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da Costa ACA, Albarello Gellen LP, Fernandes MR, Coelho RDCC, Monte N, de Moraes FCA, Calderaro MCL, de Freitas LM, Matos JA, Fernandes TFDS, Aguiar KEC, Vinagre LWMS, dos Santos SEB, dos Santos NPC. Correlation between Genomic Variants and Worldwide COVID-19 Epidemiology. J Pers Med 2024; 14:579. [PMID: 38929800 PMCID: PMC11204818 DOI: 10.3390/jpm14060579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 05/16/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024] Open
Abstract
COVID-19 is a systemic disease caused by the etiologic agent SARS-CoV-2, first reported in Hubei Province in Wuhan, China, in late 2019. The SARS-CoV-2 virus has evolved over time with distinct transmissibility subvariants from ancestral lineages. The clinical manifestations of the disease vary according to their severity and can range from asymptomatic to severe. Due to the rapid evolution to a pandemic, epidemiological studies have become essential to understand and effectively combat COVID-19, as the incidence and mortality of this disease vary between territories and populations. This study correlated epidemiological data on the incidence and mortality of COVID-19 with frequencies of important SNPs in GWAS studies associated with the susceptibility and mortality of this disease in different populations. Our results indicated significant correlations for 11 genetic variants (rs117169628, rs2547438, rs2271616, rs12610495, rs12046291, rs35705950, rs2176724, rs10774671, rs1073165, rs4804803 and rs7528026). Of these 11 variants, 7 (rs12046291, rs117169628, rs1073165, rs2547438, rs2271616, rs12610495 and rs35705950) were positively correlated with the incidence rate, these variants were more frequent in EUR populations, suggesting that this population is more susceptible to COVID-19. The rs2176724 variant was inversely related to incidence rates; therefore, the higher the frequency of the allele is, the lower the incidence rate. This variant was more frequent in the AFR population, which suggests a protective factor against SARS-CoV-2 infection in this population. The variants rs10774671, rs4804803, and rs7528026 showed a significant relationship with mortality rates. SNPs rs10774671 and rs4804803 were inversely related to mortality rates and are more frequently present in the AFR population. The rs7528026 variant, which is more frequent in the AMR population, was positively related to mortality rates. The study has the potential to identify and correlate the genetic profile with epidemiological data, identify populations that are more susceptible to severe forms of COVID-19, and relate them to incidence and mortality.
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Affiliation(s)
- Ana Caroline Alves da Costa
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
| | - Laura Patrícia Albarello Gellen
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
| | - Marianne Rodrigues Fernandes
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
- Ophir Loyola Hospital, Pará State Departament of Health, Belém 66063-240, PA, Brazil
| | - Rita de Cássia Calderaro Coelho
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
| | - Natasha Monte
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
| | - Francisco Cezar Aquino de Moraes
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
| | - Maria Clara Leite Calderaro
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
| | - Lilian Marques de Freitas
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
| | - Juliana Aires Matos
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
| | - Thamara Fernanda da Silva Fernandes
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
| | - Kaio Evandro Cardoso Aguiar
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
| | - Lui Wallacy Morikawa Souza Vinagre
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
- Ophir Loyola Hospital, Pará State Departament of Health, Belém 66063-240, PA, Brazil
| | - Sidney Emanuel Batista dos Santos
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
- Laboratory of Human and Medical Genetics, Institute of Biological Science, Federal University of Pará, Belém 66077-830, PA, Brazil
| | - Ney Pereira Carneiro dos Santos
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
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Abe K, Beer JC, Nguyen T, Ariyapala IS, Holmes TH, Feng W, Zhang B, Kuo D, Luo Y, Ma XJ, Maecker HT. Cross-Platform Comparison of Highly Sensitive Immunoassays for Inflammatory Markers in a COVID-19 Cohort. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1244-1253. [PMID: 38334457 PMCID: PMC10948291 DOI: 10.4049/jimmunol.2300729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/19/2024] [Indexed: 02/10/2024]
Abstract
A variety of commercial platforms are available for the simultaneous detection of multiple cytokines and associated proteins, often employing Ab pairs to capture and detect target proteins. In this study, we comprehensively evaluated the performance of three distinct platforms: the fluorescent bead-based Luminex assay, the proximity extension-based Olink assay, and a novel proximity ligation assay platform known as Alamar NULISAseq. These assessments were conducted on human serum samples from the National Institutes of Health IMPACC study, with a focus on three essential performance metrics: detectability, correlation, and differential expression. Our results reveal several key findings. First, the Alamar platform demonstrated the highest overall detectability, followed by Olink and then Luminex. Second, the correlation of protein measurements between the Alamar and Olink platforms tended to be stronger than the correlation of either of these platforms with Luminex. Third, we observed that detectability differences across the platforms often translated to differences in differential expression findings, although high detectability did not guarantee the ability to identify meaningful biological differences. Our study provides valuable insights into the comparative performance of these assays, enhancing our understanding of their strengths and limitations when assessing complex biological samples, as exemplified by the sera from this COVID-19 cohort.
