101
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Yu X, Ho K, Shen Z, Fu X, Huang H, Wu D, Lin Y, Lin Y, Chen W, Su M, Qiu C, Zhuang X, Su Z. The Association of Human Leukocyte Antigen and COVID-19 in Southern China. Open Forum Infect Dis 2021; 8:ofab410. [PMID: 34552996 PMCID: PMC8436377 DOI: 10.1093/ofid/ofab410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 08/06/2021] [Indexed: 12/24/2022] Open
Abstract
Human leukocyte antigen (HLA) polymorphism is hypothesized to be associated with diverse immune responses toward infectious diseases. Herein, by comparing against multiple subpopulation groups as control, we confirmed that HLA-B*15:27 and HLA-DRB1*04:06 were associated with coronavirus disease 2019 susceptibility in China. Both alleles were predicted to have weak binding affinities toward viral proteins.
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Affiliation(s)
- Xueping Yu
- Department of Infectious Disease, The First Hospital of Quanzhou, affiliated to Fujian Medical University, Quanzhou, Fujian, China
| | - Kuoting Ho
- HI. Q Biomedical Laboratory, Quanzhou, Fujian, China.,School of Biomedical Science, Huaqiao University, Quanzhou, Fujian, China
| | - Zhongliang Shen
- Department of Infectious Disease, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaoying Fu
- HI. Q Biomedical Laboratory, Quanzhou, Fujian, China
| | - Hongbo Huang
- Department of Respiratory Disease, The First Hospital of Quanzhou, affiliated to Fujian Medical University, Quanzhou, Fujian, China
| | - Delun Wu
- HI. Q Biomedical Laboratory, Quanzhou, Fujian, China
| | - Yancheng Lin
- HI. Q Biomedical Laboratory, Quanzhou, Fujian, China
| | - Yijian Lin
- Department of Respiratory Disease, The First Hospital of Quanzhou, affiliated to Fujian Medical University, Quanzhou, Fujian, China
| | - Wenhuang Chen
- Department of Infectious Disease, The First Hospital of Quanzhou, affiliated to Fujian Medical University, Quanzhou, Fujian, China
| | - Milong Su
- Department of Clinical Laboratory, The First Hospital of Quanzhou, affiliated to Fujian Medical University, Quanzhou, Fujian, China
| | - Chao Qiu
- Department of Infectious Disease, Huashan Hospital, Fudan University, Shanghai, China
| | - Xibin Zhuang
- Department of Respiratory Disease, The First Hospital of Quanzhou, affiliated to Fujian Medical University, Quanzhou, Fujian, China
| | - Zhijun Su
- Department of Infectious Disease, The First Hospital of Quanzhou, affiliated to Fujian Medical University, Quanzhou, Fujian, China
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102
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Giannini HM, Meyer NJ. Genetics of Acute Respiratory Distress Syndrome: Pathways to Precision. Crit Care Clin 2021; 37:817-834. [PMID: 34548135 DOI: 10.1016/j.ccc.2021.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Clinical risk factors alone fail to fully explain acute respiratory distress syndrome (ARDS) risk or ARDS death, suggesting that individual risk factors contribute. The goals of genomic ARDS studies include better mechanistic understanding, identifying dysregulated pathways that may be amenable to pharmacologic targeting, using genomic causal inference techniques to find measurable traits with meaning, and deconvoluting ARDS heterogeneity by proving reproducible subpopulations that may share a unique biology. This article discusses the latest advances in ARDS genomics, provides historical perspective, and highlights some of the ways that the coronavirus disease 2019 (COVID-19) pandemic is accelerating genomic ARDS research.
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Affiliation(s)
- Heather M Giannini
- University of Pennsylvania Perelman School of Medicine, 3400 Spruce Street, 5038 Gates Building, Philadelphia, PA 19104, USA
| | - Nuala J Meyer
- University of Pennsylvania Perelman School of Medicine, 3400 Spruce Street, 5038 Gates Building, Philadelphia, PA 19104, USA.
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103
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Deng H, Yan X, Yuan L. Human genetic basis of coronavirus disease 2019. Signal Transduct Target Ther 2021; 6:344. [PMID: 34545062 PMCID: PMC8450706 DOI: 10.1038/s41392-021-00736-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 07/28/2021] [Accepted: 08/08/2021] [Indexed: 02/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in considerable morbidity and mortality worldwide. COVID-19 incidence, severity, and mortality rates differ greatly between populations, genders, ABO blood groups, human leukocyte antigen (HLA) genotypes, ethnic groups, and geographic backgrounds. This highly heterogeneous SARS-CoV-2 infection is multifactorial. Host genetic factors such as variants in the angiotensin-converting enzyme gene (ACE), the angiotensin-converting enzyme 2 gene (ACE2), the transmembrane protease serine 2 gene (TMPRSS2), along with HLA genotype, and ABO blood group help to explain individual susceptibility, severity, and outcomes of COVID-19. This review is focused on COVID-19 clinical and viral characteristics, pathogenesis, and genetic findings, with particular attention on genetic diversity and variants. The human genetic basis could provide scientific bases for disease prediction and targeted therapy to address the COVID-19 scourge.
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Affiliation(s)
- Hao Deng
- Health Management Center, the Third Xiangya Hospital, Central South University, Changsha, China.
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, China.
- Disease Genome Research Center, Central South University, Changsha, China.
- Department of Neurology, the Third Xiangya Hospital, Central South University, Changsha, China.
| | - Xue Yan
- Health Management Center, the Third Xiangya Hospital, Central South University, Changsha, China
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, China
- Disease Genome Research Center, Central South University, Changsha, China
| | - Lamei Yuan
- Health Management Center, the Third Xiangya Hospital, Central South University, Changsha, China
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, China
- Disease Genome Research Center, Central South University, Changsha, China
- Department of Neurology, the Third Xiangya Hospital, Central South University, Changsha, China
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104
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Li Y, Ke Y, Xia X, Wang Y, Cheng F, Liu X, Jin X, Li B, Xie C, Liu S, Chen W, Yang C, Niu Y, Jia R, Chen Y, Liu X, Wang Z, Zheng F, Jin Y, Li Z, Yang N, Cao P, Chen H, Ping J, He F, Wang C, Zhou G. Genome-wide association study of COVID-19 severity among the Chinese population. Cell Discov 2021; 7:76. [PMID: 34465742 PMCID: PMC8408196 DOI: 10.1038/s41421-021-00318-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/29/2021] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causes a broad clinical spectrum of coronavirus disease 2019 (COVID-19). The development of COVID-19 may be the result of a complex interaction between the microbial, environmental, and host genetic components. To reveal genetic determinants of susceptibility to COVID-19 severity in the Chinese population, we performed a genome-wide association study on 885 severe or critical COVID-19 patients (cases) and 546 mild or moderate patients (controls) from two hospitals, Huoshenshan and Union hospitals at Wuhan city in China. We identified two loci on chromosome 11q23.3 and 11q14.2, which are significantly associated with the COVID-19 severity in the meta-analyses of the two cohorts (index rs1712779: odds ratio [OR] = 0.49; 95% confidence interval [CI], 0.38-0.63 for T allele; P = 1.38 × 10-8; and index rs10831496: OR = 1.66; 95% CI, 1.38-1.98 for A allele; P = 4.04 × 10-8, respectively). The results for rs1712779 were validated in other two small COVID-19 cohorts in the Asian populations (P = 0.029 and 0.031, respectively). Furthermore, we identified significant eQTL associations for REXO2, C11orf71, NNMT, and CADM1 at 11q23.3, and CTSC at 11q14.2, respectively. In conclusion, our findings highlight two loci at 11q23.3 and 11q14.2 conferring susceptibility to the severity of COVID-19, which might provide novel insights into the pathogenesis and clinical treatment of this disease.
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Affiliation(s)
- Yuanfeng Li
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China
| | - Yuehua Ke
- Center for Disease Control and Prevention of PLA, Beijing, China.,Department of Laboratory Medicine, Wuhan Huoshenshan Hospital, Wuhan, Hubei, China
| | - Xinyi Xia
- Department of Laboratory Medicine, Wuhan Huoshenshan Hospital, Wuhan, Hubei, China.,COVID-19 Research Center, Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing Clinical College of Southern Medical University, Nanjing, Jiangsu, China
| | - Yahui Wang
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China.,State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Lifeomics, Beijing, China
| | - Fanjun Cheng
- Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xinyi Liu
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China
| | - Xin Jin
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Boan Li
- Clinical Laboratory Medicine Center, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Chengyong Xie
- Medical College of Guizhou University, Guiyang, Guizhou, China
| | - Siyang Liu
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Weijun Chen
- University of Chinese Academy of Sciences, Beijing, China
| | - Chenning Yang
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China
| | - Yuguang Niu
- Department of Otolaryngology, The First Medical Center of General Hospital of PLA, Beijing, China
| | - Ruizhong Jia
- Center for Disease Control and Prevention of PLA, Beijing, China
| | - Yong Chen
- Center for Disease Control and Prevention of PLA, Beijing, China
| | - Xiong Liu
- Center for Disease Control and Prevention of PLA, Beijing, China
| | - Zhihua Wang
- Center for Disease Control and Prevention of PLA, Beijing, China
| | - Fang Zheng
- Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yan Jin
- Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zhen Li
- Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ning Yang
- Clinical Laboratory Medicine Center, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Pengbo Cao
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China
| | - Hongxia Chen
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China
| | - Jie Ping
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China
| | - Fuchu He
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Lifeomics, Beijing, China.,Guangzhou Laboratory, Guangzhou, Guangdong, China
| | - Changjun Wang
- Center for Disease Control and Prevention of PLA, Beijing, China. .,Department of Laboratory Medicine, Wuhan Huoshenshan Hospital, Wuhan, Hubei, China.
| | - Gangqiao Zhou
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China. .,Medical College of Guizhou University, Guiyang, Guizhou, China. .,Guangzhou Laboratory, Guangzhou, Guangdong, China. .,Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.
