoliner M, Girardi V, de Abreu Goes Pereira VM, Witt Hansen A, Fleck JD, Frohlich J, de-Paris F, Motta Rodrigues G, Aparecida Risczik Arruda Correa J, Machado Arlindo De Mattos E, Minuto Paiva R, Deutschendorf C, Soares Falcetta F, Proença Modena JL, Rosado Spilki F. Prolonged SARS-CoV-2 Infection and Intra-Patient Viral Evolution in an Immunodeficient Child. Pediatr Infect Dis J 2023; 42:212-217. [PMID: 36728777 PMCID: PMC9935232 DOI: 10.1097/inf.0000000000003782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/30/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND With the progression of the Coronavirus disease pandemic, the number of mutations in the viral genome has increased, showing the adaptive evolution of severe acute respiratory syndrome coronavirus 2 in humans and intensification in transmissibility. Long-term infections also allow the development of viral diversity. In this study, we report the case of a child with severe combined immu presenting a prolonged severe acute respiratory syndrome coronavirus 2 infection. We aimed to analyze 3 naso-oropharyngeal swab samples collected between August and December 2021 to describe the amino acid changes present in the sequence reads that may have a role in the emergence of new viral variants. METHODS The whole genome from clinical samples was sequenced through high throughput sequencing and analyzed using a workflow to map reads and then find variations/single-nucleotide polymorphisms. In addition, the samples were isolated in cell culture, and a plaque forming units assay was performed, which indicates the presence of viable viral particles. RESULTS The results obtained showed that the virus present in all samples is infectious. Also, there were 20 common mutations among the 3 sequence reads, found in the ORF1ab and ORF10 proteins. As well, a considerable number of uncommon mutations were found. CONCLUSIONS In conclusion, we emphasize that genomic surveillance can be a useful tool to assess possible evolution signals in long-term patients.
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Affiliation(s)
- Micheli Filippi
- From the Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Mariene Ribeiro Amorim
- Laboratório de Vírus Emergentes, Departamento de Genética, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Mariana Soares da Silva
- From the Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Juliana Schons Gularte
- From the Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Meriane Demoliner
- From the Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Viviane Girardi
- From the Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | | | - Alana Witt Hansen
- From the Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Juliane Deise. Fleck
- From the Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Júlia Frohlich
- From the Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Fernanda de-Paris
- Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | | | | | | | | | | | | | - José Luiz Proença Modena
- Laboratório de Vírus Emergentes, Departamento de Genética, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Fernando Rosado Spilki
- From the Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
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13
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Pal S, Mehta P, Pandey A, Ara A, Ghoshal U, Ghoshal UC, Pandey R, Tripathi RK, Yadav PN, Ravishankar R, Kundu TK, Rajender S. Molecular determinants associated with temporal succession of SARS-CoV-2 variants in Uttar Pradesh, India. Front Microbiol 2023; 14:986729. [PMID: 36819024 PMCID: PMC9929466 DOI: 10.3389/fmicb.2023.986729] [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: 07/05/2022] [Accepted: 01/05/2023] [Indexed: 02/04/2023] Open
Abstract
The emergence and rapid evolution of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) caused a global crisis that required a detailed characterization of the dynamics of mutational pattern of the viral genome for comprehending its epidemiology, pathogenesis and containment. We investigated the molecular evolution of the SASR-CoV-2 genome during the first, second and third waves of COVID-19 in Uttar Pradesh, India. Nanopore sequencing of the SARS-CoV-2 genome was undertaken in 544 confirmed cases of COVID-19, which included vaccinated and unvaccinated individuals. In the first wave (unvaccinated population), the 20A clade (56.32%) was superior that was replaced by 21A Delta in the second wave, which was more often seen in vaccinated individuals in comparison to unvaccinated (75.84% versus 16.17%, respectively). Subsequently, 21A delta got outcompeted by Omicron (71.8%), especially the 21L variant, in the third wave. We noticed that Q677H appeared in 20A Alpha and stayed up to Delta, D614G appeared in 20A Alpha and stayed in Delta and Omicron variants (got fixed), and several other mutations appeared in Delta and stayed in Omicron. A cross-sectional analysis of the vaccinated and unvaccinated individuals during the second wave revealed signature combinations of E156G, F157Del, L452R, T478K, D614G mutations in the Spike protein that might have facilitated vaccination breach in India. Interestingly, some of these mutation combinations were carried forward from Delta to Omicron. In silico protein docking showed that Omicron had a higher binding affinity with the host ACE2 receptor, resulting in enhanced infectivity of Omicron over the Delta variant. This work has identified the combinations of key mutations causing vaccination breach in India and provided insights into the change of [virus's] binding affinity with evolution, resulting in more virulence in Delta and more infectivity in Omicron variants of SARS-CoV-2. Our findings will help in understanding the COVID-19 disease biology and guide further surveillance of the SARS-CoV-2 genome to facilitate the development of vaccines with better efficacies.