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Affiliation(s)
- Koji Abe
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305
| | | | - Tran Nguyen
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305
| | | | - Tyson H. Holmes
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305
| | - Wei Feng
- Alamar Biosciences, Inc., Fremont, CA 94538
| | | | - Dwight Kuo
- Alamar Biosciences, Inc., Fremont, CA 94538
| | - Yuling Luo
- Alamar Biosciences, Inc., Fremont, CA 94538
| | | | - Holden T. Maecker
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305
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Chen LN, Shou ZX, Jin X. Interaction Between Genetic Susceptibility and COVID-19 Pathogenesis in Pediatric Multisystem Inflammatory Disorders: The Role of Immune Responses. Viral Immunol 2024; 37:1-11. [PMID: 38271561 DOI: 10.1089/vim.2023.0074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024] Open
Abstract
Numerous studies have highlighted the emergence of coronavirus disease (COVID-19) symptoms reminiscent of Kawasaki disease in children, including fever, heightened multisystem inflammation, and multiorgan involvement, posing a life-threatening complication. Consequently, extensive research endeavors in pediatric have aimed to elucidate the intricate relationship between COVID-19 infection and the immune system. COVID-19 profoundly impacts immune cells, culminating in a cytokine storm that particularly inflicts damage on the pulmonary system. The gravity and vulnerability to COVID-19 are closely intertwined with the vigor of the immune response. In this context, the human leukocyte antigen (HLA) molecule assumes pivotal significance in shaping immune responses. Genetic scrutiny of HLA has unveiled the presence of at least one deleterious allele in children afflicted with multisystem inflammatory syndrome in children (MIS-C). Furthermore, research has demonstrated that COVID-19 exploits the angiotensin-converting enzyme 2 (ACE-2) receptor, transmembrane serine protease type 2, and various other genes to gain entry into host cells, with individuals harboring ACE-2 polymorphisms being at higher risk. Pediatric studies have employed diverse genetic methodologies, such as genome-wide association studies (GWAS) and whole exome sequencing, to scrutinize target genes. These investigations have pinpointed two specific genomic loci linked to the severity and susceptibility of COVID-19, with the HLA locus emerging as a notable risk factor. In this comprehensive review article, we endeavor to assess the available evidence and consolidate data, offering insights into current clinical practices and delineating avenues for future research. Our objective is to advance early diagnosis, stabilization, and appropriate management strategies to mitigate genetic susceptibility's impact on the incidence of COVID-19 in pediatric patients with multisystem inflammation.
