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Kori M, Kasavi C, Arga KY. Exploring COVID-19 Pandemic Disparities with Transcriptomic Meta-analysis from the Perspective of Personalized Medicine. J Microbiol 2024:10.1007/s12275-024-00154-9. [PMID: 38980578 DOI: 10.1007/s12275-024-00154-9] [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: 03/12/2024] [Revised: 06/06/2024] [Accepted: 06/17/2024] [Indexed: 07/10/2024]
Abstract
Infection with SARS-CoV2, which is responsible for COVID-19, can lead to differences in disease development, severity and mortality rates depending on gender, age or the presence of certain diseases. Considering that existing studies ignore these differences, this study aims to uncover potential differences attributable to gender, age and source of sampling as well as viral load using bioinformatics and multi-omics approaches. Differential gene expression analyses were used to analyse the phenotypic differences between SARS-CoV-2 patients and controls at the mRNA level. Pathway enrichment analyses were performed at the gene set level to identify the activated pathways corresponding to the differences in the samples. Drug repurposing analysis was performed at the protein level, focusing on host-mediated drug candidates to uncover potential therapeutic differences. Significant differences (i.e. the number of differentially expressed genes and their characteristics) were observed for COVID-19 at the mRNA level depending on the sample source, gender and age of the samples. The results of the pathway enrichment show that SARS-CoV-2 can be combated more effectively in the respiratory tract than in the blood samples. Taking into account the different sample sources and their characteristics, different drug candidates were identified. Evaluating disease prediction, prevention and/or treatment strategies from a personalised perspective is crucial. In this study, we not only evaluated the differences in COVID-19 from a personalised perspective, but also provided valuable data for further experimental and clinical efforts. Our findings could shed light on potential pandemics.
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Affiliation(s)
- Medi Kori
- Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, 34752, Istanbul, Turkey.
- Faculty of Health Sciences, Acibadem Mehmet Ali Aydinlar University, 34752, Istanbul, Turkey.
| | - Ceyda Kasavi
- Department of Bioengineering, Marmara University, 34722, Istanbul, Turkey
| | - Kazim Yalcin Arga
- Department of Bioengineering, Marmara University, 34722, Istanbul, Turkey
- Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, 34722, Istanbul, Turkey
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Cao Z, Sun F, Ding H, Tian Z, Cui Y, Yang W, Hu S, Shi L. A retrospective analysis of the influencing factors of nucleic acid CT value fluctuation in COVID-19 patients infected with Omicron variant virus in Changchun city. Front Public Health 2024; 12:1377135. [PMID: 38947348 PMCID: PMC11211536 DOI: 10.3389/fpubh.2024.1377135] [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: 01/31/2024] [Accepted: 06/03/2024] [Indexed: 07/02/2024] Open
Abstract
Objective This study aimed to determine the risk factors associated with fluctuations in nucleic acid CT values in patients infected with the Omicron variant during an outbreak at a hospital in Changchun city. Methods A retrospective analysis was conducted on general information, medical history, vaccination history, and laboratory test data of COVID-19 patients infected with the Omicron variant and admitted to the hospital in Changchun from March 2022 to April 2022. The study aimed to explore the factors influencing nucleic acid CT value fluctuations in COVID-19 patients infected with the Omicron variant in Changchun city. Results Fluctuations in nucleic acid CT values were significantly correlated with occupation composition (p = 0.030), hospital stay duration (p = 0.000), heart rate (p = 0.026), creatinine (p = 0.011), platelet count (p = 0.000), glutamic-pyruvic transaminase (p = 0.045), and glutamic oxaloacetic transaminase (p = 0.017). Binary logistic regression analysis revealed significant correlations between hospital stay duration (p = 0.000), platelet count (p = 0.019), heart rate (p = 0.036), and nucleic acid CT value fluctuations (p < 0.05), indicating that they were independent risk factors. Red blood cell count was identified as a factor influencing nucleic acid CT value fluctuations in Group A patients. Occupation composition, direct bilirubin, and platelet count were identified as factors influencing nucleic acid CT value fluctuations in Group B patients. Further binary logistic regression analysis indicated that occupational composition and direct bilirubin are significant independent factors for nucleic acid CT value fluctuations in Group B patients, positively correlated with occupational risk and negatively correlated with direct bilirubin. Conclusion Therefore, enhancing patients' immunity, increasing physical exercise to improve myocardial oxygen consumption, reducing the length of hospital stays, and closely monitoring liver function at the onset of hospitalization to prevent liver function abnormalities are effective measures to control fluctuations in nucleic acid CT values.