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105
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Wu P, Ding L, Li X, Liu S, Cheng F, He Q, Xiao M, Wu P, Hou H, Jiang M, Long P, Wang H, Liu L, Qu M, Shi X, Jiang Q, Mo T, Ding W, Fu Y, Han S, Huo X, Zeng Y, Zhou Y, Zhang Q, Ke J, Xu X, Ni W, Shao Z, Wang J, Liu P, Li Z, Jin Y, Zheng F, Wang F, Liu L, Li W, Liu K, Peng R, Xu X, Lin Y, Gao H, Shi L, Geng Z, Mu X, Yan Y, Wang K, Wu D, Hao X, Cheng S, Qiu G, Guo H, Li K, Chen G, Sun Z, Lin X, Jin X, Wang F, Sun C, Wang C. Trans-ethnic genome-wide association study of severe COVID-19. Commun Biol 2021; 4:1034. [PMID: 34465887 PMCID: PMC8408224 DOI: 10.1038/s42003-021-02549-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 08/12/2021] [Indexed: 01/08/2023] Open
Abstract
COVID-19 has caused numerous infections with diverse clinical symptoms. To identify human genetic variants contributing to the clinical development of COVID-19, we genotyped 1457 (598/859 with severe/mild symptoms) and sequenced 1141 (severe/mild: 474/667) patients of Chinese ancestry. We further incorporated 1401 genotyped and 948 sequenced ancestry-matched population controls, and tested genome-wide association on 1072 severe cases versus 3875 mild or population controls, followed by trans-ethnic meta-analysis with summary statistics of 3199 hospitalized cases and 897,488 population controls from the COVID-19 Host Genetics Initiative. We identified three significant signals outside the well-established 3p21.31 locus: an intronic variant in FOXP4-AS1 (rs1853837, odds ratio OR = 1.28, P = 2.51 × 10-10, allele frequencies in Chinese/European AF = 0.345/0.105), a frameshift insertion in ABO (rs8176719, OR = 1.19, P = 8.98 × 10-9, AF = 0.422/0.395) and a Chinese-specific intronic variant in MEF2B (rs74490654, OR = 8.73, P = 1.22 × 10-8, AF = 0.004/0). These findings highlight an important role of the adaptive immunity and the ABO blood-group system in protection from developing severe COVID-19.
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Affiliation(s)
- Peng Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Medical Center for Major Public Health Events, Huazhong University of Science and Technology, Wuhan, China
| | - Lin Ding
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaodong Li
- Hepatic Disease Institute, Hubei Key Laboratory of Theoretical and Applied Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China
- Hubei Provincial Academy of Traditional Chinese Medicine, Wuhan, China
| | - Siyang Liu
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Fanjun Cheng
- Department of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qing He
- The Third People's Hospital of Shenzhen, National Clinical Research Center for Infectious Disease, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Mingzhong Xiao
- Hepatic Disease Institute, Hubei Key Laboratory of Theoretical and Applied Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China
- Hubei Provincial Academy of Traditional Chinese Medicine, Wuhan, China
| | - Ping Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Medical Center for Major Public Health Events, Huazhong University of Science and Technology, Wuhan, China
| | - Hongyan Hou
- National Medical Center for Major Public Health Events, Huazhong University of Science and Technology, Wuhan, China
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Minghui Jiang
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Pinpin Long
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hao Wang
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Linlin Liu
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, China
| | - Minghan Qu
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xian Shi
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qin Jiang
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tingting Mo
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wencheng Ding
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Medical Center for Major Public Health Events, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Fu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Medical Center for Major Public Health Events, Huazhong University of Science and Technology, Wuhan, China
| | - Shi Han
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, China
| | - Xixiang Huo
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, China
| | - Yingchun Zeng
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, China
| | - Yana Zhou
- Hepatic Disease Institute, Hubei Key Laboratory of Theoretical and Applied Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China
- Hubei Provincial Academy of Traditional Chinese Medicine, Wuhan, China
| | - Qing Zhang
- Hepatic Disease Institute, Hubei Key Laboratory of Theoretical and Applied Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China
- Hubei Provincial Academy of Traditional Chinese Medicine, Wuhan, China
| | - Jia Ke
- Hepatic Disease Institute, Hubei Key Laboratory of Theoretical and Applied Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China
- Hubei Provincial Academy of Traditional Chinese Medicine, Wuhan, China
| | - Xi Xu
- Hepatic Disease Institute, Hubei Key Laboratory of Theoretical and Applied Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China
- Hubei Provincial Academy of Traditional Chinese Medicine, Wuhan, China
| | - Wei Ni
- Hepatic Disease Institute, Hubei Key Laboratory of Theoretical and Applied Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China
- Hubei Provincial Academy of Traditional Chinese Medicine, Wuhan, China
| | - Zuoyu Shao
- Hepatic Disease Institute, Hubei Key Laboratory of Theoretical and Applied Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China
- Hubei Provincial Academy of Traditional Chinese Medicine, Wuhan, China
| | - Jingzhi Wang
- Hepatic Disease Institute, Hubei Key Laboratory of Theoretical and Applied Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China
- Hubei Provincial Academy of Traditional Chinese Medicine, Wuhan, China
| | - Panhong Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zilong Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yan Jin
- Department of Emergency, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fang Zheng
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fang Wang
- The Third People's Hospital of Shenzhen, National Clinical Research Center for Infectious Disease, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Lei Liu
- The Third People's Hospital of Shenzhen, National Clinical Research Center for Infectious Disease, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Wending Li
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kang Liu
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rong Peng
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuedan Xu
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuhui Lin
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Gao
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Limei Shi
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ziyue Geng
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuanwen Mu
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Yan
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kai Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Degang Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xingjie Hao
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shanshan Cheng
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Gaokun Qiu
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huan Guo
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kezhen Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Medical Center for Major Public Health Events, Huazhong University of Science and Technology, Wuhan, China
| | - Gang Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Medical Center for Major Public Health Events, Huazhong University of Science and Technology, Wuhan, China
| | - Ziyong Sun
- National Medical Center for Major Public Health Events, Huazhong University of Science and Technology, Wuhan, China
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xihong Lin
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Department of Statistics, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xin Jin
- School of Medicine, South China University of Technology, Guangzhou, China.
| | - Feng Wang
- National Medical Center for Major Public Health Events, Huazhong University of Science and Technology, Wuhan, China.
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Chaoyang Sun
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- National Medical Center for Major Public Health Events, Huazhong University of Science and Technology, Wuhan, China.
| | - Chaolong Wang
- National Medical Center for Major Public Health Events, Huazhong University of Science and Technology, Wuhan, China.
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Ministry of Education Key Laboratory of Environment and Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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106
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Aguiar VRC, Augusto DG, Castelli EC, Hollenbach JA, Meyer D, Nunes K, Petzl-Erler ML. An immunogenetic view of COVID-19. Genet Mol Biol 2021; 44:e20210036. [PMID: 34436508 PMCID: PMC8388242 DOI: 10.1590/1678-4685-gmb-2021-0036] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 06/12/2021] [Indexed: 02/06/2023] Open
Abstract
Meeting the challenges brought by the COVID-19 pandemic requires an interdisciplinary approach. In this context, integrating knowledge of immune function with an understanding of how genetic variation influences the nature of immunity is a key challenge. Immunogenetics can help explain the heterogeneity of susceptibility and protection to the viral infection and disease progression. Here, we review the knowledge developed so far, discussing fundamental genes for triggering the innate and adaptive immune responses associated with a viral infection, especially with the SARS-CoV-2 mechanisms. We emphasize the role of the HLA and KIR genes, discussing what has been uncovered about their role in COVID-19 and addressing methodological challenges of studying these genes. Finally, we comment on questions that arise when studying admixed populations, highlighting the case of Brazil. We argue that the interplay between immunology and an understanding of genetic associations can provide an important contribution to our knowledge of COVID-19.
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Affiliation(s)
- Vitor R. C. Aguiar
- Universidade de São Paulo, Departamento de Genética e Biologia
Evolutiva, São Paulo, SP, Brazil
| | - Danillo G. Augusto
- University of California, UCSF Weill Institute for Neurosciences,
Department of Neurology, San Francisco, CA, USA
- Universidade Federal do Paraná, Departamento de Genética, Curitiba,
PR, Brazil
| | - Erick C. Castelli
- Universidade Estadual Paulista, Faculdade de Medicina de Botucatu,
Departamento de Patologia, Botucatu, SP, Brazil
| | - Jill A. Hollenbach
- University of California, UCSF Weill Institute for Neurosciences,
Department of Neurology, San Francisco, CA, USA
| | - Diogo Meyer
- Universidade de São Paulo, Departamento de Genética e Biologia
Evolutiva, São Paulo, SP, Brazil
| | - Kelly Nunes
- Universidade de São Paulo, Departamento de Genética e Biologia
Evolutiva, São Paulo, SP, Brazil
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107
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Colona VL, Vasiliou V, Watt J, Novelli G, Reichardt JKV. Update on human genetic susceptibility to COVID-19: susceptibility to virus and response. Hum Genomics 2021; 15:57. [PMID: 34429158 PMCID: PMC8384585 DOI: 10.1186/s40246-021-00356-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Vito Luigi Colona
- Department of Biomedicine and Prevention, "Tor Vergata" University of Rome, 00133, Rome, Italy
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, USA
| | - Jessica Watt
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Smithfield, QLD, Australia
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, "Tor Vergata" University of Rome, 00133, Rome, Italy
- IRCCS Neuromed, Pozzilli, IS, Italy
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, NV, 89557, USA
| | - Juergen K V Reichardt
- Australian Institute of Tropical Health and Medicine, James Cook University, Smithfield, QLD, 4878, Australia.