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Affiliation(s)
- Smita Pal
- CSIR-Central Drug Research Institute, Lucknow (CSIR-CDRI), Lucknow, India
| | - Poonam Mehta
- CSIR-Central Drug Research Institute, Lucknow (CSIR-CDRI), Lucknow, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ankita Pandey
- Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Anam Ara
- CSIR-Central Drug Research Institute, Lucknow (CSIR-CDRI), Lucknow, India
| | - Ujjala Ghoshal
- Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Uday C. Ghoshal
- Department of Gastroenterology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Rajesh Pandey
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India,CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Raj Kamal Tripathi
- CSIR-Central Drug Research Institute, Lucknow (CSIR-CDRI), Lucknow, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Prem N. Yadav
- CSIR-Central Drug Research Institute, Lucknow (CSIR-CDRI), Lucknow, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ramachandran Ravishankar
- CSIR-Central Drug Research Institute, Lucknow (CSIR-CDRI), Lucknow, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Tapas K. Kundu
- CSIR-Central Drug Research Institute, Lucknow (CSIR-CDRI), Lucknow, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India,Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, India
| | - Singh Rajender
- CSIR-Central Drug Research Institute, Lucknow (CSIR-CDRI), Lucknow, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India,*Correspondence: Singh Rajender, ✉
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14
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Sadeghdoust M, Aligolighasemabadi F, Dehesh T, Taefehshokr N, Sadeghdoust A, Kotfis K, Hashemiattar A, Ravandi A, Aligolighasemabadi N, Vakili O, Grabarek B, Staszkiewicz R, Łos MJ, Mokarram P, Ghavami S. The Effects of Statins on Respiratory Symptoms and Pulmonary Fibrosis in COVID-19 Patients with Diabetes Mellitus: A Longitudinal Multicenter Study. Arch Immunol Ther Exp (Warsz) 2023; 71:8. [PMID: 36853269 PMCID: PMC9972324 DOI: 10.1007/s00005-023-00672-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/14/2022] [Indexed: 03/01/2023]
Abstract
The aim of this prospective cohort study was to explore the effect of statins on long-term respiratory symptoms and pulmonary fibrosis in coronavirus disease 2019 (COVID-19) patients with diabetes mellitus (DM). Patients were recruited from three tertiary hospitals, categorized into Statin or Non-statin groups, and assessed on days 0, 28, and 90 after symptoms onset to record the duration of symptoms. Pulmonary fibrosis was scored at baseline and follow-up time points by high-resolution computed tomography scans. Each group comprised 176 patients after propensity score matching. Data analysis revealed that the odds of having cough and dyspnea were significantly higher in the Non-statin group compared to the Statin group during the follow-up period. Overall, there was no significant difference in the change in pulmonary fibrosis score between groups. However, Non-statin patients with > 5 years of DM were more likely to exhibit a significantly higher fibrosis score during the follow-up period as compared to their peers in the Statin group. Our results suggest that the use of statins is associated with a lower risk of developing chronic cough and dyspnea in diabetic patients with COVID-19, and may reduce pulmonary fibrosis associated with COVID-19 in patients with long-term (> 5 years) DM.