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Affiliation(s)
- Zhenghua Cao
- Changchun University of Traditional Chinese Medicine, Changchun, Jilin, China
| | - Feng Sun
- Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, Jilin, China
| | - Huan Ding
- Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, Jilin, China
| | - Zhiyu Tian
- Changchun University of Traditional Chinese Medicine, Changchun, Jilin, China
| | - Yingzi Cui
- Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, Jilin, China
| | - Wei Yang
- Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, Jilin, China
| | - Shaodan Hu
- Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, Jilin, China
| | - Li Shi
- Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, Jilin, China
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Acer Ö, Genç Bahçe Y, Özüdoğru O. Homologous and Heterologous Covid-19 Booster Vaccinations Against SARS-CoV-2 Infection in the Elderly. Curr Microbiol 2024; 81:171. [PMID: 38739274 DOI: 10.1007/s00284-024-03689-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 04/04/2024] [Indexed: 05/14/2024]
Abstract
A third booster doses for the 2019 coronavirus disease (COVID-19) is widely used all over the world, especially in risky individuals, with the recommendation of WHO. The purpose of this study was to evaluate the effectiveness of mRNA (BNT162b2), and CoronaVac (Sinovac Biotech) vaccines as a reminder dose following two doses of CoronaVac against COVID-19 infection, serious illness, and mortality in the geriatric population aged 75 and older during the delta variant dominant period. Our study comprised 2730 individuals the age of 75 and older in total, of which 1082 (39.6%) were male and 1648 (60.4%) were female. The vaccine effectiveness (VE) of 2 doses of CoronaVac + 1 dose of BNT162b2 vaccine combination against COVID-19 was determined as 89.2% (95% Confidence interval (CI) 80.7-93.9%), while the VE of 3 doses of CoronaVac vaccine was determined as 80.4% (95% CI 60.5-90.2%). Geriatric patients who received three doses of CoronaVac vaccine did not need intensive care. No deaths were observed in the vaccinated groups. While the VE of vaccination with 2 doses of CoronaVac + 1 dose of BNT162b2 was 41.8% (95% CI 0-74.1%) against hospitalization, 64.4% (95% CI 0-94.7%) against intensive care unit admission, the VE of vaccination with three doses of the CoronaVac was 78.2% (95% CI 0-96.5%) against hospitalization. In conclusion, our research showed that, even with the emergence of viral variants, a third dose of the CoronaVac and BNT162b2 vaccines is highly effective against symptomatic SARS-CoV-2 infection. Third-dose vaccination regimens, including heterologous and homologous vaccines, can be an effective tool in controlling the COVID-19 pandemic and the emergence of new variants.
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Affiliation(s)
- Ömer Acer
- Department of Medical Microbiology, Medical Faculty, Siirt University, 56100, Siirt, Türkiye.
| | - Yasemin Genç Bahçe
- Microbiology Laboratory, Siirt Training and Research Hospital, 56100, Siirt, Türkiye
| | - Osman Özüdoğru
- Department of Internal Medicine, Medical Faculty, Erzincan Binali Yıldırım University, 24100, Erzincan, Türkiye
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Sila T, Surasombatpattana S, Rajborirug S, Laochareonsuk W, Choochuen P, Kongkamol C, Ingviya T, Prompat N, Mahasirimongkol S, Sangkhathat S, Aiewsakun P. SARS-CoV-2 variant with the spike protein mutation F306L in the southern border provinces of Thailand. Sci Rep 2024; 14:7729. [PMID: 38565881 PMCID: PMC10987673 DOI: 10.1038/s41598-024-56646-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 03/08/2024] [Indexed: 04/04/2024] Open
Abstract
The southernmost part of Thailand is a unique and culturally diverse region that has been greatly affected by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) outbreak during the coronavirus disease-2019 pandemic. To gain insights into this situation, we analyzed 1942 whole-genome sequences of SARS-CoV-2 obtained from the five southernmost provinces of Thailand between April 2021 and March 2022, together with those publicly available in the Global Initiative on Sharing All Influenza Data database. Our analysis revealed evidence for transboundary transmissions of the virus in and out of the five southernmost provinces during the study period, from both domestic and international sources. The most prevalent viral variant in our sequence dataset was the Delta B.1.617.2.85 variant, also known as the Delta AY.85 variant, with many samples carrying a non-synonymous mutation F306L in their spike protein. Protein-protein docking and binding interface analyses suggested that the mutation may enhance the binding between the spike protein and host cell receptor protein angiotensin-converting enzyme 2, and we found that the mutation was significantly associated with an increased fatality rate. This mutation has also been observed in other SARS-CoV-2 variants, suggesting that it is of particular interest and should be monitored.