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108
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Meng Z, Guo S, Zhou Y, Li M, Wang M, Ying B. Applications of laboratory findings in the prevention, diagnosis, treatment, and monitoring of COVID-19. Signal Transduct Target Ther 2021; 6:316. [PMID: 34433805 PMCID: PMC8386162 DOI: 10.1038/s41392-021-00731-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 07/21/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
The worldwide pandemic of coronavirus disease 2019 (COVID-19) presents us with a serious public health crisis. To combat the virus and slow its spread, wider testing is essential. There is a need for more sensitive, specific, and convenient detection methods of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Advanced detection can greatly improve the ability and accuracy of the clinical diagnosis of COVID-19, which is conducive to the early suitable treatment and supports precise prophylaxis. In this article, we combine and present the latest laboratory diagnostic technologies and methods for SARS-CoV-2 to identify the technical characteristics, considerations, biosafety requirements, common problems with testing and interpretation of results, and coping strategies of commonly used testing methods. We highlight the gaps in current diagnostic capacity and propose potential solutions to provide cutting-edge technical support to achieve a more precise diagnosis, treatment, and prevention of COVID-19 and to overcome the difficulties with the normalization of epidemic prevention and control.
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Affiliation(s)
- Zirui Meng
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Shuo Guo
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Yanbing Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Mengjiao Li
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Minjin Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China.
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109
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Angiotensin-Converting Enzyme 2 (ACE2) in the Context of Respiratory Diseases and Its Importance in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection. Pharmaceuticals (Basel) 2021; 14:ph14080805. [PMID: 34451902 PMCID: PMC8398530 DOI: 10.3390/ph14080805] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/02/2021] [Accepted: 08/11/2021] [Indexed: 12/14/2022] Open
Abstract
Angiotensin-Converting Enzyme 2 (ACE2) is an 805 amino acid protein encoded by the ACE2 gene expressed in various human cells, especially in those located in the epithelia. The primary function of ACE2 is to produce angiotensin (1–7) from angiotensin II (Ang II). The current research has described the importance of ACE2 and Ang (1–7) in alternative routes of the renin-angiotensin system (RAS) that promote the downregulation of fibrosis, inflammation, and oxidative stress processes in a great variety of diseases, such as hypertension, acute lung injury, liver cirrhosis, and kidney abnormalities. Investigations into the recent outbreak of the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have revealed the importance of ACE2 during infection and its role in recognizing viral binding proteins through interactions with specific amino acids of this enzyme. Additionally, the ACE2 expression in several organs has allowed us to understand the clinical picture related to the infection caused by SARS-CoV-2. This review aims to provide context for the functions and importance of ACE2 with regards to SARS-CoV-2 in the general clinical aspect and its impact on other diseases, especially respiratory diseases.
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110
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Migliorini F, Torsiello E, Spiezia F, Oliva F, Tingart M, Maffulli N. Association between HLA genotypes and COVID-19 susceptibility, severity and progression: a comprehensive review of the literature. Eur J Med Res 2021; 26:84. [PMID: 34344463 PMCID: PMC8329616 DOI: 10.1186/s40001-021-00563-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/27/2021] [Indexed: 01/08/2023] Open
Abstract
The COVID-19 pandemic has markedly impacted on cultural, political, and economic structures all over the world. Several aspects of its pathogenesis and related clinical consequences have not yet been elucidated. Infection rates, as well morbidity and mortality differed within countries. It is intriguing for scientists to understand how patient genetics may influence the outcome of the condition, to clarify which aspects could be related the clinical variability of SARS-CoV-2 disease. We reviewed the studies exploring the role of human leukocyte antigens (HLA) genotypes on individual responses to SARS-CoV-2 infection and/or progression, discussing also the contribution of the immunological patterns MHC-related. In March 2021, the main online databases were accessed. All the articles that investigated the possible association between the HLA genotypes and related polymorphisms with susceptibility, severity and progression of COVID-19 were considered. Although both genetic and environmental factors are certainly expected to influence the susceptibility to or protection of individuals, the HLA and related polymorphisms can influence susceptibility, progression and severity of SARS-CoV-2 infection. The crucial role played by HLA molecules in the immune response, especially through pathogen-derived peptide presentation, and the huge molecular variability of HLA alleles in the human populations could be responsible for the different rates of infection and the different patients following COVID-19 infection.
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Affiliation(s)
- Filippo Migliorini
- Department of Orthopaedic and Trauma Surgery, RWTH University Hospital, Pauwelsstraße 30, 52074, Aachen, Germany.
| | - Ernesto Torsiello
- Department of Medicine, Surgery and Dentistry, University of Salerno, Via S. Allende, 84081, Baronissi, SA, Italy
| | - Filippo Spiezia
- Ospedale San Carlo Potenza, Via Potito Petrone, 85100, Potenza, Italy
| | - Francesco Oliva
- Department of Medicine, Surgery and Dentistry, University of Salerno, Via S. Allende, 84081, Baronissi, SA, Italy
| | - Markus Tingart
- Department of Orthopaedic and Trauma Surgery, RWTH University Hospital, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Nicola Maffulli
- Department of Medicine, Surgery and Dentistry, University of Salerno, Via S. Allende, 84081, Baronissi, SA, Italy
- Faculty of Medicine, School of Pharmacy and Bioengineering, Keele University, Thornburrow Drive, Stoke on Trent, England
- Barts and the London School of Medicine and Dentistry, Centre for Sports and Exercise Medicine, Mile End Hospital, Queen Mary University of London, 275 Bancroft Road, London, E1 4DG, England
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111
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De Marco R, Faria TC, Mine KL, Cristelli M, Medina‐Pestana JO, Tedesco‐Silva H, Gerbase‐DeLima M. HLA-A homozygosis is associated with susceptibility to COVID-19. HLA 2021; 98:122-131. [PMID: 34165257 PMCID: PMC8446943 DOI: 10.1111/tan.14349] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/01/2021] [Accepted: 06/14/2021] [Indexed: 12/11/2022]
Abstract
The purpose of this single center retrospective study was to investigate the relationship between HLA and ABO polymorphisms and COVID-19 susceptibility and severity in kidney transplant recipients. It included 720 recipients who had COVID-19 and 1680 controls composed by recipients in follow-up who did not contact the transplantation center for COVID-19 symptoms, up to the moment of their inclusion in the study. HLA-A, -B, and -DRB1 allele groups and ABO frequencies were compared between recipients with COVID-19 (all cases, or separately mild/moderate and severe disease) and controls. The HLA association study was conducted in two case-control series and only associations that showed a p-value <0.05 in both series were considered. No HLA association regarding COVID-19 occurrence or severity met this criterion. Homozygosity at HLA-A locus was associated with COVID-19 susceptibility (odds ratio 1.4) but not severity. Blood groups A and O were associated with susceptibility and resistance to COVID-19, respectively. COVID-19 severity was associated only with older age and cardiac disease, in a multivariate analysis. We conclude that an influence of HLA on COVID-19 susceptibility is supported by the association with homozygosity at HLA-A locus but that there is no evidence for a role of any particular HLA-A, -B, or -DRB1 polymorphism. Thus, we suggest that what matters is the overall capability of an individual's HLA molecules to present SARS-CoV-2 peptides to T cells, a factor that might have a great influence on the breadth of the immune response.
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Affiliation(s)
- Renato De Marco
- Instituto de ImunogenéticaAssociação Fundo de Incentivo à PesquisaSão PauloBrazil
| | - Tathyane C. Faria
- Instituto de ImunogenéticaAssociação Fundo de Incentivo à PesquisaSão PauloBrazil
| | - Karina L. Mine
- Instituto de ImunogenéticaAssociação Fundo de Incentivo à PesquisaSão PauloBrazil
| | - Marina Cristelli
- Nephrology DivisionHospital do Rim, Universidade Federal de São PauloSão PauloBrazil
| | | | - Hélio Tedesco‐Silva
- Nephrology DivisionHospital do Rim, Universidade Federal de São PauloSão PauloBrazil
| | - Maria Gerbase‐DeLima
- Instituto de ImunogenéticaAssociação Fundo de Incentivo à PesquisaSão PauloBrazil
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112
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Kotsev SV, Miteva D, Krayselska S, Shopova M, Pishmisheva-Peleva M, Stanilova SA, Velikova T. Hypotheses and facts for genetic factors related to severe COVID-19. World J Virol 2021; 10:137-155. [PMID: 34367930 PMCID: PMC8316875 DOI: 10.5501/wjv.v10.i4.137] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 05/19/2021] [Accepted: 05/23/2021] [Indexed: 02/06/2023] Open
Abstract
Genome-wide association analysis allows the identification of potential candidate genes involved in the development of severe coronavirus disease 2019 (COVID-19). Hence, it seems that genetics matters here, as well. Nevertheless, the virus's nature, including its RNA structure, determines the rate of mutations leading to new viral strains with all epidemiological and clinical consequences. Given these observations, we herein comment on the current hypotheses about the possible role of the genes in association with COVID-19 severity. We discuss some of the major candidate genes that have been identified as potential genetic factors associated with the COVID-19 severity and infection susceptibility: HLA, ABO, ACE2, TLR7, ApoE, TYK2, OAS, DPP9, IFNAR2, CCR2, etc. Further study of genes and genetic variants will be of great benefit for the prevention and assessment of the individual risk and disease severity in different populations. These scientific data will serve as a basis for the development of clinically applicable diagnostic and prognostic tests for patients at high risk of COVID-19.