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Affiliation(s)
- Li-Na Chen
- Department of Pediatric, Affiliated Hospital of Shaoxing University, Shaoxing, China
| | - Zhang-Xuan Shou
- Department of Pharmacy, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Xue Jin
- Department of Pharmacy, Center for Clinical Pharmacy, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
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Abe K, Beer JC, Nguyen T, Ariyapala IS, Holmes TH, Feng W, Zhang B, Kuo D, Luo Y, Ma XJ, Maecker HT. Cross-platform comparison of highly-sensitive immunoassays for inflammatory markers in a COVID-19 cohort 1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.24.563866. [PMID: 37961126 PMCID: PMC10634816 DOI: 10.1101/2023.10.24.563866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
A variety of commercial platforms are available for the simultaneous detection of multiple cytokines and associated proteins, often employing antibody pairs to capture and detect target proteins. In this study, we comprehensively evaluated the performance of three distinct platforms: the fluorescent bead-based Luminex assay, the proximity extension-based Olink assay, and a novel proximity ligation assay platform known as Alamar NULISAseq. These assessments were conducted on serum samples from the NIH IMPACC study, with a focus on three essential performance metrics: detectability, correlation, and differential expression. Our results reveal several key findings. Firstly, the Alamar platform demonstrated the highest overall detectability, followed by Olink and then Luminex. Secondly, the correlation of protein measurements between the Alamar and Olink platforms tended to be stronger than the correlation of either of these platforms with Luminex. Thirdly, we observed that detectability differences across the platforms often translated to differences in differential expression findings, although high detectability did not guarantee the ability to identify meaningful biological differences. Our study provides valuable insights into the comparative performance of these assays, enhancing our understanding of their strengths and limitations when assessing complex biological samples, as exemplified by the sera from this COVID-19 cohort.
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Muacevic A, Adler JR, Dharmalingam A, Bhaskar E, Anil AA, Senthil N. Post-acute Sequelae of SARS-CoV-2 Infection: Do Indians Fare Better? Cureus 2022; 14:e32159. [PMID: 36601150 PMCID: PMC9807184 DOI: 10.7759/cureus.32159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2022] [Indexed: 12/05/2022] Open
Abstract
INTRODUCTION The uplift of SARS-CoV-2 infection has necessitated the understanding of long-term consequences in the affected population. This study was driven by a lack of Indian studies to estimate the torment of post-coronavirus disease 2019 (COVID-19) symptoms and the quality of life. METHODS This prospective observational study was conducted in a tertiary care centre in South India, between August and November 2020. SARS-CoV-2 hospitalised patients were telephonically questioned regarding the persistence of symptoms along with an assessment of the quality of life using the 15D questionnaire in the first, second, and fourth weeks. Since a majority of the patients had resolution of symptoms by four weeks, the study was not extended for a longer period. RESULTS The study included 476 patients whose mean length of hospital stay was 7.67 days. Of the patients, 68.7% had mild severity, 24.8% had moderate disease, and 6.5% had severe disease. About 28.4% required oxygen, 8.2% required ICU care, and 1.3% required mechanical ventilation. Myalgia (13.9%), cough (1.3%), and dyspnoea (6.1%) were the predominant persistent symptoms in the fourth-week post-discharge. All the symptoms of health-related quality of life and physical performance improved by the fourth week, which was statistically significant. CONCLUSION Our study findings are in stark contrast to the studies published from other regions of the world, which show a significant worsening of quality of life even among those with mild illness.
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Al-Karaawi IA, Al-bassam WW, Ismaeel HM, Ad'hiah AH. Interleukin-38 promoter variants and risk of COVID-19 among Iraqis. Immunobiology 2022; 227:152301. [PMID: 36375233 PMCID: PMC9651960 DOI: 10.1016/j.imbio.2022.152301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 10/13/2022] [Accepted: 11/05/2022] [Indexed: 11/11/2022]
Abstract
Coronavirus disease-19 (COVID-19) has recently emerged as a respiratory infection with a significant impact on health and society. The pathogenesis is primarily attributed to a dysregulation of cytokines, especially those with pro-inflammatory and anti-inflammatory effects. Interleukin-38 (IL-38) is a recently identified anti-inflammatory cytokine with a proposed involvement in mediating COVID-19 pathogenesis, while the association between IL38 gene variants and disease susceptibility has not been explored. Therefore, a pilot study was designed to evaluate the association of three gene variants in the promoter region of IL38 gene (rs7599662 T/A/C/G, rs28992497 T/C and rs28992498 C/A/T) with COVID-19 risk. DNA sequencing was performed to identify these variants. The study included 148 Iraqi patients with COVID-19 and 113 healthy controls (HC). Only rs7599662 showed a significant negative association with susceptibility to COVID-19. The mutant T allele was presented at a significantly lower frequency in patients compared to HC. Analysis of recessive, dominant and codominant models demonstrated that rs7599662 TT genotype frequency was significantly lower in patients than in HC. In terms of haplotypes (in order: rs7599662, rs28992497 and rs28992498), frequency of CTC haplotype was significantly increased in patients compared to HC, while TTC haplotype showed significantly lower frequency in patients. The three SNPs influenced serum IL-38 levels and homozygous genotypes of mutant alleles were associated with elevated levels. In conclusion, this study indicated that IL38 gene in terms of promoter variants and haplotypes may have important implications for COVID-19 risk.