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Affiliation(s)
- Thanit Sila
- Department of Pathology, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Smonrapat Surasombatpattana
- Department of Pathology, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Songyos Rajborirug
- Department of Epidemiology, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Wison Laochareonsuk
- Division of Surgery, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Pongsakorn Choochuen
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Chanon Kongkamol
- Department of Family Medicine and Preventive Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Thammasin Ingviya
- Department of Family Medicine and Preventive Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Napat Prompat
- Faculty of Medical Technology, Medical of Technology Service Center, Prince of Songkla University, Songkhla, 90110, Thailand
| | - Surakameth Mahasirimongkol
- Department of Medical Sciences, Genetics Center, Medical Life Sciences Institute, Ministry of Public Health, Nonthaburi, 11000, Thailand
| | - Surasak Sangkhathat
- Division of Surgery, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand.
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand.
| | - Pakorn Aiewsakun
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
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Choi G, Lim AY, Choi S, Park K, Lee SY, Kim JH. Viral shedding patterns of symptomatic SARS-CoV-2 infections by periods of variant predominance and vaccination status in Gyeonggi Province, Korea. Epidemiol Health 2022; 45:e2023008. [PMID: 36596734 PMCID: PMC10581894 DOI: 10.4178/epih.e2023008] [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: 10/17/2022] [Accepted: 12/21/2022] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVES We compared the viral cycle threshold (Ct) values of infected patients to better understand viral kinetics by vaccination status during different periods of variant predominance in Gyeonggi Province, Korea. METHODS We obtained case-specific data from the coronavirus disease 2019 (COVID-19) surveillance system, Gyeonggi in-depth epidemiological report system, and Health Insurance Review & Assessment Service from January 2020 to January 2022. We defined periods of variant predominance and explored Ct values by analyzing viral sequencing test results. Using a generalized additive model, we performed a nonlinear regression analysis to determine viral kinetics over time. RESULTS Cases in the Delta variant's period of predominance had higher viral shedding patterns than cases in other periods. The temporal change of viral shedding did not vary by vaccination status in the Omicron-predominant period, but viral shedding decreased in patients who had completed their third vaccination in the Delta-predominant period. During the Delta-predominant and Omicron-predominant periods, the time from symptom onset to peak viral shedding based on the E gene was approximately 2.4 days (95% confidence interval [CI], 2.2 to 2.5) and 2.1 days (95% CI, 2.0 to 2.1), respectively. CONCLUSIONS In one-time tests conducted to diagnose COVID-19 in a large population, although no adjustment for individual characteristics was conducted, it was confirmed that viral shedding differed by the predominant strain and vaccination history. These results show the value of utilizing hundreds of thousands of test data produced at COVID-19 screening test centers.
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Affiliation(s)
- Gawon Choi
- Gyeonggi Infectious Disease Control Center, Health Bureau, Gyeonggi Provincial Government, Suwon, Korea
| | - Ah-Young Lim
- Department of Social and Preventive Medicine, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Sojin Choi
- Gyeonggi Infectious Disease Control Center, Health Bureau, Gyeonggi Provincial Government, Suwon, Korea
| | - Kunhee Park
- Gyeonggi Infectious Disease Control Center, Health Bureau, Gyeonggi Provincial Government, Suwon, Korea
| | - Soon Young Lee
- Department of Preventive Medicine and Public Health, Ajou University School of Medicine, Suwon, Korea
| | - Jong-Hun Kim
- Gyeonggi Infectious Disease Control Center, Health Bureau, Gyeonggi Provincial Government, Suwon, Korea
- Department of Social and Preventive Medicine, Sungkyunkwan University School of Medicine, Suwon, Korea
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Amidei A, Dobrovolny HM. Estimation of virus-mediated cell fusion rate of SARS-CoV-2. Virology 2022; 575:91-100. [PMID: 36088794 PMCID: PMC9449781 DOI: 10.1016/j.virol.2022.08.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/27/2022] [Accepted: 08/28/2022] [Indexed: 12/22/2022]
Abstract
Several viruses have the ability to form large multinucleated cells known as syncytia. Many properties of syncytia and the role they play in the evolution of a viral infection are not well understood. One basic question that has not yet been answered is how quickly syncytia form. We use a novel mathematical model of cell-cell fusion assays and apply it to experimental data from SARS-CoV-2 fusion assays to provide the first estimates of virus-mediated cell fusion rate. We find that for SARS-CoV2, the fusion rate is in the range of 6 × 10−4–12×10−4/h. We also use our model to compare fusion rates when the protease TMPRSS2 is overexpressed (2–4 times larger fusion rate), when the protease furin is removed (one third the original fusion rate), and when the spike protein is altered (1/10th the original fusion rate). The use of mathematical models allows us to provide additional quantitative information about syncytia formation.
