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Lee JH, Sergi C, Kast RE, Kanwar BA, Bourbeau J, Oh S, Sohn MG, Lee CJ, Coleman MD. Aggravating mechanisms from COVID-19. Virol J 2024; 21:228. [PMID: 39334442 PMCID: PMC11430051 DOI: 10.1186/s12985-024-02506-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Accepted: 09/16/2024] [Indexed: 09/30/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces immune-mediated diseases. The pathophysiology of COVID-19 uses the following three mechanisms: (1) inflammasome activation mechanism; (2) cGAS-STING signaling mechanism; and (3) SAMHD1 tetramerization mechanism, which leads to IFN-I production. Interactions between the host and virus govern induction, resulting in multiorgan impacts. The NLRP3 with cGAS-STING constitutes the primary immune response. The expression of SARS-CoV-2 ORF3a, NSP6, NSP7, and NSP8 blocks innate immune activation and facilitates virus replication by targeting the RIG-I/MDA5, TRIF, and cGAS-STING signaling. SAMHD1 has a target motif for CDK1 to protect virion assembly, threonine 592 to modulate a catalytically active tetramer, and antiviral IFN responses to block retroviral infection. Plastic and allosteric nucleic acid binding of SAMHD1 modulates the antiretroviral activity of SAMHD1. Therefore, inflammasome activation, cGAS-STING signaling, and SAMHD1 tetramerization explain acute kidney injury, hepatic, cardiac, neurological, and gastrointestinal injury of COVID-19. It might be necessary to effectively block the pathological courses of diverse diseases.
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Affiliation(s)
- Jong Hoon Lee
- Science and Research Center, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
- Department of Geriatrics, Gyeonggi Medical Center Pocheon Hospital, 1648 Pocheon-ro Sin-eup-dong, Pocheon-si, Gyeonggi-do, 11142, Republic of Korea.
| | - Consolato Sergi
- Division of Anatomical Pathology, Children's Hospital of Eastern Ontario (CHEO), University of Ottawa, 401 Smyth Road, Ottawa, ON, K1H 8L1, Canada
| | - Richard E Kast
- IIAIGC Study Center, 11 Arlington Ct, Burlington, 05408 VT, USA
| | - Badar A Kanwar
- Haider Associates, 1999 Forest Ridge Dr, Bedford, TX, 76021, USA
| | - Jean Bourbeau
- Respiratory Epidemiology and Clinical Research Unit, McGill University Health Centre, Montréal, QC, Canada
| | - Sangsuk Oh
- Department of Food Engineering, Food Safety Laboratory, Memory Unit, Ewha Womans University, Seoul, 03670, Korea
| | - Mun-Gi Sohn
- Department of Food Science, KyungHee University College of Life Science, Seoul, 17104, Republic of Korea
| | - Chul Joong Lee
- Department of Anesthesiology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Michael D Coleman
- College of Health and Life Sciences, Aston University, Birmingham, B4 7ET, UK.
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Ma X, Lu Y, Xu S. Adaptive Evolution of Two Distinct Adaptive Haplotypes of Neanderthal Origin at the Immunoglobulin Heavy-chain Locus in East Asian and European Populations. Mol Biol Evol 2024; 41:msae147. [PMID: 39011558 DOI: 10.1093/molbev/msae147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 07/05/2024] [Accepted: 07/11/2024] [Indexed: 07/17/2024] Open
Abstract
Immunoglobulins (Igs) have a crucial role in humoral immunity. Two recent studies have reported a high-frequency Neanderthal-introgressed haplotype throughout Eurasia and a high-frequency Neanderthal-introgressed haplotype specific to southern East Asia at the immunoglobulin heavy-chain (IGH) gene locus on chromosome 14q32.33. Surprisingly, we found the previously reported high-frequency Neanderthal-introgressed haplotype does not exist throughout Eurasia. Instead, our study identified two distinct high-frequency haplotypes of putative Neanderthal origin in East Asia and Europe, although they shared introgressed alleles. Notably, the alleles of putative Neanderthal origin reduced the expression of IGHG1 and increased the expression of IGHG2 and IGHG3 in various tissues. These putatively introgressed alleles also affected the production of IgG1 upon antigen stimulation and increased the risk of systemic lupus erythematosus. Additionally, the greatest genetic differentiation across the whole genome between southern and northern East Asians was observed for the East Asian haplotype of putative Neanderthal origin. The frequency decreased from southern to northern East Asia and correlated positively with the genome-wide proportion of southern East Asian ancestry, indicating that this putative positive selection likely occurred in the common ancestor of southern East Asian populations before the admixture with northern East Asian populations.
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Affiliation(s)
- Xixian Ma
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Yan Lu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai China
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
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Aneli S, Ceccatelli Berti C, Gilea AI, Birolo G, Mutti G, Pavesi A, Baruffini E, Goffrini P, Capelli C. Functional characterization of archaic-specific variants in mitonuclear genes: insights from comparative analysis in S. cerevisiae. Hum Mol Genet 2024; 33:1152-1163. [PMID: 38558123 DOI: 10.1093/hmg/ddae057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/29/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024] Open
Abstract
Neanderthal and Denisovan hybridisation with modern humans has generated a non-random genomic distribution of introgressed regions, the result of drift and selection dynamics. Cross-species genomic incompatibility and more efficient removal of slightly deleterious archaic variants have been proposed as selection-based processes involved in the post-hybridisation purge of archaic introgressed regions. Both scenarios require the presence of functionally different alleles across Homo species onto which selection operated differently according to which populations hosted them, but only a few of these variants have been pinpointed so far. In order to identify functionally divergent archaic variants removed in humans, we focused on mitonuclear genes, which are underrepresented in the genomic landscape of archaic humans. We searched for non-synonymous, fixed, archaic-derived variants present in mitonuclear genes, rare or absent in human populations. We then compared the functional impact of archaic and human variants in the model organism Saccharomyces cerevisiae. Notably, a variant within the mitochondrial tyrosyl-tRNA synthetase 2 (YARS2) gene exhibited a significant decrease in respiratory activity and a substantial reduction of Cox2 levels, a proxy for mitochondrial protein biosynthesis, coupled with the accumulation of the YARS2 protein precursor and a lower amount of mature enzyme. Our work suggests that this variant is associated with mitochondrial functionality impairment, thus contributing to the purging of archaic introgression in YARS2. While different molecular mechanisms may have impacted other mitonuclear genes, our approach can be extended to the functional screening of mitonuclear genetic variants present across species and populations.