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Nhung VP, Ton ND, Ngoc TTB, Thuong MTH, Hai NTT, Oanh KTP, Hien LTT, Thach PN, Hai NV, Ha NH. Host Genetic Risk Factors Associated with COVID-19 Susceptibility and Severity in Vietnam. Genes (Basel) 2022; 13:genes13101884. [PMID: 36292769 PMCID: PMC9601961 DOI: 10.3390/genes13101884] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/14/2022] [Accepted: 10/15/2022] [Indexed: 11/16/2022] Open
Abstract
Since the emergence and rapid transmission of SARS-CoV-2, numerous scientific reports have searched for the association of host genetic variants with COVID-19, but the data are mostly acquired from Europe. In the current work, we explored the link between host genes (SARS-CoV-2 entry and immune system related to COVID-19 sensitivity/severity) and ABO blood types with COVID-19 from whole-exome data of 200 COVID-19 patients and 100 controls in Vietnam. The O blood type was found to be a protective factor that weakens the worst outcomes of infected individuals. For SARS-CoV-2 susceptibility, rs2229207 (TC genotype, allele C) and rs17860118 (allele T) of IFNAR2 increased the risk of infection, but rs139940581 (CT genotype, allele T) of SLC6A20 reduced virus sensitivity. For COVID-19 progress, the frequencies of rs4622692 (TG genotype) and rs1048610 (TC genotype) of ADAM17 were significantly higher in the moderate group than in the severe/fatal group. The variant rs12329760 (AA genotype) of TMPRSS2 was significantly associated with asymptomatic/mild symptoms. Additionally, rs2304255 (CT genotype, allele T) of TYK2 and rs2277735 (AG genotype) of DPP9 were associated with severe/fatal outcomes. Studies on different populations will give better insights into the pathogenesis, which is ethnic-dependent, and thus decipher the genetic factor’s contribution to mechanisms that predispose people to being more vulnerable to COVID-19.
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Affiliation(s)
- Vu Phuong Nhung
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
| | - Nguyen Dang Ton
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
- Faculty of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
| | - Tran Thi Bich Ngoc
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
| | - Ma Thi Huyen Thuong
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
- Faculty of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
| | - Nguyen Thi Thanh Hai
- National Hospital for Tropical Disease, Kim Chung, Dong Anh, Hanoi 100000, Vietnam
- Department of Biochemistry, Hanoi Medical University, 1 Ton That Tung, Dong Da, Hanoi 100000, Vietnam
| | - Kim Thi Phuong Oanh
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
- Faculty of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
| | - Le Thi Thu Hien
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
- Faculty of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
| | - Pham Ngoc Thach
- National Hospital for Tropical Disease, Kim Chung, Dong Anh, Hanoi 100000, Vietnam
| | - Nong Van Hai
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
- Faculty of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
| | - Nguyen Hai Ha
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
- Faculty of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
- Correspondence: ; Tel.: +84-385-368-368
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Pourazizi M, Eshraghi B, Azad R, Afshar K, Mohammadbeigy I. Father–Son
COVID
‐19‐associated mucormycosis: Important role of genetic susceptibility in combination with environmental factors. Clin Case Rep 2022; 10:e6312. [PMID: 36101784 PMCID: PMC9459102 DOI: 10.1002/ccr3.6312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/22/2022] [Accepted: 08/25/2022] [Indexed: 12/15/2022] Open
Abstract
In this report, a father with a history of diabetes mellitus and his son without a remarkable past medical history, both got COVID‐19‐ associated mucormycosis (CAM) as evidenced by their clinical and radiological findings. This suggests the possible role of genetics in combination with the environment in susceptibility to CAM. The simultaneous infection of a diabetic father and his son who did not have any known risk factors for COVID‐19‐associated mucormycosis (CAM) may indicate the possible role of genetics and the environment in CAM infection.