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Affiliation(s)
- Stanislav Vasilev Kotsev
- Department of Infectious Diseases, Pazardzhik Multiprofile Hospital for Active Treatment, Pazardzhik 4400, Bulgaria
| | - Dimitrina Miteva
- Department of Genetics, Sofia University “St. Kliment Ohridski”, Sofia 1000, Bulgaria
| | | | - Martina Shopova
- Department of Infectious Diseases, Pazardzhik Multiprofile Hospital for Active Treatment, Pazardzhik 4400, Bulgaria
| | - Maria Pishmisheva-Peleva
- Department of Infectious Diseases, Pazardzhik Multiprofile Hospital for Active Treatment, Pazardzhik 4400, Bulgaria
| | - Spaska Angelova Stanilova
- Department of Molecular Biology, Immunology and Medical Genetics, Medical Faculty, Trakia University, Stara Zagora 6000, Bulgaria
| | - Tsvetelina Velikova
- Department of Clinical Immunology, University Hospital Lozenetz, Sofia 1407, Bulgaria
- Medical Faculty, Sofia University “St. Kliment Ohridski”, Sofia 1407, Bulgaria
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113
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Nikonova AA, Faizuloev EB, Gracheva AV, Isakov IY, Zverev VV. Genetic Diversity and Evolution of the Biological Features of the Pandemic SARS-CoV-2. Acta Naturae 2021; 13:77-88. [PMID: 34707899 PMCID: PMC8526184 DOI: 10.32607/actanaturae.11337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/13/2021] [Indexed: 01/08/2023] Open
Abstract
The new coronavirus infection (COVID-19) represents a challenge for global health. Since the outbreak began, the number of confirmed cases has exceeded 117 million, with more than 2.6 million deaths worldwide. With public health measures aimed at containing the spread of the disease, several countries have faced a crisis in the availability of intensive care units. Currently, a large-scale effort is underway to identify the nucleotide sequences of the SARS-CoV-2 coronavirus that is an etiological agent of COVID-19. Global sequencing of thousands of viral genomes has revealed many common genetic variants, which enables the monitoring of the evolution of SARS-CoV-2 and the tracking of its spread over time. Understanding the current evolution of SARS-CoV-2 is necessary not only for a retrospective analysis of the new coronavirus infection spread, but also for the development of approaches to the therapy and prophylaxis of COVID-19. In this review, we have focused on the general characteristics of SARS-CoV-2 and COVID-19. Also, we have analyzed available publications on the genetic diversity of the virus and the relationship between the diversity and the biological properties of SARS-CoV-2, such as virulence and contagiousness.
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Affiliation(s)
- A. A. Nikonova
- Mechnikov Research Institute for Vaccines and Sera, Moscow, 105064 Russia
| | - E. B. Faizuloev
- Mechnikov Research Institute for Vaccines and Sera, Moscow, 105064 Russia
| | - A. V. Gracheva
- Mechnikov Research Institute for Vaccines and Sera, Moscow, 105064 Russia
| | - I. Yu. Isakov
- Mechnikov Research Institute for Vaccines and Sera, Moscow, 105064 Russia
| | - V. V. Zverev
- Mechnikov Research Institute for Vaccines and Sera, Moscow, 105064 Russia
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114
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Zhang S, Cooper-Knock J, Weimer AK, Harvey C, Julian TH, Wang C, Li J, Furini S, Frullanti E, Fava F, Renieri A, Pan C, Song J, Billing-Ross P, Gao P, Shen X, Timpanaro IS, Kenna KP, Davis MM, Tsao PS, Snyder MP. Common and rare variant analyses combined with single-cell multiomics reveal cell-type-specific molecular mechanisms of COVID-19 severity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.06.15.21258703. [PMID: 34189540 PMCID: PMC8240695 DOI: 10.1101/2021.06.15.21258703] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The determinants of severe COVID-19 in non-elderly adults are poorly understood, which limits opportunities for early intervention and treatment. Here we present novel machine learning frameworks for identifying common and rare disease-associated genetic variation, which outperform conventional approaches. By integrating single-cell multiomics profiling of human lungs to link genetic signals to cell-type-specific functions, we have discovered and validated over 1,000 risk genes underlying severe COVID-19 across 19 cell types. Identified risk genes are overexpressed in healthy lungs but relatively downregulated in severely diseased lungs. Genetic risk for severe COVID-19, within both common and rare variants, is particularly enriched in natural killer (NK) cells, which places these immune cells upstream in the pathogenesis of severe disease. Mendelian randomization indicates that failed NKG2D-mediated activation of NK cells leads to critical illness. Network analysis further links multiple pathways associated with NK cell activation, including type-I-interferon-mediated signalling, to severe COVID-19. Our rare variant model, PULSE, enables sensitive prediction of severe disease in non-elderly patients based on whole-exome sequencing; individualized predictions are accurate independent of age and sex, and are consistent across multiple populations and cohorts. Risk stratification based on exome sequencing has the potential to facilitate post-exposure prophylaxis in at-risk individuals, potentially based around augmentation of NK cell function. Overall, our study characterizes a comprehensive genetic landscape of COVID-19 severity and provides novel insights into the molecular mechanisms of severe disease, leading to new therapeutic targets and sensitive detection of at-risk individuals.
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115
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Tadić B, Melnik R. Microscopic dynamics modeling unravels the role of asymptomatic virus carriers in SARS-CoV-2 epidemics at the interplay between biological and social factors. Comput Biol Med 2021; 133:104422. [PMID: 33930762 PMCID: PMC8078086 DOI: 10.1016/j.compbiomed.2021.104422] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 12/25/2022]
Abstract
The recent experience of SARS-CoV-2 epidemics spreading revealed the importance of passive forms of infection transmissions. Apart from the virus survival outside the host, the latent infection transmissions caused by asymptomatic and presymptomatic hosts represent major challenges for controlling the epidemics. In this regard, social mixing and various biological factors play their subtle, but often critical, role. For example, a life-threatening condition may result in the infection contracted from an asymptomatic virus carrier. Here, we use a new recently developed microscopic agent-based modelling framework to shed light on the role of asymptomatic hosts and unravel the interplay between the biological and social factors of these nonlinear stochastic processes at high temporal resolution. The model accounts for each human actor's susceptibility and the virus survival time, as well as traceability along the infection path. These properties enable an efficient dissection of the infection events caused by asymptomatic carriers from those which involve symptomatic hosts before they develop symptoms and become removed to a controlled environment. Consequently, we assess how their relative proportions in the overall infection curve vary with changing model parameters. Our results reveal that these proportions largely depend on biological factors in the process, specifically, the virus transmissibility and the critical threshold for developing symptoms, which can be affected by the virus pathogenicity. Meanwhile, social participation activity is crucial for the overall infection level, further modulated by the virus transmissibility.
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Affiliation(s)
- Bosiljka Tadić
- Department of Theoretical Physics, Jožef Stefan Institute, Jamova 39, Ljubljana, Slovenia; Complexity Science Hub, Josefstaedter Strasse 39, Vienna, Austria.
| | - Roderick Melnik
- MS2Discovery Interdisciplinary Research Institute, M2NeT Laboratory and Department of Mathematics, Wilfrid Laurier University, Waterloo, ON, Canada; BCAM - Basque Center for Applied Mathematics, Alameda de Mazarredo 14, E-48009, Bilbao, Spain
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116
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Dukhinova M, Kokinos E, Kuchur P, Komissarov A, Shtro A. Macrophage-derived cytokines in pneumonia: Linking cellular immunology and genetics. Cytokine Growth Factor Rev 2021; 59:46-61. [PMID: 33342718 PMCID: PMC8035975 DOI: 10.1016/j.cytogfr.2020.11.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 12/16/2022]
Abstract
Macrophages represent the first line of anti-pathogen defense - they encounter invading pathogens to perform the phagocytic activity, to deliver the plethora of pro- and anti-inflammatory cytokines, and to shape the tissue microenvironment. Throughout pneumonia course, alveolar macrophages and infiltrated blood monocytes produce increasing cytokine amounts, which activates the antiviral/antibacterial immunity but can also provoke the risk of the so-called cytokine "storm" and normal tissue damage. Subsequently, the question of how the cytokine spectrum is shaped and balanced in the pneumonia context remains a hot topic in medical immunology, particularly in the COVID19 pandemic era. The diversity in cytokine profiles, involved in pneumonia pathogenesis, is determined by the variations in cytokine-receptor interactions, which may lead to severe cytokine storm and functional decline of particular tissues and organs, for example, cardiovascular and respiratory systems. Cytokines and their receptors form unique profiles in individual patients, depending on the (a) microenvironmental context (comorbidities and associated treatment), (b) lung monocyte heterogeneity, and (c) genetic variations. These multidisciplinary strategies can be proactively considered beforehand and during the pneumonia course and potentially allow the new age of personalized immunotherapy.