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Affiliation(s)
- Serena Aneli
- Department of Public Health Sciences and Pediatrics, University of Turin, C.so Galileo Galilei 22, Turin 10126, Italy
| | - Camilla Ceccatelli Berti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Alexandru Ionut Gilea
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Giovanni Birolo
- Department of Medical Sciences, University of Turin, Via Santena 5, Turin 10126, Italy
| | - Giacomo Mutti
- Barcelona Supercomputing Centre (BSC-CNS), Department of Life Sciences, Plaça Eusebi Güell, 1-3, Barcelona 08034, Spain
- Institute for Research in Biomedicine (IRB Barcelona), Department of Mechanisms of Disease, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Angelo Pavesi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Enrico Baruffini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Paola Goffrini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Cristian Capelli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
- Department of Biology, University of Oxford, 11a Mansfield Rd, Oxford OX1 3SZ, United Kingdom
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Yousfi FZE, Haroun AE, Nebhani C, Belayachi J, Askander O, Fahime EE, Fares H, Ennibi K, Abouqal R, Razine R, Bouhouche A. Prevalence of the protective OAS1 rs10774671-G allele against severe COVID-19 in Moroccans: implications for a North African Neanderthal connection. Arch Virol 2024; 169:109. [PMID: 38658463 PMCID: PMC11043147 DOI: 10.1007/s00705-024-06038-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 02/26/2024] [Indexed: 04/26/2024]
Abstract
The clinical presentation of COVID-19 shows high variability among individuals, which is partly due to genetic factors. The OAS1/2/3 cluster has been found to be strongly associated with COVID-19 severity. We examined this locus in the Moroccan population for the occurrence of the critical variant rs10774671 and its respective haplotype blocks. The frequency of single-nucleotide polymorphisms (SNPs) in the cluster of OAS immunity genes in 157 unrelated individuals of Moroccan origin was determined using an in-house exome database. OAS1 exon 6 of 71 SARS-CoV-2-positive individuals with asymptomatic/mild disease and 74 with moderate/severe disease was sequenced by the Sanger method. The genotypic, allelic, and haplotype frequencies of three SNPs were compared between these two groups. Finally, males in our COVID-19 series were genotyped for the Berber-specific marker E-M81. The prevalence of the OAS1 rs10774671-G allele in present-day Moroccans was found to be 40.4%, which is similar to that found in Europeans. However, it was found equally in both the Neanderthal GGG haplotype and the African GAC haplotype, with a frequency of 20% each. These two haplotypes, and hence the rs10774671-G allele, were significantly associated with protection against severe COVID-19 (p = 0.034, p = 0.041, and p = 0.008, respectively). Surprisingly, in men with the Berber-specific uniparental markers, the African haplotype was absent, while the prevalence of the Neanderthal haplotype was similar to that in Europeans. The protective rs10774671-G allele of OAS1 was found only in the Neanderthal haplotype in Berbers, the indigenous people of North Africa, suggesting that this region may have served as a stepping-stone for the passage of hominids to other continents.
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Affiliation(s)
- Fatima Zahra El Yousfi
- Laboratory of Human Genetics, Medical School and Pharmacy, University Mohammed V in Rabat, Rabat, Morocco
| | - Abbas Ermilo Haroun
- Laboratory of Biostatistics, Clinical and Epidemiological Research, Department of Public Health, Medical School and Pharmacy, University Mohammed V in Rabat, Rabat, Morocco
- Laboratory of Community Health, Department of Public Health, Medical School and Pharmacy, University Mohammed V in Rabat, Rabat, Morocco
| | - Chaimae Nebhani
- Laboratory of Human Genetics, Medical School and Pharmacy, University Mohammed V in Rabat, Rabat, Morocco
| | - Jihane Belayachi
- Laboratory of Biostatistics, Clinical and Epidemiological Research, Department of Public Health, Medical School and Pharmacy, University Mohammed V in Rabat, Rabat, Morocco
- Acute Medical Unit, Ibn Sina University Hospital, Rabat, Morocco
| | - Omar Askander
- Faculty of Medical Science, Mohammed VI Polytechnic University, Benguerir, Morocco
| | - Elmostafa El Fahime
- Molecular Biology and Functional Genomics Platform, National Center for Scientific and Technical Research, Rabat, Morocco
| | - Hakima Fares
- Intensive Care Department, Cheikh Zaid International Universitary Hospital, Rabat, Morocco
| | - Khalid Ennibi
- Virology, Infectious and Tropical Diseases Center, Hopital Militaire d'Instruction Mohammed V, Rabat, Morocco
| | - Redouane Abouqal
- Laboratory of Biostatistics, Clinical and Epidemiological Research, Department of Public Health, Medical School and Pharmacy, University Mohammed V in Rabat, Rabat, Morocco
- Laboratory of Community Health, Department of Public Health, Medical School and Pharmacy, University Mohammed V in Rabat, Rabat, Morocco
| | - Rachid Razine
- Laboratory of Biostatistics, Clinical and Epidemiological Research, Department of Public Health, Medical School and Pharmacy, University Mohammed V in Rabat, Rabat, Morocco
- Laboratory of Community Health, Department of Public Health, Medical School and Pharmacy, University Mohammed V in Rabat, Rabat, Morocco
| | - Ahmed Bouhouche
- Laboratory of Human Genetics, Medical School and Pharmacy, University Mohammed V in Rabat, Rabat, Morocco.
- Genomic Center of the Cheikh Zaid Foundation, Abulcasis International University of Health Sciences, Rabat, Morocco.