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Affiliation(s)
- Mohammadamin Sadeghdoust
- grid.411768.d0000 0004 1756 1744Department of Internal Medicine, Mashhad Medical Sciences Branch, Islamic Azad University, Mashhad, Iran
| | - Farnaz Aligolighasemabadi
- grid.411768.d0000 0004 1756 1744Department of Internal Medicine, Mashhad Medical Sciences Branch, Islamic Azad University, Mashhad, Iran
| | - Tania Dehesh
- grid.412105.30000 0001 2092 9755Department of Biostatistics and Epidemiology, School of Public Health, Kerman University of Medical Sciences, Kerman, Iran
| | - Nima Taefehshokr
- grid.39381.300000 0004 1936 8884Department of Microbiology and Immunology, Center for Human Immunology, The University of Western Ontario, London, ON Canada
| | - Adel Sadeghdoust
- grid.412237.10000 0004 0385 452XDepartment of Internal Medicine, School of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Katarzyna Kotfis
- grid.107950.a0000 0001 1411 4349Department of Anesthesiology, Intensive Therapy and Acute Intoxications, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Amirhossein Hashemiattar
- grid.411768.d0000 0004 1756 1744Department of Radiology, Mashhad Medical Sciences Branch, Islamic Azad University, Mashhad, Iran
| | - Amir Ravandi
- grid.21613.370000 0004 1936 9609Institute of Cardiovascular Sciences, Sr. Boniface Research Centre, University of Manitoba, Winnipeg, Canada
| | - Neda Aligolighasemabadi
- grid.411874.f0000 0004 0571 1549Department of Internal Medicine, School of Medicine, Razi Hospital, Guilan University of Medical Sciences, Rasht, Iran
| | - Omid Vakili
- grid.411036.10000 0001 1498 685XDepartment of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Beniamin Grabarek
- Department of Histology, Cytophysiology and Embryology, Faculty of Medicine in Zabrze, Academy of Silesia in Katowice, Zabrze, Poland ,Department of Gynaecology and Obstetrics, Faculty of Medicine in Zabrze, Academy of Silesia in Katowice, Zabrze, Poland ,Laboratory of Molecular Biology and Virology, GynCentrum, Katowice, Poland
| | - Rafał Staszkiewicz
- Department of Histology, Cytophysiology and Embryology, Faculty of Medicine in Zabrze, Academy of Silesia in Katowice, Zabrze, Poland ,Department of Neurosurgery, 5Th Military Clinical Hospital with the SP ZOZ Polyclinic in Krakow, Krakow, Poland
| | - Marek J. Łos
- grid.6979.10000 0001 2335 3149Biotechnology Center, Silesian University of Technology, Gliwice, Poland ,grid.412571.40000 0000 8819 4698Autophagy Research Center, Department of Biochemistry, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Pooneh Mokarram
- Autophagy Research Center, Department of Biochemistry, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Saeid Ghavami
- Autophagy Research Center, Department of Biochemistry, Shiraz University of Medical Sciences, Shiraz, Iran. .,Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada. .,Faculty of Medicine in Zabrze, University of Technology in Katowice, Academia of Silesia, Zabrze, Poland. .,Research Institute of Oncology and Hematology, Cancer Care, Manitoba University of Manitoba, Winnipeg, Canada. .,Biology of Breathing Theme, Children Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, Canada.
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15
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Ahmadi K, Shahbazi B, Zakeri AJ, Gouklani H. Characterization of SARS-CoV-2 omicron variants from Iran and evaluation of the effect of mutations on the spike, nucleocapsid, ORF8, and ORF9b proteins function. J Biomol Struct Dyn 2022; 41:11415-11430. [PMID: 36576175 DOI: 10.1080/07391102.2022.2162131] [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: 09/23/2022] [Accepted: 12/18/2022] [Indexed: 12/29/2022]
Abstract
The SARS-CoV-2 'Omicron' strain, with 15 mutations in the receptor binding domain (RBD), was detected in South Africa and rapidly spread worldwide. SARS-CoV-2 ORF9b protein by binding to the TOM70 receptor and ORF8 protein by binding to MHC-I, IF3 receptors inhibit the host's immune response. In this study, genomics variations were evaluated for 96 samples isolated from Iran from March to July 2022 using the Nextclade web server and informatics tools. We identified the mutations occurring in the SARS-CoV-2 proteins. We also evaluated the effect of mutations on spike protein interaction with the ACE2 receptor, ORF9b protein interaction with the TOM70 receptor, and structural stability of ORF8 and nucleocapsid proteins using docking and molecular dynamics. Results indicated that during March and April 2022, the BA.2 strain was dominant in the south of Iran, while during June 2022, the BA.5 strain was dominant. BF.5 strain had the most divergence among SARS-CoV-2 strains reported from south of Iran. The binding affinity of BA.5 and BF.5 strains spike protein to ACE2 receptor is similar, and compared to BA.2 strain, was stronger. The BF.5 ORF9b K40R mutation causes a better binding affinity of the protein to the TOM70 receptor. Also, mutations that occurred in the ORF8 protein led to instability in the dimer formation of this protein and improved immune response for mutations that occurred in BA.2 strain, while this mutation did not occur in BF.5 strain. The mutations that were detected in nucleocapsid protein CTD and NTD domains caused the stability of these domains.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Khadijeh Ahmadi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Behzad Shahbazi