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Affiliation(s)
- Mohsen Pourazizi
- Department of Ophthalmology, Isfahan Eye Research Center Isfahan University of Medical Sciences Isfahan Iran
| | - Bahram Eshraghi
- Department of Ophthalmology, Isfahan Eye Research Center Isfahan University of Medical Sciences Isfahan Iran
| | - Roya Azad
- Department of Radiology, Faculty of Medicine Isfahan University of Medical Sciences Isfahan Iran
| | - Kimia Afshar
- Student Research Committee Isfahan University of Medical Sciences Isfahan Iran
| | - Iman Mohammadbeigy
- Isfahan Eye Research Center Isfahan University of Medical Sciences Isfahan Iran
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Vakil MK, Mansoori Y, Al‐Awsi GRL, Hosseinipour A, Ahsant S, Ahmadi S, Ekrahi M, Montaseri Z, Pezeshki B, Mohaghegh P, Sohrabpour M, Bahmanyar M, Daraei A, Dadkhah Jouybari T, Tavassoli A, Ghasemian A. Individual genetic variability mainly of Proinflammatory cytokines, cytokine receptors, and toll-like receptors dictates pathophysiology of COVID-19 disease. J Med Virol 2022; 94:4088-4096. [PMID: 35538614 PMCID: PMC9348290 DOI: 10.1002/jmv.27849] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 05/02/2022] [Accepted: 05/06/2022] [Indexed: 11/12/2022]
Abstract
Innate and acquired immunity responses are crucial for viral infection elimination. However, genetic variations in coding genes may exacerbate the inflammation or initiate devastating cytokine storms which poses severe respiratory conditions in coronavirus disease-19 (COVID-19). Host genetic variations in particular those related to the immune responses determine the patients' susceptibility and COVID-19 severity and pathophysiology. Gene polymorphisms such as single nucleotide polymorphisms (SNPs) of interferons, TNF, IL1, IL4, IL6, IL7, IL10, and IL17 predispose patients to the severe form of COVID-19 or severe acute respiratory syndrome coronavirus-2 (SARS-COV-2). These variations mainly alter the gene expression and cause a severe response by B cells, T cells, monocytes, neutrophils, and natural killer cells participating in a cytokine storm. Moreover, cytokines and chemokines SNPs are associated with the severity of COVID-19 and clinical outcomes depending on the corresponding effect. Additionally, genetic variations in genes encoding toll-like receptors (TLRs) mainly TLR3, TLR7, and TLR9 have been related to the COVID-19 severe respiratory symptoms. The specific relation of these mutations with the novel variants of concern (VOCs) infection remains to be elucidated. Genetic variations mainly within genes encoding proinflammatory cytokines, cytokine receptors, and TLRs predispose patients to COVID-19 disease severity. Understanding host immune gene variations associated with the SARS-COV-2 infection opens insights to control the pathophysiology of emerging viral infections.