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Affiliation(s)
- Marina Dukhinova
- International Institute "Solution Chemistry of Advanced Materials and Technology", ITMO University, St. Petersburg, Russia.
| | - Elena Kokinos
- International Institute "Solution Chemistry of Advanced Materials and Technology", ITMO University, St. Petersburg, Russia
| | - Polina Kuchur
- International Institute "Solution Chemistry of Advanced Materials and Technology", ITMO University, St. Petersburg, Russia
| | - Alexey Komissarov
- International Institute "Solution Chemistry of Advanced Materials and Technology", ITMO University, St. Petersburg, Russia
| | - Anna Shtro
- International Institute "Solution Chemistry of Advanced Materials and Technology", ITMO University, St. Petersburg, Russia; Department of Chemotherapy, Smorodintsev Research Institute of Influenza, St. Petersburg, Russia
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117
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Yildirim Z, Sahin OS, Yazar S, Bozok Cetintas V. Genetic and epigenetic factors associated with increased severity of Covid-19. Cell Biol Int 2021; 45:1158-1174. [PMID: 33590936 PMCID: PMC8014716 DOI: 10.1002/cbin.11572] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 02/14/2021] [Indexed: 01/07/2023]
Abstract
Since December 2019, a new form of severe acute respiratory syndrome (SARS) from a novel strain of coronavirus (SARS coronavirus 2 [SARS-CoV-2]) has been spreading worldwide. The disease caused by SARS-CoV-2 was named Covid-19 and declared as a pandemic by the World Health Organization in March 2020. Clinical symptoms of Covid-19 range from common cold to more severe disease defined as pneumonia, hypoxia, and severe respiratory distress. In the next stage, disease can become more critical with respiratory failure, sepsis, septic shock, and/or multiorgan failure. Outcomes of Covid-19 indicate large gaps between the male-female and the young-elder groups. Several theories have been proposed to explain variations, such as gender, age, comorbidity, and genetic factors. It is likely that mixture of genetic and nongenetic factors interplays between virus and host genetics and determines the severity of disease outcome. In this review, we aimed to summarize current literature in terms of potential host genetic and epigenetic factors that associated with increased severity of Covid-19. Several studies indicated that the genetic variants of the SARS-CoV-2 entry mechanism-related (angiotensin-converting enzymes, transmembrane serine protease-2, furin) and host innate immune response-related genes (interferons [IFNs], interleukins, toll-like receptors), and human leukocyte antigen, ABO, 3p21.31, and 9q34.2 loci are critical host determinants related to Covid-19 severity. Epigenetic mechanisms also affect Covid-19 outcomes by regulating IFN signaling, angiotensin-converting enzyme-2, and immunity-related genes that particularly escape from X chromosome inactivation. Enhanced understanding of host genetic and epigenetic factors and viral interactions of SARS-CoV-2 is critical for improved prognostic tools and innovative therapeutics.
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Affiliation(s)
- Zafer Yildirim
- Department of Medical Biology, Faculty of MedicineEge UniversityIzmirTurkey
| | - Oyku Semahat Sahin
- Department of Medical Biology, Faculty of MedicineEge UniversityIzmirTurkey
| | - Seyhan Yazar
- Garvan‐Weizmann Centre for Cellular GenomicsGarvan Institute of Medical ResearchSydneyNew South WalesAustralia
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118
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MHC Haplotyping of SARS-CoV-2 Patients: HLA Subtypes Are Not Associated with the Presence and Severity of COVID-19 in the Israeli Population. J Clin Immunol 2021; 41:1154-1161. [PMID: 34050837 PMCID: PMC8164405 DOI: 10.1007/s10875-021-01071-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/19/2021] [Indexed: 02/07/2023]
Abstract
HLA haplotypes were found to be associated with increased risk for viral infections or disease severity in various diseases, including SARS. Several genetic variants are associated with COVID-19 severity. Studies have proposed associations, based on a very small sample and a large number of tested HLA alleles, but no clear association between HLA and COVID-19 incidence or severity has been reported. We conducted a large-scale HLA analysis of Israeli individuals who tested positive for SARS-CoV-2 infection by PCR. Overall, 72,912 individuals with known HLA haplotypes were included in the study, of whom 6413 (8.8%) were found to have SARS-CoV-2 by PCR. A total of 20,937 subjects were of Ashkenazi origin (at least 2/4 grandparents). One hundred eighty-one patients (2.8% of the infected) were hospitalized due to the disease. None of the 66 most common HLA loci (within the five HLA subgroups: A, B, C, DQB1, DRB1) was found to be associated with SARS-CoV-2 infection or hospitalization in the general Israeli population. Similarly, no association was detected in the Ashkenazi Jewish subset. Moreover, no association was found between heterozygosity in any of the HLA loci and either infection or hospitalization. We conclude that HLA haplotypes are not a major risk/protecting factor among the Israeli population for SARS-CoV-2 infection or severity. Our results suggest that if any HLA association exists with the disease it is very weak, and of limited effect on the pandemic.
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119
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Dubé MP, Lemaçon A, Barhdadi A, Lemieux Perreault LP, Oussaïd E, Asselin G, Provost S, Sun M, Sandoval J, Legault MA, Mongrain I, Dubois A, Valois D, Dedelis E, Lousky J, Choi J, Goulet E, Savard C, Chicoine LM, Cossette M, Chabot-Blanchet M, Guertin MC, de Denus S, Bouabdallaoui N, Marchand R, Bassevitch Z, Nozza A, Gaudet D, L'Allier PL, Hussin J, Boivin G, Busseuil D, Tardif JC. Genetics of symptom remission in outpatients with COVID-19. Sci Rep 2021; 11:10847. [PMID: 34035401 PMCID: PMC8149390 DOI: 10.1038/s41598-021-90365-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/11/2021] [Indexed: 01/09/2023] Open
Abstract
We conducted a genome-wide association study of time to remission of COVID-19 symptoms in 1723 outpatients with at least one risk factor for disease severity from the COLCORONA clinical trial. We found a significant association at 5p13.3 (rs1173773; P = 4.94 × 10-8) near the natriuretic peptide receptor 3 gene (NPR3). By day 15 of the study, 44%, 54% and 59% of participants with 0, 1, or 2 copies of the effect allele respectively, had symptom remission. In 851 participants not treated with colchicine (placebo), there was a significant association at 9q33.1 (rs62575331; P = 2.95 × 10-8) in interaction with colchicine (P = 1.19 × 10-5) without impact on risk of hospitalisations, highlighting a possibly shared mechanistic pathway. By day 15 of the study, 46%, 62% and 64% of those with 0, 1, or 2 copies of the effect allele respectively, had symptom remission. The findings need to be replicated and could contribute to the biological understanding of COVID-19 symptom remission.
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Affiliation(s)
- Marie-Pierre Dubé
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada. .,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada. .,Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, Canada.
| | - Audrey Lemaçon
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada.,Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Amina Barhdadi
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada
| | - Louis-Philippe Lemieux Perreault
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada
| | - Essaïd Oussaïd
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada
| | - Géraldine Asselin
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada
| | - Sylvie Provost
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada
| | - Maxine Sun
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada.,Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Johanna Sandoval
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada
| | - Marc-André Legault
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada.,Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Ian Mongrain
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada
| | - Anick Dubois
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada
| | - Diane Valois
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada
| | - Emma Dedelis
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada
| | - Jennifer Lousky
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada
| | - Julie Choi
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada
| | - Elisabeth Goulet
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada
| | - Christiane Savard
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada
| | - Lea-Mei Chicoine
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada
| | - Mariève Cossette
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Montreal Health Innovations Coordinating Centre, Montreal, Canada
| | - Malorie Chabot-Blanchet
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Montreal Health Innovations Coordinating Centre, Montreal, Canada
| | - Marie-Claude Guertin
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Montreal Health Innovations Coordinating Centre, Montreal, Canada
| | - Simon de Denus
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada.,Faculty of Pharmacy, Université de Montréal, Montreal, Canada
| | | | - Richard Marchand
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada
| | - Zohar Bassevitch
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Montreal Health Innovations Coordinating Centre, Montreal, Canada
| | - Anna Nozza
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Montreal Health Innovations Coordinating Centre, Montreal, Canada
| | - Daniel Gaudet
- Ecogene-21 and Department of Medicine, Université de Montréal, Chicoutimi, Canada
| | | | - Julie Hussin
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, Canada.,Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Guy Boivin
- Centre Hospitalier de l'Université Laval, Quebec City, Canada
| | - David Busseuil
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada
| | - Jean-Claude Tardif
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada. .,Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, Canada.
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120
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Wulandari L, Hamidah B, Pakpahan C, Damayanti NS, Kurniati ND, Adiatmaja CO, Wigianita MR, Soedarsono, Husada D, Tinduh D, Prakoeswa CRS, Endaryanto A, Puspaningsih NNT, Mori Y, Lusida MI, Shimizu K, Oceandy D. Initial study on TMPRSS2 p.Val160Met genetic variant in COVID-19 patients. Hum Genomics 2021; 15:29. [PMID: 34001248 PMCID: PMC8127183 DOI: 10.1186/s40246-021-00330-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/04/2021] [Indexed: 11/19/2022] Open
Abstract
Background Coronavirus disease 2019 (COVID-19) is a global health problem that causes millions of deaths worldwide. The clinical manifestation of COVID-19 widely varies from asymptomatic infection to severe pneumonia and systemic inflammatory disease. It is thought that host genetic variability may affect the host’s response to the virus infection and thus cause severity of the disease. The SARS-CoV-2 virus requires interaction with its receptor complex in the host cells before infection. The transmembrane protease serine 2 (TMPRSS2) has been identified as one of the key molecules involved in SARS-CoV-2 virus receptor binding and cell invasion. Therefore, in this study, we investigated the correlation between a genetic variant within the human TMPRSS2 gene and COVID-19 severity and viral load. Results We genotyped 95 patients with COVID-19 hospitalised in Dr Soetomo General Hospital and Indrapura Field Hospital (Surabaya, Indonesia) for the TMPRSS2 p.Val160Met polymorphism. Polymorphism was detected using a TaqMan assay. We then analysed the association between the presence of the genetic variant and disease severity and viral load. We did not observe any correlation between the presence of TMPRSS2 genetic variant and the severity of the disease. However, we identified a significant association between the p.Val160Met polymorphism and the SARS-CoV-2 viral load, as estimated by the Ct value of the diagnostic nucleic acid amplification test. Furthermore, we observed a trend of association between the presence of the C allele and the mortality rate in patients with severe COVID-19. Conclusion Our data indicate a possible association between TMPRSS2 p.Val160Met polymorphism and SARS-CoV-2 infectivity and the outcome of COVID-19. Supplementary Information The online version contains supplementary material available at 10.1186/s40246-021-00330-7.