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Abdul-Jabbar Zakeri
- Social Determinants in Health Promotion Research Center, Research Institute for Health, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Hamed Gouklani
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
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16
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da Cruz Freire JE, Júnior JEM, Pinheiro DP, da Cruz Paiva Lima GE, do Amaral CL, Veras VR, Madeira MP, Freire EBL, Ozório RG, Fernandes VO, Montenegro APDR, Montenegro RC, Colares JKB, Júnior RMM. Evaluation of the anti-diabetic drug sitagliptin as a novel attenuate to SARS-CoV-2 evidence-based in silico: molecular docking and molecular dynamics. 3 Biotech 2022; 12:344. [PMCID: PMC9640538 DOI: 10.1007/s13205-022-03406-w] [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: 07/30/2022] [Accepted: 09/30/2022] [Indexed: 11/09/2022] Open
Abstract
The current outbreak of COVID-19 cases worldwide has been responsible for a significant number of deaths, especially in hospitalized patients suffering from comorbidities, such as obesity, diabetes, hypertension. The disease not only has prompted an interest in the pathophysiology, but also it has propelled a massive race to find new anti-SARS-CoV-2 drugs. In this scenario, known drugs commonly used to treat other diseases have been suggested as alternative or complementary therapeutics. Herein we propose the use of sitagliptin, an inhibitor of dipeptidyl peptidase-4 (DPP4) used to treat type-II diabetes, as an agent to block and inhibit the activity of two proteases, 3CLpro and PLpro, related to the processing of SARS-CoV-2 structural proteins. Inhibition of these proteases may possibly reduce the viral load and infection on the host by hampering the synthesis of new viruses, thus promoting a better outcome. In silico assays consisting in the modeling of the ligand sitagliptin and evaluation of its capacity to interact with 3CLpro and PLpro through the prediction of the ligand bioactivity, molecular docking, overlapping of crystal structures, and molecular dynamic simulations were conducted. The experiments indicate that sitagliptin can interact and bind to both targets. However, this interaction seems to be stronger and more stable to 3CLpro (ΔG = −7.8 kcal mol−1), when compared to PLpro (ΔG = −7.5 kcal mol−1). This study suggests that sitagliptin may be suitable to treat COVID-19 patients, beyond its common use as an anti-diabetic medication. In vivo studies may further support this hypothesis.
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17
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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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18
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Alahdal M, Elkord E. Promising use of immune cell-derived exosomes in the treatment of SARS-CoV-2 infections. Clin Transl Med 2022; 12:e1026. [PMID: 35988156 PMCID: PMC9393056 DOI: 10.1002/ctm2.1026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/01/2022] [Accepted: 08/08/2022] [Indexed: 12/11/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is persistently threatening the lives of thousands of individuals globally. It triggers pulmonary oedema, driving to dyspnoea and lung failure. Viral infectivity of coronavirus disease 2019 (COVID-19) is a genuine challenge due to the mutagenic genome and mysterious immune-pathophysiology. Early reports highlighted that extracellular vesicles (exosomes, Exos) work to enhance COVID-19 progression by mediating viral transmission, replication and mutations. Furthermore, recent studies revealed that Exos derived from immune cells play an essential role in the promotion of immune cell exhaustion by transferring regulatory lncRNAs and miRNAs from exhausted cells to the active cells. Fortunately, there are great chances to modulate the immune functions of Exos towards a sustained repression of COVID-19. Engineered Exos hold promising immunotherapeutic opportunities for remodelling cytotoxic T cells' function. Immune cell-derived Exos may trigger a stable epigenetic repression of viral infectivity, restore functional cytokine-producing T cells and rebalance immune response in severe infections by inducing functional T regulatory cells (Tregs). This review introduces a view on the current outcomes of immunopathology, and immunotherapeutic applications of immune cell-derived Exos in COVID-19, besides new perspectives to develop novel patterns of engineered Exos triggering novel anti-SARS-CoV-2 immune responses.
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Affiliation(s)
- Murad Alahdal
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Eyad Elkord
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman.,Biomedical Research Center, School of Science, Engineering and Environment, University of Salford, Manchester, United Kingdom
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