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Affiliation(s)
- Mohammad Kazem Vakil
- Noncommunicable Diseases Research CenterFasa University of Medical SciencesFasaIran
| | - Yaser Mansoori
- Noncommunicable Diseases Research CenterFasa University of Medical SciencesFasaIran
| | - Ghaidaa Raheem Lateef Al‐Awsi
- University of Al‐QadisiyahCollege of ScienceAl DiwaniyahIraq
- Department of Radiological TechniquesAl‐Mustaqbal University CollegeBabylonIraq
| | - Ali Hosseinipour
- Department of Internal MedicineFasa University of Medical SciencesFasaIran
| | - Samaneh Ahsant
- Noncommunicable Diseases Research CenterFasa University of Medical SciencesFasaIran
| | - Sedigheh Ahmadi
- Noncommunicable Diseases Research CenterFasa University of Medical SciencesFasaIran
| | - Mohammad Ekrahi
- Noncommunicable Diseases Research CenterFasa University of Medical SciencesFasaIran
| | - Zahra Montaseri
- Department of Infectious DiseasesFasa University of Medical SciencesFasaIran
| | - Babak Pezeshki
- Noncommunicable Diseases Research CenterFasa University of Medical SciencesFasaIran
| | - Poopak Mohaghegh
- Pediatrics Department, School of MedicineFasa University of Medical SciencesFasaIran
| | - Mojtaba Sohrabpour
- Noncommunicable Diseases Research CenterFasa University of Medical SciencesFasaIran
| | - Maryam Bahmanyar
- Pediatrics Department, School of MedicineFasa University of Medical SciencesFasaIran
| | - Abdolreza Daraei
- Department of Medical Genetics, School of MedicineBabol University of Medical SciencesBabolIran
| | | | | | - Abdolmajid Ghasemian
- Noncommunicable Diseases Research CenterFasa University of Medical SciencesFasaIran
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10
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Glessner JT, Chang X, Mentch F, Qu H, Abrams DJ, Thomas A, Sleiman PMA, Hakonarson H. COVID-19 in pediatrics: Genetic susceptibility. Front Genet 2022; 13:928466. [PMID: 36051697 PMCID: PMC9425045 DOI: 10.3389/fgene.2022.928466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/13/2022] [Indexed: 11/21/2022] Open
Abstract
The uptick in SARS-CoV-2 infection has resulted in a worldwide COVID-19 pandemic, which has created troublesome health and economic problems. We performed case–control meta-analyses in both African and European ethnicity COVID-19 disease cases based on laboratory test and phenotypic criteria. The cases had laboratory-confirmed SARS-CoV-2 infection. We uniquely investigated COVID infection genetics in a pediatric population. Our cohort has a large African ancestry component, also unique to our study. We tested for genetic variant association in 498 cases vs. 1,533 controls of African ancestry and 271 cases vs. 855 controls of European ancestry. We acknowledge that the sample size is relatively small, owing to the low prevalence of COVID infection among pediatric individuals. COVID-19 cases averaged 13 years of age. Pediatric genetic studies enhance the ability to detect genetic associations with a limited possible environment impact. Our findings support the notion that some genetic variants, most notably at the SEMA6D, FMN1, ACTN1, PDS5B, NFIA, ADGRL3, MMP27, TENM3, SPRY4, MNS1, and RSU1 loci, play a role in COVID-19 infection susceptibility. The pediatric cohort also shows nominal replication of previously reported adult study results: CCR9, CXCR6, FYCO1, LZTFL1, TDGF1, CCR1, CCR2, CCR3, CCR5, MAPT-AS1, and IFNAR2 gene variants. Reviewing the biological roles of genes implicated here, NFIA looks to be the most interesting as it binds to a palindromic sequence observed in both viral and cellular promoters and in the adenovirus type 2 origin of replication.