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Affiliation(s)
- Ava Amidei
- Department of Chemistry & Biochemistry, Texas Christian University, Fort Worth, TX, USA
| | - Hana M Dobrovolny
- Department of Physics & Astronomy, Texas Christian University, Fort Worth, TX, USA.
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Fan C, Wu Y, Rui X, Yang Y, Ling C, Liu S, Liu S, Wang Y. Animal models for COVID-19: advances, gaps and perspectives. Signal Transduct Target Ther 2022; 7:220. [PMID: 35798699 PMCID: PMC9261903 DOI: 10.1038/s41392-022-01087-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/20/2022] [Accepted: 06/27/2022] [Indexed: 01/08/2023] Open
Abstract
COVID-19, caused by SARS-CoV-2, is the most consequential pandemic of this century. Since the outbreak in late 2019, animal models have been playing crucial roles in aiding the rapid development of vaccines/drugs for prevention and therapy, as well as understanding the pathogenesis of SARS-CoV-2 infection and immune responses of hosts. However, the current animal models have some deficits and there is an urgent need for novel models to evaluate the virulence of variants of concerns (VOC), antibody-dependent enhancement (ADE), and various comorbidities of COVID-19. This review summarizes the clinical features of COVID-19 in different populations, and the characteristics of the major animal models of SARS-CoV-2, including those naturally susceptible animals, such as non-human primates, Syrian hamster, ferret, minks, poultry, livestock, and mouse models sensitized by genetically modified, AAV/adenoviral transduced, mouse-adapted strain of SARS-CoV-2, and by engraftment of human tissues or cells. Since understanding the host receptors and proteases is essential for designing advanced genetically modified animal models, successful studies on receptors and proteases are also reviewed. Several improved alternatives for future mouse models are proposed, including the reselection of alternative receptor genes or multiple gene combinations, the use of transgenic or knock-in method, and different strains for establishing the next generation of genetically modified mice.
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Affiliation(s)
- Changfa Fan
- Division of Animal Model Research, Institute for Laboratory Animal Resources, National Institutes for Food and Drug Control (NIFDC), National Rodent Laboratory Animal Resources Center, Beijing, 102629, China
| | - Yong Wu
- Division of Animal Model Research, Institute for Laboratory Animal Resources, National Institutes for Food and Drug Control (NIFDC), National Rodent Laboratory Animal Resources Center, Beijing, 102629, China
| | - Xiong Rui
- Division of Animal Model Research, Institute for Laboratory Animal Resources, National Institutes for Food and Drug Control (NIFDC), National Rodent Laboratory Animal Resources Center, Beijing, 102629, China
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100083, China
| | - Yuansong Yang
- Division of Animal Model Research, Institute for Laboratory Animal Resources, National Institutes for Food and Drug Control (NIFDC), National Rodent Laboratory Animal Resources Center, Beijing, 102629, China
| | - Chen Ling
- Division of Animal Model Research, Institute for Laboratory Animal Resources, National Institutes for Food and Drug Control (NIFDC), National Rodent Laboratory Animal Resources Center, Beijing, 102629, China
- College of Life Sciences, Northwest University; Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, 710069, China
| | - Susu Liu
- Division of Animal Model Research, Institute for Laboratory Animal Resources, National Institutes for Food and Drug Control (NIFDC), National Rodent Laboratory Animal Resources Center, Beijing, 102629, China
| | - Shunan Liu
- Division of Animal Model Research, Institute for Laboratory Animal Resources, National Institutes for Food and Drug Control (NIFDC), National Rodent Laboratory Animal Resources Center, Beijing, 102629, China
| | - Youchun Wang
- Division of HIV/AIDS and Sexually Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, China.
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