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Perez-Favila A, Sanchez-Macias S, De Lara SAO, Garza-Veloz I, Araujo-Espino R, Castañeda-Lopez ME, Mauricio-Gonzalez A, Vazquez-Reyes S, Velasco-Elizondo P, Trejo-Ortiz PM, Montaño FEM, Castruita-De la Rosa C, Martinez-Fierro ML. Gene Variants of the OAS/RNase L Pathway and Their Association with Severity of Symptoms and Outcome of SARS-CoV-2 Infection. J Pers Med 2024; 14:426. [PMID: 38673053 PMCID: PMC11051515 DOI: 10.3390/jpm14040426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 04/05/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
INTRODUCTION The interferon pathway plays a critical role in triggering the immune response to SARS-CoV-2, and these gene variants may be involved in the severity of COVID-19. This study aimed to analyze the frequency of three gene variants of OAS and RNASEL with the occurrence of COVID-19 symptoms and disease outcome. METHODS This cross-sectional study included 104 patients with SARS-CoV-2 infection, of which 34 were asymptomatic COVID-19, and 70 were symptomatic cases. The variants rs486907 (RNASEL), rs10774671 (OAS1), rs1293767 (OAS2), and rs2285932 (OAS3) were screened and discriminated using a predesigned 5'-nuclease assay with TaqMan probes. RESULTS Patients with the allele C of the OAS2 gene rs1293767 (OR = 0.36, 95% CI: 0.15-0.83, p = 0.014) and allele T of the OAS3 gene rs2285932 (OR = 0.39, 95% CI: 0.2-0.023, p = 0.023) have lower susceptibility to developing symptomatic COVID-19. The genotype frequencies (G/G, G/C, and C/C) of rs1293767 for that comparison were 64.7%, 29.4%, and 5.9% in the asymptomatic group and 95.2%, 4.8%, and 0% in severe disease (p < 0.05). CONCLUSIONS Our data indicate that individuals carrying the C allele of the OAS2 gene rs1293767 and the T allele of the OAS3 gene rs2285932 are less likely to develop symptomatic COVID-19, suggesting these genetic variations may confer a protective effect among the Mexican study population. Furthermore, the observed differences in genotype frequencies between asymptomatic individuals and those with severe disease emphasize the potential of these variants as markers for disease severity. These insights enhance our understanding of the genetic factors that may influence the course of COVID-19 and underscore the potential for genetic screening in identifying individuals at increased risk for severe disease outcomes.
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Affiliation(s)
- Aurelio Perez-Favila
- Laboratorio de Medicina Molecular, Unidad Académica de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (A.P.-F.); (S.S.-M.); (S.A.O.D.L.); (I.G.-V.); (C.C.-D.l.R.)
- Doctorado en Ciencias con Orientación en Medicina Molecular, Unidad Académica de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (R.A.-E.); (M.E.C.-L.); (A.M.-G.); (S.V.-R.); (P.V.-E.); (P.M.T.-O.); (F.E.M.M.)
| | - Sonia Sanchez-Macias
- Laboratorio de Medicina Molecular, Unidad Académica de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (A.P.-F.); (S.S.-M.); (S.A.O.D.L.); (I.G.-V.); (C.C.-D.l.R.)
| | - Sergio A. Oropeza De Lara
- Laboratorio de Medicina Molecular, Unidad Académica de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (A.P.-F.); (S.S.-M.); (S.A.O.D.L.); (I.G.-V.); (C.C.-D.l.R.)
| | - Idalia Garza-Veloz
- Laboratorio de Medicina Molecular, Unidad Académica de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (A.P.-F.); (S.S.-M.); (S.A.O.D.L.); (I.G.-V.); (C.C.-D.l.R.)
- Doctorado en Ciencias con Orientación en Medicina Molecular, Unidad Académica de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (R.A.-E.); (M.E.C.-L.); (A.M.-G.); (S.V.-R.); (P.V.-E.); (P.M.T.-O.); (F.E.M.M.)
| | - Roxana Araujo-Espino
- Doctorado en Ciencias con Orientación en Medicina Molecular, Unidad Académica de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (R.A.-E.); (M.E.C.-L.); (A.M.-G.); (S.V.-R.); (P.V.-E.); (P.M.T.-O.); (F.E.M.M.)
| | - Maria E. Castañeda-Lopez
- Doctorado en Ciencias con Orientación en Medicina Molecular, Unidad Académica de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (R.A.-E.); (M.E.C.-L.); (A.M.-G.); (S.V.-R.); (P.V.-E.); (P.M.T.-O.); (F.E.M.M.)
| | - Alejandro Mauricio-Gonzalez
- Doctorado en Ciencias con Orientación en Medicina Molecular, Unidad Académica de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (R.A.-E.); (M.E.C.-L.); (A.M.-G.); (S.V.-R.); (P.V.-E.); (P.M.T.-O.); (F.E.M.M.)
| | - Sodel Vazquez-Reyes
- Doctorado en Ciencias con Orientación en Medicina Molecular, Unidad Académica de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (R.A.-E.); (M.E.C.-L.); (A.M.-G.); (S.V.-R.); (P.V.-E.); (P.M.T.-O.); (F.E.M.M.)
| | - Perla Velasco-Elizondo
- Doctorado en Ciencias con Orientación en Medicina Molecular, Unidad Académica de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (R.A.-E.); (M.E.C.-L.); (A.M.-G.); (S.V.-R.); (P.V.-E.); (P.M.T.-O.); (F.E.M.M.)
| | - Perla M. Trejo-Ortiz
- Doctorado en Ciencias con Orientación en Medicina Molecular, Unidad Académica de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (R.A.-E.); (M.E.C.-L.); (A.M.-G.); (S.V.-R.); (P.V.-E.); (P.M.T.-O.); (F.E.M.M.)
| | - Fabiana E. Mollinedo Montaño
- Doctorado en Ciencias con Orientación en Medicina Molecular, Unidad Académica de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (R.A.-E.); (M.E.C.-L.); (A.M.-G.); (S.V.-R.); (P.V.-E.); (P.M.T.-O.); (F.E.M.M.)
| | - Claudia Castruita-De la Rosa
- Laboratorio de Medicina Molecular, Unidad Académica de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (A.P.-F.); (S.S.-M.); (S.A.O.D.L.); (I.G.-V.); (C.C.-D.l.R.)
| | - Margarita L. Martinez-Fierro
- Laboratorio de Medicina Molecular, Unidad Académica de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (A.P.-F.); (S.S.-M.); (S.A.O.D.L.); (I.G.-V.); (C.C.-D.l.R.)