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Affiliation(s)
- Joseph T. Glessner
- Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- *Correspondence: Joseph T. Glessner,
| | - Xiao Chang
- Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Frank Mentch
- Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Huiqi Qu
- Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Debra J. Abrams
- Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Alexandria Thomas
- Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Patrick M. A. Sleiman
- Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Hakon Hakonarson
- Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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11
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SARS-CoV-2 Antibody Response against Mild-to-Moderate Breakthrough COVID-19 in Home Isolation Setting in Thailand. Vaccines (Basel) 2022; 10:vaccines10071131. [PMID: 35891295 PMCID: PMC9318962 DOI: 10.3390/vaccines10071131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 12/03/2022] Open
Abstract
Background: In December 2021, Omicron replaced Delta as the dominant coronavirus disease 2019 (COVID-19) variant in Thailand. Both variants embody diverse epidemiological trends and immunogenicity. We investigated whether Delta and Omicron patients’ biological and clinical characteristics and immunogenicity differed post-COVID-19 infection. Methods: This retrospective cohort study investigated the clinical outcomes and laboratory data of 5181 patients with mild-to-moderate COVID-19 (Delta, 2704; Omicron, 2477) under home isolation. We evaluated anti-receptor-binding domain immunoglobulin G (anti-RBD IgG) and surrogate viral neutralizing (sVNT) activity in 495 individuals post-COVID-19 infection during the Delta pandemic. Results: Approximately 84% of all patients received favipiravir. The median cycle threshold (Ct) values were lower for Omicron patients than Delta patients (19 vs. 21; p < 0.001), regardless of vaccination status. Upper respiratory tract symptoms were more frequent with Omicron patients than Delta patients. There were no significant associations between Ct and Omicron symptoms (95% confidence interval 0.98−1.02). A two-dose vaccine regimen reduced hospital readmission by 10% to 30% and death by under 1%. Anti-RBD IgG and sVNT against Delta were higher among older individuals post-COVID-19 infection. Older individuals expressed anti-RBD IgG and sVNT for a more extended period after two-dose vaccination than other age groups. Conclusions: After a full vaccination course, breakthrough mild-to-moderate Delta and Omicron infections have limited immunogenicity. Prior infections exert reduced protection against later reinfection or infection from novel variants. However, this protection may be sufficient to prevent hospitalization and death, particularly in countries where vaccine supplies are limited.
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12
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Biancolella M, Colona VL, Mehrian-Shai R, Watt JL, Luzzatto L, Novelli G, Reichardt JKV. COVID-19 2022 update: transition of the pandemic to the endemic phase. Hum Genomics 2022; 16:19. [PMID: 35650595 PMCID: PMC9156835 DOI: 10.1186/s40246-022-00392-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/26/2022] [Indexed: 02/06/2023] Open
Abstract
COVID-19, which is caused by the SARS-CoV-2, has ravaged the world for the past 2 years. Here, we review the current state of research into the disease with focus on its history, human genetics and genomics and the transition from the pandemic to the endemic phase. We are particularly concerned by the lack of solid information from the initial phases of the pandemic that highlighted the necessity for better preparation to face similar future threats. On the other hand, we are gratified by the progress into human genetic susceptibility investigations and we believe now is the time to explore the transition from the pandemic to the endemic phase. The latter will require worldwide vigilance and cooperation, especially in emerging countries. In the transition to the endemic phase, vaccination rates have lagged and developed countries should assist, as warranted, in bolstering vaccination rates worldwide. We also discuss the current status of vaccines and the outlook for COVID-19.
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Affiliation(s)
| | - Vito Luigi Colona
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133, Rome, Italy
| | - Ruty Mehrian-Shai
- Sheba Medical Center, Pediatric Hemato-Oncology, Edmond and Lilly Safra Children's Hospital, Tel Hashomer 2 Sheba Road, 52621, Ramat Gan, Israel
| | - Jessica Lee Watt
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Smithfield, QLD, 4878, Australia
| | - Lucio Luzzatto
- Department of Haematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania.,University of Florence, Florence, Italy
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133, Rome, Italy. .,IRCCS Neuromed, Pozzilli, Isernia, Italy. .,Department of Pharmacology, School of Medicine, University of Nevada, Reno, NV, USA. .,Department of Biomedicine and Prevention, School of Medicine and Surgery, Via Montpellier 1, 00133, Rome, Italy.
| | - Juergen K V Reichardt
- Australian Institute of Tropical Health and Medicine, James Cook University, Smithfield, QLD, 4878, Australia
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