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Affiliation(s)
- Laksmi Wulandari
- Department of Pulmonology and Respiratory Medicine, Faculty of Medicine, Universitas Airlangga/Dr Soetomo General Academic Hospital, Surabaya, Indonesia
| | - Berliana Hamidah
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Cennikon Pakpahan
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia.,Andrology Program, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
| | | | - Neneng Dewi Kurniati
- Department of Medical Microbiology, Faculty of Medicine, Universitas Airlangga/Clinical Microbiology Unit, Central Laboratory Installation, Dr Soetomo General Academic Hospital, Surabaya, Indonesia
| | - Christophorus Oetama Adiatmaja
- Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia.,Clinical Pathology Program, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
| | | | - Soedarsono
- Department of Pulmonology and Respiratory Medicine, Faculty of Medicine, Universitas Airlangga/Dr Soetomo General Academic Hospital, Surabaya, Indonesia
| | - Dominicus Husada
- Department of Child Health, Faculty of Medicine, Universitas Airlangga/Dr Soetomo General Academic Hospital, Surabaya, Indonesia
| | - Damayanti Tinduh
- Department of Physical Medicine and Rehabilitation, Faculty of Medicine, Universitas Airlangga/Dr Soetomo General Academic Hospital, Surabaya, Indonesia
| | - Cita Rosita Sigit Prakoeswa
- Department of Dermatology Venerology, Faculty of Medicine, Universitas Airlangga/Dr. Soetomo General Academic Hospital, Surabaya, Indonesia
| | - Anang Endaryanto
- Department of Child Health, Faculty of Medicine, Universitas Airlangga/Dr Soetomo General Academic Hospital, Surabaya, Indonesia
| | - Ni Nyoman Tri Puspaningsih
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia.,Laboratory of Proteomic, University CoE-Research Center for Bio-Molecule Engineering, Universitas Airlangga, Surabaya, Indonesia
| | - Yasuko Mori
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kusunoki-cho, Chuo-ku, Kobe, Japan
| | - Maria Inge Lusida
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.,Department of Microbiology, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Kazufumi Shimizu
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kusunoki-cho, Chuo-ku, Kobe, Japan.,CRC-ERID, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Delvac Oceandy
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK.
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121
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Novelli G, Biancolella M, Mehrian-Shai R, Colona VL, Brito AF, Grubaugh ND, Vasiliou V, Luzzatto L, Reichardt JKV. COVID-19 one year into the pandemic: from genetics and genomics to therapy, vaccination, and policy. Hum Genomics 2021; 15:27. [PMID: 33966626 PMCID: PMC8107019 DOI: 10.1186/s40246-021-00326-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/15/2021] [Indexed: 12/14/2022] Open
Abstract
COVID-19 has engulfed the world and it will accompany us all for some time to come. Here, we review the current state at the milestone of 1 year into the pandemic, as declared by the WHO (World Health Organization). We review several aspects of the on-going pandemic, focusing first on two major topics: viral variants and the human genetic susceptibility to disease severity. We then consider recent and exciting new developments in therapeutics, such as monoclonal antibodies, and in prevention strategies, such as vaccines. We also briefly discuss how advances in basic science and in biotechnology, under the threat of a worldwide emergency, have accelerated to an unprecedented degree of the transition from the laboratory to clinical applications. While every day we acquire more and more tools to deal with the on-going pandemic, we are aware that the path will be arduous and it will require all of us being community-minded. In this respect, we lament past delays in timely full investigations, and we call for bypassing local politics in the interest of humankind on all continents.
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Affiliation(s)
- Giuseppe Novelli
- Department of Biomedicine and Prevention, "Tor Vergata" University of Rome, 00133, Rome, Italy.
- IRCCS Neuromed, Pozzilli, IS, Italy.
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, NV, 89557, USA.
| | | | - Ruty Mehrian-Shai
- Pediatric Hemato-Oncology, Sheba Medical Center, Tel Hashomer, Israel
| | - Vito Luigi Colona
- Department of Biomedicine and Prevention, "Tor Vergata" University of Rome, 00133, Rome, Italy
| | - Anderson F Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Lucio Luzzatto
- Haematology, Muhimbili University of Health and Allied Sciences, Dar-es Salaam, Tanzania
| | - Juergen K V Reichardt
- Australian Institute of Tropical Health and Medicine, James Cook University, Smithfield, Queensland, 4878, Australia
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122
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Andolfo I, Russo R, Lasorsa VA, Cantalupo S, Rosato BE, Bonfiglio F, Frisso G, Abete P, Cassese GM, Servillo G, Esposito G, Gentile I, Piscopo C, Villani R, Fiorentino G, Cerino P, Buonerba C, Pierri B, Zollo M, Iolascon A, Capasso M. Common variants at 21q22.3 locus influence MX1 and TMPRSS2 gene expression and susceptibility to severe COVID-19. iScience 2021; 24:102322. [PMID: 33748697 PMCID: PMC7968217 DOI: 10.1016/j.isci.2021.102322] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/15/2021] [Accepted: 03/15/2021] [Indexed: 12/15/2022] Open
Abstract
The established risk factors of coronavirus disease 2019 (COVID-19) are advanced age, male sex, and comorbidities, but they do not fully explain the wide spectrum of disease manifestations. Genetic factors implicated in the host antiviral response provide for novel insights into its pathogenesis. We performed an in-depth genetic analysis of chromosome 21 exploiting the genome-wide association study data, including 6,406 individuals hospitalized for COVID-19 and 902,088 controls with European genetic ancestry from the COVID-19 Host Genetics Initiative. We found that five single nucleotide polymorphisms within TMPRSS2 and near MX1 gene show associations with severe COVID-19. The minor alleles of the five single nucleotide polymorphisms (SNPs) correlated with a reduced risk of developing severe COVID-19 and high level of MX1 expression in blood. Our findings demonstrate that host genetic factors can influence the different clinical presentations of COVID-19 and that MX1 could be a potential therapeutic target.
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Affiliation(s)
- Immacolata Andolfo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples, Federico II, 80145 Naples, Italy
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Napoli, Italy
| | - Roberta Russo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples, Federico II, 80145 Naples, Italy
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Napoli, Italy
| | - Vito Alessandro Lasorsa
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples, Federico II, 80145 Naples, Italy
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Napoli, Italy
| | - Sueva Cantalupo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples, Federico II, 80145 Naples, Italy
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Napoli, Italy
| | - Barbara Eleni Rosato
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples, Federico II, 80145 Naples, Italy
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Napoli, Italy
| | - Ferdinando Bonfiglio
- Dipartimento di Ingegneria chimica, dei Materiali e della Produzione industriale, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Giulia Frisso
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples, Federico II, 80145 Naples, Italy
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Napoli, Italy
| | - Pasquale Abete
- COVID Hospital, P.O.S. Anna e SS. Madonna della Neve di Boscotrecase, Ospedali Riuniti Area Vesuviana, Napoli, Italy
| | - Gian Marco Cassese
- COVID Hospital, P.O.S. Anna e SS. Madonna della Neve di Boscotrecase, Ospedali Riuniti Area Vesuviana, Napoli, Italy
| | - Giuseppe Servillo
- Dipartimento di Neuroscienze e Scienze riproduttive ed odontostomatologiche, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Gabriella Esposito
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples, Federico II, 80145 Naples, Italy
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Napoli, Italy
| | - Ivan Gentile
- Dipartimento di Medicina clinica e Chirurgia, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Carmelo Piscopo
- Medical and Laboratory Genetics Unit, A.O.R.N. ‘Antonio Cardarelli’, Napoli, Italy
| | - Romolo Villani
- Poison Centre, A.O.R.N. ‘Antonio Cardarelli’, Napoli, Italy
| | | | - Pellegrino Cerino
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Napoli, Italy
| | - Carlo Buonerba
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Napoli, Italy
| | - Biancamaria Pierri
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Napoli, Italy
- Dipartimento di Medicina, Chirurgia e Odontoiatria "Scuola Medica Salernitana", Università di Salerno, Baronissi, Italy
| | - Massimo Zollo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples, Federico II, 80145 Naples, Italy
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Napoli, Italy
| | - Achille Iolascon
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples, Federico II, 80145 Naples, Italy
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Napoli, Italy
| | - Mario Capasso
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples, Federico II, 80145 Naples, Italy
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Napoli, Italy
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Khor SS, Omae Y, Nishida N, Sugiyama M, Kinoshita N, Suzuki T, Suzuki M, Suzuki S, Izumi S, Hojo M, Ohmagari N, Mizokami M, Tokunaga K. HLA-A*11:01:01:01, HLA-C*12:02:02:01-HLA-B*52:01:02:02, Age and Sex Are Associated With Severity of Japanese COVID-19 With Respiratory Failure. Front Immunol 2021; 12:658570. [PMID: 33968060 PMCID: PMC8100314 DOI: 10.3389/fimmu.2021.658570] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/22/2021] [Indexed: 12/21/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus causing coronavirus disease 2019 (COVID-19) was announced as an outbreak by the World Health Organization (WHO) in January 2020 and as a pandemic in March 2020. The majority of infected individuals have experienced no or only mild symptoms, ranging from fully asymptomatic cases to mild pneumonic disease. However, a minority of infected individuals develop severe respiratory symptoms. The objective of this study was to identify susceptible HLA alleles and clinical markers that can be used in risk prediction model for the early identification of severe COVID-19 among hospitalized COVID-19 patients. A total of 137 patients with mild COVID-19 (mCOVID-19) and 53 patients with severe COVID-19 (sCOVID-19) were recruited from the Center Hospital of the National Center for Global Health and Medicine (NCGM), Tokyo, Japan for the period of February–August 2020. High-resolution sequencing-based typing for eight HLA genes was performed using next-generation sequencing. In the HLA association studies, HLA-A*11:01:01:01 [Pc = 0.013, OR = 2.26 (1.27–3.91)] and HLA-C*12:02:02:01-HLA-B*52:01:01:02 [Pc = 0.020, OR = 2.25 (1.24–3.92)] were found to be significantly associated with the severity of COVID-19. After multivariate analysis controlling for other confounding factors and comorbidities, HLA-A*11:01:01:01 [P = 3.34E-03, OR = 3.41 (1.50–7.73)], age at diagnosis [P = 1.29E-02, OR = 1.04 (1.01–1.07)] and sex at birth [P = 8.88E-03, OR = 2.92 (1.31–6.54)] remained significant. The area under the curve of the risk prediction model utilizing HLA-A*11:01:01:01, age at diagnosis, and sex at birth was 0.772, with sensitivity of 0.715 and specificity of 0.717. To the best of our knowledge, this is the first article that describes associations of HLA alleles with COVID-19 at the 4-field (highest) resolution level. Early identification of potential sCOVID-19 could help clinicians prioritize medical utility and significantly decrease mortality from COVID-19.