- Doctorado en Ciencias con Orientación en Medicina Molecular, Unidad Académica de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (R.A.-E.); (M.E.C.-L.); (A.M.-G.); (S.V.-R.); (P.V.-E.); (P.M.T.-O.); (F.E.M.M.)
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Angulo-Aguado M, Carrillo-Martinez JC, Contreras-Bravo NC, Morel A, Parra-Abaunza K, Usaquén W, Fonseca-Mendoza DJ, Ortega-Recalde O. Next-generation sequencing of host genetics risk factors associated with COVID-19 severity and long-COVID in Colombian population. Sci Rep 2024; 14:8497. [PMID: 38605121 PMCID: PMC11009356 DOI: 10.1038/s41598-024-57982-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 03/24/2024] [Indexed: 04/13/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19) was considered a major public health burden worldwide. Multiple studies have shown that susceptibility to severe infections and the development of long-term symptoms is significantly influenced by viral and host factors. These findings have highlighted the potential of host genetic markers to identify high-risk individuals and develop target interventions to reduce morbimortality. Despite its importance, genetic host factors remain largely understudied in Latin-American populations. Using a case-control design and a custom next-generation sequencing (NGS) panel encompassing 81 genetic variants and 74 genes previously associated with COVID-19 severity and long-COVID, we analyzed 56 individuals with asymptomatic or mild COVID-19 and 56 severe and critical cases. In agreement with previous studies, our results support the association between several clinical variables, including male sex, obesity and common symptoms like cough and dyspnea, and severe COVID-19. Remarkably, thirteen genetic variants showed an association with COVID-19 severity. Among these variants, rs11385942 (p < 0.01; OR = 10.88; 95% CI = 1.36-86.51) located in the LZTFL1 gene, and rs35775079 (p = 0.02; OR = 8.53; 95% CI = 1.05-69.45) located in CCR3 showed the strongest associations. Various respiratory and systemic symptoms, along with the rs8178521 variant (p < 0.01; OR = 2.51; 95% CI = 1.27-4.94) in the IL10RB gene, were significantly associated with the presence of long-COVID. The results of the predictive model comparison showed that the mixed model, which incorporates genetic and non-genetic variables, outperforms clinical and genetic models. To our knowledge, this is the first study in Colombia and Latin-America proposing a predictive model for COVID-19 severity and long-COVID based on genomic analysis. Our study highlights the usefulness of genomic approaches to studying host genetic risk factors in specific populations. The methodology used allowed us to validate several genetic variants previously associated with COVID-19 severity and long-COVID. Finally, the integrated model illustrates the importance of considering genetic factors in precision medicine of infectious diseases.
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Affiliation(s)
- Mariana Angulo-Aguado
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, D.C, Colombia
| | - Juan Camilo Carrillo-Martinez
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, D.C, Colombia
| | - Nora Constanza Contreras-Bravo
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, D.C, Colombia
| | - Adrien Morel
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, D.C, Colombia
| | | | - William Usaquén
- Populations Genetics and Identification Group, Institute of Genetics, Universidad Nacional de Colombia, Bogotá, D.C, Colombia
| | - Dora Janeth Fonseca-Mendoza
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, D.C, Colombia
| | - Oscar Ortega-Recalde
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, D.C, Colombia.
- Departamento de Morfología, Facultad de Medicina e Instituto de Genética, Universidad Nacional de Colombia, Bogotá, D.C, Colombia.
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7
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Montenegro AFL, Clementino MAF, Yaochite JNU. Type I interferon pathway genetic variants in severe COVID-19. Virus Res 2024; 342:199339. [PMID: 38354910 PMCID: PMC10901847 DOI: 10.1016/j.virusres.2024.199339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/09/2024] [Accepted: 02/11/2024] [Indexed: 02/16/2024]
Abstract
Coronavirus Disease 2019 (COVID-19) is an infectious disease caused by SARS-CoV-2. According to the World Health Organization (WHO), there have been over 760 million reported cases and over 6 million deaths caused by this disease worldwide. The severity of COVID-19 is based on symptoms presented by the patient and is divided as asymptomatic, mild, moderate, severe, and critical. The manifestations are interconnected with genetic variations. The innate immunity is the quickest response mechanism of an organism against viruses. Type I interferon pathway plays a key role in antiviral responses due to viral replication inhibition in infected cells and adaptive immunity stimulation induced by interferon molecules. Thus, variants in type I interferon pathway's genes are being studied in different COVID-19 manifestations. This review summarizes the role of variants in type I interferon pathway's genes on prognosis and severity progression of COVID-19.
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Affiliation(s)
- A F L Montenegro
- Laboratório de Imunologia Celular e Molecular, Departamento de Análises Clínicas e Toxicológicas da Faculdade de Farmácia, Odontologia e Enfermagem, Universidade Federal do Ceará - UFC, Rua Pastor Samuel Munguba, 1210 - Rodolfo Teófilo, Fortaleza, Ceará, Brasil
| | - M A F Clementino
- Laboratório de Toxinologia Molecular, NUBIMED - Núcleo de Biomedicina, Universidade Federal do Ceará - UFC. Fortaleza, Ceará, Brasil
| | - J N U Yaochite
- Laboratório de Imunologia Celular e Molecular, Departamento de Análises Clínicas e Toxicológicas da Faculdade de Farmácia, Odontologia e Enfermagem, Universidade Federal do Ceará - UFC, Rua Pastor Samuel Munguba, 1210 - Rodolfo Teófilo, Fortaleza, Ceará, Brasil.
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8
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Gamero-de-Luna EJ, Sánchez-Jaén MR. [Genetic factors associated with long COVID]. Semergen 2024; 50:102187. [PMID: 38277732 DOI: 10.1016/j.semerg.2023.102187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 10/01/2023] [Indexed: 01/28/2024]
Abstract
INTRODUCTION The variability in expression and evolution of COVID is not completely explained by clinical factors. In fact, genetic factors play an important role. Moreover, it is unknown whether the genetic factor that contribute to susceptibility and severity are also involved in the onset and evolution of long-COVID. The objective of this review is to gather information from literature to understand which genetic factors are involved in the onset of persistent COVID. MATERIAL AND METHODS Systematic review in PubMed and bioRxiv and medRxiv repositories based on MeSH-descriptors and MeSH-terms related to COVID and genetic factors. Using these terms 2715 articles were pooled. An initial screening performed by authors independently, selected 205 articles of interest. A final deeper screening a total of 85 articles were chosen for complete reading and summarized in this review. RESULTS Although ACE2 and TMPSS6 are involved in COVID susceptibility, their involvement in long-COVID has not been found. On the other hand, the severity of the disease and the onset of long-COVID has been associated with different genes involved in the inflammatory and immune response. Particularly interesting has been the association found with the FOXP4 locus. CONCLUSIONS Although studies on long-COVID are insufficient to fully comprehend the cause, it is clear that the current identified genetic factors do not fully explain the progression and onset of long-COVID. Other factors such as polygenic action, pleiotropic genes, the microbiota and epigenetic changes must be considered and studied.
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Affiliation(s)
- E J Gamero-de-Luna
- Medicina Familiar y Comunitaria, Centro de Salud El Juncal, Sevilla, España; GT Medicina Genómica Personalizada y Enfermedades Raras, SEMERGEN, España.
| | - M R Sánchez-Jaén
- GT Medicina Genómica Personalizada y Enfermedades Raras, SEMERGEN, España; Medicina Familiar y Comunitaria, Centro de Salud de Fabero, León, España
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9
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Zhang F, Zhou P, Wang L, Liao X, Liu X, Ke C, Wen S, Shu Y. Polymorphisms of IFN signaling genes and FOXP4 influence the severity of COVID-19. BMC Infect Dis 2024; 24:270. [PMID: 38429664 PMCID: PMC10905836 DOI: 10.1186/s12879-024-09040-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 01/20/2024] [Indexed: 03/03/2024] Open
Abstract
BACKGROUND The clinical manifestations of COVID-19 range from asymptomatic, mild to moderate, severe, and critical disease. Host genetic variants were recognized to affect the disease severity. However, the genetic landscape differs among various populations. Therefore, we explored the variants associated with COVID-19 severity in the Guangdong population. METHODS A total of 314 subjects were selected, of which the severe and critical COVID-19 patients were defined as "cases", and the mild and moderate patients were defined as "control". Twenty-two variants in interferon-related genes and FOXP4 were genotyped using the MassARRAY technology platform. RESULTS IFN signaling gene MX1 rs17000900 CA + AA genotype was correlated with a reduced risk of severe COVID-19 in males (P = 0.001, OR = 0.050, 95%CI = 0.008-0.316). The AT haplotype comprised of MX1 rs17000900 and rs2071430 was more likely to protect against COVID-19 severity (P = 6.3E-03). FOXP4 rs1886814 CC genotype (P = 0.001, OR = 3.747, 95%CI = 1.746-8.043) and rs2894439 GA + AA genotype (P = 0.001, OR = 5.703, 95% CI = 2.045-15.903) were correlated with increased risk of severe COVID-19. Haplotype CA comprised of rs1886814 and rs2894439 was found to be correlated with adverse outcomes (P = 7.0E-04). FOXP4 rs1886814 CC (P = 0.0004) and rs2894439 GA + AA carriers had higher neutralizing antibody titers (P = 0.0018). The CA + AA genotype of MX1 rs17000900 tended to be correlated with lower neutralizing antibody titers than CC genotype (P = 0.0663), but the difference was not statistically significant. CONCLUSION Our study found a possible association between MX1 and FOXP4 polymorphisms and the severity of COVID-19. Distinguishing high-risk patients who develop severe COVID-19 will provide clues for early intervention and individual treatment strategies.
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Affiliation(s)
- Feng Zhang
- School of Public Health (Shenzhen), Sun Yat-Sen University, Shenzhen, 518107, P. R. China
| | - Pingping Zhou
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, P. R. China
| | - Liangliang Wang
- School of Public Health (Shenzhen), Sun Yat-Sen University, Shenzhen, 518107, P. R. China
| | - Xinzhong Liao
- School of Public Health (Shenzhen), Sun Yat-Sen University, Shenzhen, 518107, P. R. China
| | - Xuejie Liu
- School of Public Health (Shenzhen), Sun Yat-Sen University, Shenzhen, 518107, P. R. China
| | - Changwen Ke
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, P. R. China
| | - Simin Wen
- Guangzhou First People's Hospital, the Second Affiliated Hospital of South China University of Technology, Guangzhou, P. R. China.
| | - Yuelong Shu
- School of Public Health (Shenzhen), Sun Yat-Sen University, Shenzhen, 518107, P. R. China.
- Key Laboratory of Pathogen Infection Prevention and Control (MOE), State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 102629, P. R. China.
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10
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Chen Y, Yu XY, Xu SJ, Shi XQ, Zhang XX, Sun C. An indel introduced by Neanderthal introgression, rs3835124:ATTTATT > ATT, might contribute to prostate cancer risk by regulating PDK1 expression. Ann Hum Genet 2024; 88:126-137. [PMID: 37846608 DOI: 10.1111/ahg.12533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 07/25/2023] [Accepted: 08/04/2023] [Indexed: 10/18/2023]
Abstract
INTRODUCTION Prostate cancer is one of the most common cancer types in males and rs12621278:A > G has been suggested to be associated with this disease by previous genome-wide association studies. One thousand genomes project data analysis indicated that rs12621278:A > G is within two long-core haplotypes. However, the origin, causal variant(s), and molecular function of these haplotypes were remaining unclear. MATERIALS AND METHODS Population genetics analysis and functional genomics work was performed for this locus. RESULTS Phylogeny analysis verified that the rare haplotype is derived from Neanderthal introgression. Genome annotation suggested that three genetic variants in the core haplotypes, rs116108611:G > A, rs139972066:AAAAAAAA > AAAAAAAAA, and rs3835124:ATTTATT > ATT, are located in functional regions. Luciferase assay indicated that rs139972066:AAAAAAAA > AAAAAAAAA and rs116108611:G > A are not able to alter ITGA6 (integrin alpha 6) and ITGA6 antisense RNA 1 expression, respectively. In contrast, rs3835124:ATTTATT > ATT can significantly influence PDK1 (pyruvate dehydrogenase kinase 1) expression, which was verified by expression quantitative trait locus analysis. This genetic variant can alter transcription factor cut like homeobox 1 interaction efficiency. The introgressed haplotype was observed to be subject to positive selection in East Asian populations. The molecular function of the haplotype suggested that Neanderthal should be with lower PDK1 expression and further different energy homeostasis from modern human. CONCLUSION This study provided new insight into the contribution of Neanderthal introgression to human phenotypes.