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Affiliation(s)
- Seik-Soon Khor
- Genome Medical Science Project, National Center for Global Health and Medicine Hospital, Tokyo, Japan
| | - Yosuke Omae
- Genome Medical Science Project, National Center for Global Health and Medicine Hospital, Tokyo, Japan
| | - Nao Nishida
- Genome Medical Sciences Project, National Center for Global Health and Medicine, Ichikawa, Japan
| | - Masaya Sugiyama
- Genome Medical Sciences Project, National Center for Global Health and Medicine, Ichikawa, Japan
| | - Noriko Kinoshita
- Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, Tokyo, Japan
| | - Tetsuya Suzuki
- Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, Tokyo, Japan
| | - Michiyo Suzuki
- Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, Tokyo, Japan
| | - Satoshi Suzuki
- Biobank, National Center for Global Health and Medicine, Tokyo, Japan
| | - Shinyu Izumi
- Department of Respiratory Medicine, National Center for Global Health and Medicine Hospital, Tokyo, Japan
| | - Masayuki Hojo
- Department of Respiratory Medicine, National Center for Global Health and Medicine Hospital, Tokyo, Japan
| | - Norio Ohmagari
- Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, Tokyo, Japan
| | - Masashi Mizokami
- Genome Medical Sciences Project, National Center for Global Health and Medicine, Ichikawa, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine Hospital, Tokyo, Japan
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124
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Fricke-Galindo I, Falfán-Valencia R. Genetics Insight for COVID-19 Susceptibility and Severity: A Review. Front Immunol 2021; 12:622176. [PMID: 33868239 PMCID: PMC8047200 DOI: 10.3389/fimmu.2021.622176] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/16/2021] [Indexed: 12/15/2022] Open
Abstract
Coronavirus disease (COVID-19) presents a broad spectrum of clinical manifestations ranging from an asymptomatic to a severe clinical course. The host genetic background influence on the susceptibility and outcome of multiples infectious diseases has been previously reported. Herein, we aimed to describe relevant identified genetic variants and those potentially related to the inter-individual variability of COVID-19 susceptibility and/or severity considering the physiopathological pathway of the disease The HLA-A*25:01, -B*15:27, -B*46:01, -C*01:02, and -C*07:29 alleles have been associated with COVID-19 susceptibility; while HLA-A*02:02, -B*15:03, and -C*12:03 have been identified as low-risk alleles. Variants in cytokine genes such as IL1B, IL1R1, IL1RN, IL6, IL17A, FCGR2A, and TNF could be related to disease susceptibility and cytokine storm, and/or COVID-19 complications (e.g., venous thrombosis). Several variants in ACE2 and TMPRSS2 affecting the expression of the receptors related to COVID-19 have been associated with the disease susceptibility and risk factors. Finally, two GWAS have identified the loci 3p21.31 (LZTFL1, SLC6A20, CCR9, FYCO1, CXCR6, and XCR1) and 9q34.2 (ABO) with COVID-19 severity. Heterogeneous results in the association of genetic variants with COVID-19 susceptibility and severity were observed. The mechanism of identified risk-genes and studies in different populations are still warranted.
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Affiliation(s)
| | - Ramcés Falfán-Valencia
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
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Guilger-Casagrande M, de Barros CT, Antunes VAN, de Araujo DR, Lima R. Perspectives and Challenges in the Fight Against COVID-19: The Role of Genetic Variability. Front Cell Infect Microbiol 2021; 11:598875. [PMID: 33791232 PMCID: PMC8005637 DOI: 10.3389/fcimb.2021.598875] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 02/15/2021] [Indexed: 12/12/2022] Open
Abstract
In the last year, the advent of the COVID-19 pandemic brought a new consideration for the multidisciplinary sciences. The unknown mechanisms of infection used by SARS-CoV-2 and the absence of effective antiviral pharmacological therapy, diagnosis methods, and vaccines evoked scientific efforts on the COVID-19 outcome. In general, COVID-19 clinical features are a result of local and systemic inflammatory processes that are enhanced by some preexistent comorbidities, such as diabetes, obesity, cardiovascular, and pulmonary diseases, and biological factors, like gender and age. However, the discrepancies in COVID-19 clinical signs observed among those patients lead to investigations about the critical factors that deeply influence disease severity and death. Herein, we present the viral infection mechanisms and its consequences after blocking the angiotensin-converting enzyme 2 (ACE2) axis in different tissues and the progression of inflammatory and immunological reactions, especially the influence of genetic features on those differential clinical responses. Furthermore, we discuss the role of genotype as an essential indicator of COVID-19 susceptibility, considering the expression profiles, polymorphisms, gene identification, and epigenetic modifications of viral entry factors and their recognition, as well as the infection effects on cell signaling molecule expression, which amplifies disease severity.
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Affiliation(s)
- Mariana Guilger-Casagrande
- Institute of Science and Technology, São Paulo State University–UNESP, Sorocaba, Brazil
- Laboratory for Evaluation of the Bioactivity and Toxicology of Nanomaterials, University of Sorocaba-UNISO, Sorocaba, Brazil
| | - Cecilia T. de Barros
- Laboratory for Evaluation of the Bioactivity and Toxicology of Nanomaterials, University of Sorocaba-UNISO, Sorocaba, Brazil
| | - Vitória A. N. Antunes
- Laboratory for Evaluation of the Bioactivity and Toxicology of Nanomaterials, University of Sorocaba-UNISO, Sorocaba, Brazil
| | - Daniele R. de Araujo
- Human and Natural Sciences Center, Federal University of ABC, Santo André, Brazil
| | - Renata Lima
- Laboratory for Evaluation of the Bioactivity and Toxicology of Nanomaterials, University of Sorocaba-UNISO, Sorocaba, Brazil
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Pojero F, Candore G, Caruso C, Di Bona D, Groneberg DA, Ligotti ME, Accardi G, Aiello A. The Role of Immunogenetics in COVID-19. Int J Mol Sci 2021; 22:2636. [PMID: 33807915 PMCID: PMC7961811 DOI: 10.3390/ijms22052636] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/26/2021] [Accepted: 03/03/2021] [Indexed: 12/14/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is induced by SARS-CoV-2 and may arise as a variety of clinical manifestations, ranging from an asymptomatic condition to a life-threatening disease associated with cytokine storm, multiorgan and respiratory failure. The molecular mechanism behind such variability is still under investigation. Several pieces of experimental evidence suggest that genetic variants influencing the onset, maintenance and resolution of the immune response may be fundamental in predicting the evolution of the disease. The identification of genetic variants behind immune system reactivity and function in COVID-19 may help in the elaboration of personalized therapeutic strategies. In the frenetic look for universally shared treatment plans, those genetic variants that are common to other diseases/models may also help in addressing future research in terms of drug repurposing. In this paper, we discuss the most recent updates about the role of immunogenetics in determining the susceptibility to and the history of SARS-CoV-2 infection. We propose a narrative review of available data, speculating about lessons that we have learnt from other viral infections and immunosenescence, and discussing what kind of aspects of research should be deepened in order to improve our knowledge of how host genetic variability impacts the outcome for COVID-19 patients.