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Affiliation(s)
- Ying Chen
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, P. R. China
| | - Xin-Yi Yu
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, P. R. China
| | - Shuang-Jia Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, P. R. China
| | - Xiao-Qian Shi
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, P. R. China
| | - Xin-Xin Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, P. R. China
| | - Chang Sun
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, P. R. China
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11
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Zeberg H, Jakobsson M, Pääbo S. The genetic changes that shaped Neandertals, Denisovans, and modern humans. Cell 2024; 187:1047-1058. [PMID: 38367615 DOI: 10.1016/j.cell.2023.12.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/20/2023] [Accepted: 12/20/2023] [Indexed: 02/19/2024]
Abstract
Modern human ancestors diverged from the ancestors of Neandertals and Denisovans about 600,000 years ago. Until about 40,000 years ago, these three groups existed in parallel, occasionally met, and exchanged genes. A critical question is why modern humans, and not the other two groups, survived, became numerous, and developed complex cultures. Here, we discuss genetic differences among the groups and some of their functional consequences. As more present-day genome sequences become available from diverse groups, we predict that very few, if any, differences will distinguish all modern humans from all Neandertals and Denisovans. We propose that the genetic basis of what constitutes a modern human is best thought of as a combination of genetic features, where perhaps none of them is present in each and every present-day individual.
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Affiliation(s)
- Hugo Zeberg
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Physiology and Pharmacology, Karolinska Institutet, 17165 Stockholm, Sweden.
| | - Mattias Jakobsson
- Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Okinawa Institute of Science and Technology, Onnason 904-0495, Okinawa, Japan.
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12
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Kerdoncuff E, Skov L, Patterson N, Zhao W, Lueng YY, Schellenberg GD, Smith JA, Dey S, Ganna A, Dey AB, Kardia SL, Lee J, Moorjani P. 50,000 years of Evolutionary History of India: Insights from ~2,700 Whole Genome Sequences. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.15.580575. [PMID: 38405782 PMCID: PMC10888882 DOI: 10.1101/2024.02.15.580575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
India has been underrepresented in whole genome sequencing studies. We generated 2,762 high coverage genomes from India-including individuals from most geographic regions, speakers of all major languages, and tribal and caste groups-providing a comprehensive survey of genetic variation in India. With these data, we reconstruct the evolutionary history of India through space and time at fine scales. We show that most Indians derive ancestry from three ancestral groups related to ancient Iranian farmers, Eurasian Steppe pastoralists and South Asian hunter-gatherers. We uncover a common source of Iranian-related ancestry from early Neolithic cultures of Central Asia into the ancestors of Ancestral South Indians (ASI), Ancestral North Indians (ANI), Austro-asiatic-related and East Asian-related groups in India. Following these admixtures, India experienced a major demographic shift towards endogamy, resulting in extensive homozygosity and identity-by-descent sharing among individuals. At deep time scales, Indians derive around 1-2% of their ancestry from gene flow from archaic hominins, Neanderthals and Denisovans. By assembling the surviving fragments of archaic ancestry in modern Indians, we recover ~1.5 Gb (or 50%) of the introgressing Neanderthal and ~0.6 Gb (or 20%) of the introgressing Denisovan genomes, more than any other previous archaic ancestry study. Moreover, Indians have the largest variation in Neanderthal ancestry, as well as the highest amount of population-specific Neanderthal segments among worldwide groups. Finally, we demonstrate that most of the genetic variation in Indians stems from a single major migration out of Africa that occurred around 50,000 years ago, with minimal contribution from earlier migration waves. Together, these analyses provide a detailed view of the population history of India and underscore the value of expanding genomic surveys to diverse groups outside Europe.
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Affiliation(s)
- Elise Kerdoncuff
- Department of Molecular and Cell Biology, University of California, Berkeley, United States of America
| | - Laurits Skov
- Department of Molecular and Cell Biology, University of California, Berkeley, United States of America
| | - Nick Patterson
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Wei Zhao
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yuk Yee Lueng
- Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, United States of America
| | - Gerard D. Schellenberg
- Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, United States of America
| | - Jennifer A. Smith
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Sharmistha Dey
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, Helsinki, Finland
| | - AB Dey
- Department of Geriatric Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Sharon L.R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jinkook Lee
- Department of Economics, and Center for Economic & Social Research, University of Southern California, Los Angeles, California, United States of America
| | - Priya Moorjani
- Department of Molecular and Cell Biology, University of California, Berkeley, United States of America
- Center for Computational Biology, University of California, Berkeley, United States of America