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Affiliation(s)
- Fanny Pojero
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neuroscience and Advanced Diagnostic, University of Palermo, 90134 Palermo, Italy; (F.P.); (G.C.); (M.E.L.); (G.A.)
| | - Giuseppina Candore
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neuroscience and Advanced Diagnostic, University of Palermo, 90134 Palermo, Italy; (F.P.); (G.C.); (M.E.L.); (G.A.)
| | - Calogero Caruso
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neuroscience and Advanced Diagnostic, University of Palermo, 90134 Palermo, Italy; (F.P.); (G.C.); (M.E.L.); (G.A.)
| | - Danilo Di Bona
- Department of Emergency and Organ Transplantation, University of Bari Aldo Moro, 70124 Bari, Italy;
| | - David A. Groneberg
- Institute of Occupational, Social and Environmental Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60596 Frankfurt, Germany;
| | - Mattia E. Ligotti
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neuroscience and Advanced Diagnostic, University of Palermo, 90134 Palermo, Italy; (F.P.); (G.C.); (M.E.L.); (G.A.)
| | - Giulia Accardi
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neuroscience and Advanced Diagnostic, University of Palermo, 90134 Palermo, Italy; (F.P.); (G.C.); (M.E.L.); (G.A.)
| | - Anna Aiello
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neuroscience and Advanced Diagnostic, University of Palermo, 90134 Palermo, Italy; (F.P.); (G.C.); (M.E.L.); (G.A.)
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Signorini C, Pignatti P, Coccini T. How Do Inflammatory Mediators, Immune Response and Air Pollution Contribute to COVID-19 Disease Severity? A Lesson to Learn. Life (Basel) 2021; 11:182. [PMID: 33669011 PMCID: PMC7996623 DOI: 10.3390/life11030182] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/16/2021] [Accepted: 02/21/2021] [Indexed: 02/07/2023] Open
Abstract
Inflammatory and immune processes are defensive mechanisms that aim to remove harmful agents. As a response to infections, inflammation and immune response contribute to the pathophysiological mechanisms of diseases. Coronavirus disease 2019 (COVID-19), whose underlying mechanisms remain not fully elucidated, has posed new challenges for the knowledge of pathophysiology. Chiefly, the inflammatory process and immune response appear to be unique features of COVID-19 that result in developing a hyper-inflammatory syndrome, and air pollution, the world's largest health risk factor, may partly explain the behaviour and fate of COVID-19. Understanding the mechanisms involved in the progression of COVID-19 is of fundamental importance in order to avoid the late stage of the disease, associated with a poor prognosis. Here, the role of the inflammatory and immune mediators in COVID-19 pathophysiology is discussed.
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Affiliation(s)
- Cinzia Signorini
- Department of Molecular and Developmental Medicine, University of Siena, Via Aldo Moro, 53100 Siena, Italy
| | - Patrizia Pignatti
- Allergy and Immunology Unit, Istituti Clinici Scientifici Maugeri IRCCS, 27100 Pavia, Italy;
| | - Teresa Coccini
- Laboratory of Clinical and Experimental Toxicology, Pavia Poison Centre, National Toxicology Information Centre, Toxicology Unit, Istituti Clinici Scientifici Maugeri IRCCS, 27100 Pavia, Italy;
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Hartog N, Faber W, Frisch A, Bauss J, Bupp CP, Rajasekaran S, Prokop JW. SARS-CoV-2 infection: molecular mechanisms of severe outcomes to suggest therapeutics. Expert Rev Proteomics 2021; 18:105-118. [PMID: 33779460 PMCID: PMC8022340 DOI: 10.1080/14789450.2021.1908894] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/22/2021] [Indexed: 02/06/2023]
Abstract
Introduction:The year 2020 was defined by the 29,903 base pairs of RNA that codes for the SARS-CoV-2 genome. SARS-CoV-2 infects humans to cause COVID-19, spreading from patient-to-patient yet impacts patients very divergently.Areas covered: Within this review, we address the known molecular mechanisms and supporting data for COVID-19 clinical course and pathology, clinical risk factors and molecular signatures, therapeutics of severe COVID-19, and reinfection/vaccination. Literature and published datasets were reviewed using PubMed, Google Scholar, and NCBI SRA tools. The combination of exaggerated cytokine signaling, pneumonia, NETosis, pyroptosis, thrombocytopathy, endotheliopathy, multiple organ dysfunction syndrome (MODS), and acute respiratory distress syndrome (ARDS) create a positive feedback loop of severe damage in patients with COVID-19 that impacts the entire body and may persist for months following infection. Understanding the molecular pathways of severe COVID-19 opens the door for novel therapeutic design. We summarize the current insights into pathology, risk factors, secondary infections, genetics, omics, and drugs being tested to treat severe COVID-19.Expert opinion: A growing level of support suggests the need for stronger integration of biomarkers and precision medicine to guide treatment strategies of severe COVID-19, where each patient has unique outcomes and thus require guided treatment.
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Affiliation(s)
- Nicholas Hartog
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
- Allergy & Immunology, Spectrum Health, Grand Rapids, MI, USA
| | - William Faber
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
- Department of Chemistry, Grand Rapids Community College, Grand Rapids, MI, USA
| | - Austin Frisch
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Jacob Bauss
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Caleb P Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
- Spectrum Health Medical Genetics, Grand Rapids, MI, USA
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
- Pediatric Intensive Care Unit, Helen DeVos Children’s Hospital, Grand Rapids, MI, USA
- Office of Research, Office of Research, Spectrum Health, Grand Rapids, MI, USA
| | - Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, USA
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Abstract
Currently, there are no specific and efficient vaccines or drugs for COVID-19, particularly in severe cases. A wide range of variations in the clinical symptoms of different patients attributed to genomic differences. Therefore, personalized treatments seem to play a critical role in improving these symptoms and even similar conditions. Prompted by the uncertainties in the area of COVID-19 therapies, we reviewed the published papers and concepts to gather and provide useful information to clinicians and researchers interested in personalized medicine and cell-based therapy. One novel aspect of this study focuses on the potential application of personalized medicine in treating severe cases of COVID-19. However, it is theoretical, as any real-world examples of the use of genuinely personalized medicine have not existed yet. Nevertheless, we know that stem cells, especially MSCs, have immune-modulatory effects and can be stored for future personalized medicine applications. This theory has been conjugated with some evidence that we review in the present study. Besides, we discuss the importance of personalized medicine and its possible aspects in COVID-19 treatment, then review the cell-based therapy studies for COVID-19 with a particular focus on stem cell-based therapies as a primary personalized tool medicine. However, the idea of cell-based therapy has not been accepted by several scientific communities due to some concerns of lack of satisfactory clinical studies; still, the MSCs and their clinical outcomes have been revealed the safety and potency of this therapeutic approach in several diseases, especially in the immune-mediated inflammatory diseases and some incurable diseases. Promising outcomes have resulted in that clinical studies are going to continue.
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Weighted Gene Co-Expression Network Analysis Identifies Key Modules and Hub Genes Associated with Mycobacterial Infection of Human Macrophages. Antibiotics (Basel) 2021; 10:antibiotics10020097. [PMID: 33498280 PMCID: PMC7909288 DOI: 10.3390/antibiotics10020097] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 12/28/2020] [Accepted: 01/14/2021] [Indexed: 02/04/2023] Open
Abstract
Tuberculosis (TB) is still a leading cause of death worldwide. Treatments remain unsatisfactory due to an incomplete understanding of the underlying host–pathogen interactions during infection. In the present study, weighted gene co-expression network analysis (WGCNA) was conducted to identify key macrophage modules and hub genes associated with mycobacterial infection. WGCNA was performed combining our own transcriptomic results using Mycobacterium aurum-infected human monocytic macrophages (THP1) with publicly accessible datasets obtained from three types of macrophages infected with seven different mycobacterial strains in various one-to-one combinations. A hierarchical clustering tree of 11,533 genes was built from 198 samples, and 47 distinct modules were revealed. We identified a module, consisting of 226 genes, which represented the common response of host macrophages to different mycobacterial infections that showed significant enrichment in innate immune stimulation, bacterial pattern recognition, and leukocyte chemotaxis. Moreover, by network analysis applied to the 74 genes with the best correlation with mycobacteria infection, we identified the top 10 hub-connecting genes: NAMPT, IRAK2, SOCS3, PTGS2, CCL20, IL1B, ZC3H12A, ABTB2, GFPT2, and ELOVL7. Interestingly, apart from the well-known Toll-like receptor and inflammation-associated genes, other genes may serve as novel TB diagnosis markers and potential therapeutic targets.
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Li M, Schifanella L, Larsen PA. Alu retrotransposons and COVID-19 susceptibility and morbidity. Hum Genomics 2021; 15:2. [PMID: 33390179 PMCID: PMC7779329 DOI: 10.1186/s40246-020-00299-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/14/2020] [Indexed: 12/22/2022] Open
Abstract
SARS-CoV-2 has spread rapidly across the world and is negatively impacting the global human population. COVID-19 patients display a wide variety of symptoms and clinical outcomes, including those attributed to genetic ancestry. Alu retrotransposons have played an important role in human evolution, and their variants influence host response to viral infection. Intronic Alus regulate gene expression through several mechanisms, including both genetic and epigenetic pathways. With respect to SARS-CoV-2, an intronic Alu within the ACE gene is hypothesized to be associated with COVID-19 susceptibility and morbidity. Here, we review specific Alu polymorphisms that are of particular interest when considering host response to SARS-CoV-2 infection, especially polymorphic Alu insertions in genes associated with immune response and coagulation/fibrinolysis cascade. We posit that additional research focused on Alu-related pathways could yield novel biomarkers capable of predicting clinical outcomes as well as patient-specific treatment strategies for COVID-19 and related infectious diseases.
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Affiliation(s)
- Manci Li
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN, 55108, USA
| | - Luca Schifanella
- Department of Surgery, Division of Surgical Outcomes and Precision Medicine Research, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Peter A Larsen
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN, 55108, USA.
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