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English A, McDaid D, Lynch SM, McLaughlin J, Cooper E, Wingfield B, Kelly M, Bhavsar M, McGilligan V, Irwin RE, Bucholc M, Zhang SD, Shukla P, Rai TS, Bjourson AJ, Murray E, Gibson DS, Walsh C. Genomic, Proteomic, and Phenotypic Biomarkers of COVID-19 Severity: Protocol for a Retrospective Observational Study. JMIR Res Protoc 2024; 13:e50733. [PMID: 38354037 PMCID: PMC10868637 DOI: 10.2196/50733] [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: 07/11/2023] [Revised: 10/23/2023] [Accepted: 11/09/2023] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND Health organizations and countries around the world have found it difficult to control the spread of COVID-19. To minimize the future impact on the UK National Health Service and improve patient care, there is a pressing need to identify individuals who are at a higher risk of being hospitalized because of severe COVID-19. Early targeted work was successful in identifying angiotensin-converting enzyme-2 receptors and type II transmembrane serine protease dependency as drivers of severe infection. Although a targeted approach highlights key pathways, a multiomics approach will provide a clearer and more comprehensive picture of severe COVID-19 etiology and progression. OBJECTIVE The COVID-19 Response Study aims to carry out an integrated multiomics analysis to identify biomarkers in blood and saliva that could contribute to host susceptibility to SARS-CoV-2 and the development of severe COVID-19. METHODS The COVID-19 Response Study aims to recruit 1000 people who recovered from SARS-CoV-2 infection in both community and hospital settings on the island of Ireland. This protocol describes the retrospective observational study component carried out in Northern Ireland (NI; Cohort A); the Republic of Ireland cohort will be described separately. For all NI participants (n=519), SARS-CoV-2 infection has been confirmed by reverse transcription-quantitative polymerase chain reaction. A prospective Cohort B of 40 patients is also being followed up at 1, 3, 6, and 12 months postinfection to assess longitudinal symptom frequency and immune response. Data will be sourced from whole blood, saliva samples, and clinical data from the electronic care records, the general health questionnaire, and a 12-item general health questionnaire mental health survey. Saliva and blood samples were processed to extract DNA and RNA before whole-genome sequencing, RNA sequencing, DNA methylation analysis, microbiome analysis, 16S ribosomal RNA gene sequencing, and proteomic analysis were performed on the plasma. Multiomics data will be combined with clinical data to produce sensitive and specific prognostic models for severity risk. RESULTS An initial demographic and clinical profile of the NI Cohort A has been completed. A total of 249 hospitalized patients and 270 nonhospitalized patients were recruited, of whom 184 (64.3%) were female, and the mean age was 45.4 (SD 13) years. High levels of comorbidity were evident in the hospitalized cohort, with cardiovascular disease and metabolic and respiratory disorders being the most significant (P<.001), grouped according to the International Classification of Diseases 10 codes. CONCLUSIONS This study will provide a comprehensive opportunity to study the mechanisms of COVID-19 severity in recontactable participants. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) DERR1-10.2196/50733.
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Affiliation(s)
- Andrew English
- Personalised Medicine Centre, School of Medicine, Ulster University, Derry/Londonderry, United Kingdom
- National Horizons Centre, Teesside University, Middlesbrough, United Kingdom
| | - Darren McDaid
- Personalised Medicine Centre, School of Medicine, Ulster University, Derry/Londonderry, United Kingdom
| | - Seodhna M Lynch
- Personalised Medicine Centre, School of Medicine, Ulster University, Derry/Londonderry, United Kingdom
| | - Joseph McLaughlin
- Personalised Medicine Centre, School of Medicine, Ulster University, Derry/Londonderry, United Kingdom
| | - Eamonn Cooper
- Personalised Medicine Centre, School of Medicine, Ulster University, Derry/Londonderry, United Kingdom
| | - Benjamin Wingfield
- Personalised Medicine Centre, School of Medicine, Ulster University, Derry/Londonderry, United Kingdom
| | - Martin Kelly
- Western Health Social Care Trust, Londonderry, United Kingdom
| | - Manav Bhavsar
- Western Health Social Care Trust, Londonderry, United Kingdom
| | - Victoria McGilligan
- Personalised Medicine Centre, School of Medicine, Ulster University, Derry/Londonderry, United Kingdom
| | - Rachelle E Irwin
- Personalised Medicine Centre, School of Medicine, Ulster University, Derry/Londonderry, United Kingdom
| | - Magda Bucholc
- Personalised Medicine Centre, School of Medicine, Ulster University, Derry/Londonderry, United Kingdom
| | - Shu-Dong Zhang
- Personalised Medicine Centre, School of Medicine, Ulster University, Derry/Londonderry, United Kingdom
| | - Priyank Shukla
- Personalised Medicine Centre, School of Medicine, Ulster University, Derry/Londonderry, United Kingdom
| | - Taranjit Singh Rai
- Personalised Medicine Centre, School of Medicine, Ulster University, Derry/Londonderry, United Kingdom
| | - Anthony J Bjourson
- Personalised Medicine Centre, School of Medicine, Ulster University, Derry/Londonderry, United Kingdom
| | - Elaine Murray
- Personalised Medicine Centre, School of Medicine, Ulster University, Derry/Londonderry, United Kingdom
| | - David S Gibson
- Personalised Medicine Centre, School of Medicine, Ulster University, Derry/Londonderry, United Kingdom
| | - Colum Walsh
- Department of Biomedical and Clinical Sciences, Linköping University, Uppsala, Sweden
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14
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Hubáček JA, Šedová L, Hellerová V, Adámková V, Tóthová V. Increased prevalence of the COVID-19 associated Neanderthal mutations in the Central European Roma population. Ann Hum Biol 2024; 51:2341727. [PMID: 38771659 DOI: 10.1080/03014460.2024.2341727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/26/2024] [Indexed: 05/23/2024]
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and subsequent COVID-19 has spread world-wide and become pandemic with about 7 million deaths reported so far. Interethnic variability of the disease has been described, but a significant part of the differences remain unexplained and may be attributable to genetic factors. AIM To analyse genetic factors potentially influencing COVID-19 susceptibility and severity in European Roma minority. SUBJECTS AND METHODS Two genetic determinants, within OAS-1 (2-prime,5-prime-oligoadenylate synthetase 1, a key protein in the defence against viral infection; it activates RNases that degrade viral RNAs; rs4767027 has been analysed) and LZTFL1 (leucine zipper transcription factor-like 1, expressed in the lung respiratory epithelium; rs35044562 has been analysed) genes were screened in a population-sample of Czech Roma (N = 302) and majority population (N = 2,559). RESULTS For both polymorphisms, Roma subjects were more likely carriers of at least one risky allele for both rs4767027-C (p < 0.001) and rs35044562-G (p < 0.00001) polymorphism. There were only 5.3% Roma subjects without at least one risky allele in comparison with 10.1% in the majority population (p < 0.01). CONCLUSIONS It is possible that different genetic background plays an important role in increased prevalence of COVID-19 in the Roma minority.
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Affiliation(s)
- Jaroslav A Hubáček
- Experimental Medicine Centre, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
- 3rd Department of Internal Medicine, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Lenka Šedová
- Faculty of Health and Social Sciences, University of South Bohemia, České Budějovice, Czech Republic
| | - Věra Hellerová
- Faculty of Health and Social Sciences, University of South Bohemia, České Budějovice, Czech Republic
| | - Věra Adámková
- Department of Preventive Cardiology, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Valérie Tóthová
- Faculty of Health and Social Sciences, University of South Bohemia, České Budějovice, Czech Republic
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Peyrégne S, Slon V, Kelso J. More than a decade of genetic research on the Denisovans. Nat Rev Genet 2024; 25:83-103. [PMID: 37723347 DOI: 10.1038/s41576-023-00643-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2023] [Indexed: 09/20/2023]
Abstract
Denisovans, a group of now extinct humans who lived in Eastern Eurasia in the Middle and Late Pleistocene, were first identified from DNA sequences just over a decade ago. Only ten fragmentary remains from two sites have been attributed to Denisovans based entirely on molecular information. Nevertheless, there has been great interest in using genetic data to understand Denisovans and their place in human history. From the reconstruction of a single high-quality genome, it has been possible to infer their population history, including events of admixture with other human groups. Additionally, the identification of Denisovan DNA in the genomes of present-day individuals has provided insights into the timing and routes of dispersal of ancient modern humans into Asia and Oceania, as well as the contributions of archaic DNA to the physiology of present-day people. In this Review, we synthesize more than a decade of research on Denisovans, reconcile controversies and summarize insights into their population history and phenotype. We also highlight how our growing knowledge about Denisovans has provided insights into our own evolutionary history.
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Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Viviane Slon
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anatomy and Anthropology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, Tel Aviv, Israel
| | - Janet Kelso
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
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16
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Lei H, Li J, Zhao B, Kou SH, Xiao F, Chen T, Wang SM. Evolutionary origin of germline pathogenic variants in human DNA mismatch repair genes. Hum Genomics 2024; 18:5. [PMID: 38287404 PMCID: PMC10823654 DOI: 10.1186/s40246-024-00573-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 01/17/2024] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND Mismatch repair (MMR) system is evolutionarily conserved for genome stability maintenance. Germline pathogenic variants (PVs) in MMR genes that lead to MMR functional deficiency are associated with high cancer risk. Knowing the evolutionary origin of germline PVs in human MMR genes will facilitate understanding the biological base of MMR deficiency in cancer. However, systematic knowledge is lacking to address the issue. In this study, we performed a comprehensive analysis to know the evolutionary origin of human MMR PVs. METHODS We retrieved MMR gene variants from the ClinVar database. The genomes of 100 vertebrates were collected from the UCSC genome browser and ancient human sequencing data were obtained through comprehensive data mining. Cross-species conservation analysis was performed based on the phylogenetic relationship among 100 vertebrates. Rescaled ancient sequencing data were used to perform variant calling for archeological analysis. RESULTS Using the phylogenetic approach, we traced the 3369 MMR PVs identified in modern humans in 99 non-human vertebrate genomes but found no evidence for cross-species conservation as the source for human MMR PVs. Using the archeological approach, we searched the human MMR PVs in over 5000 ancient human genomes dated from 45,045 to 100 years before present and identified a group of MMR PVs shared between modern and ancient humans mostly within 10,000 years with similar quantitative patterns. CONCLUSION Our study reveals that MMR PVs in modern humans were arisen within the recent human evolutionary history.
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Affiliation(s)
- Huijun Lei
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310018, Zhejiang, China
- Department of Cancer Prevention, Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang, China
| | - Jiaheng Li
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Bojin Zhao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Si Hoi Kou
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Fengxia Xiao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Tianhui Chen
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310018, Zhejiang, China.
- Department of Cancer Prevention, Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang, China.
| | - San Ming Wang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China.
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Kato S, Arakaki S, Nagano AJ, Kikuchi K, Hirase S. Genomic landscape of introgression from the ghost lineage in a gobiid fish uncovers the generality of forces shaping hybrid genomes. Mol Ecol 2023. [PMID: 38047388 DOI: 10.1111/mec.17216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/23/2023] [Accepted: 10/26/2023] [Indexed: 12/05/2023]
Abstract
Extinct lineages can leave legacies in the genomes of extant lineages through ancient introgressive hybridization. The patterns of genomic survival of these extinct lineages provide insight into the role of extinct lineages in current biodiversity. However, our understanding on the genomic landscape of introgression from extinct lineages remains limited due to challenges associated with locating the traces of unsampled 'ghost' extinct lineages without ancient genomes. Herein, we conducted population genomic analyses on the East China Sea (ECS) lineage of Chaenogobius annularis, which was suspected to have originated from ghost introgression, with the aim of elucidating its genomic origins and characterizing its landscape of introgression. By combining phylogeographic analysis and demographic modelling, we demonstrated that the ECS lineage originated from ancient hybridization with an extinct ghost lineage. Forward simulations based on the estimated demography indicated that the statistic γ of the HyDe analysis can be used to distinguish the differences in local introgression rates in our data. Consistent with introgression between extant organisms, we found reduced introgression from extinct lineage in regions with low recombination rates and with functional importance, thereby suggesting a role of linked selection that has eliminated the extinct lineage in shaping the hybrid genome. Moreover, we identified enrichment of repetitive elements in regions associated with ghost introgression, which was hitherto little known but was also observed in the re-analysis of published data on introgression between extant organisms. Overall, our findings underscore the unexpected similarities in the characteristics of introgression landscapes across different taxa, even in cases of ghost introgression.
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Affiliation(s)
- Shuya Kato
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Hamamatsu, Shizuoka, Japan
| | - Seiji Arakaki
- Amakusa Marine Biological Laboratory, Kyushu University, Amakusa, Kumamoto, Japan
| | - Atsushi J Nagano
- Department of Life Sciences, Faculty of Agriculture, Ryukoku University, Ōtsu, Shiga, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Kiyoshi Kikuchi
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Hamamatsu, Shizuoka, Japan
| | - Shotaro Hirase
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Hamamatsu, Shizuoka, Japan
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18
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Wroblewski TH, Witt KE, Lee SB, Malhi RS, Peede D, Huerta-Sánchez E, Villanea FA, Claw KG. Pharmacogenetic Variation in Neanderthals and Denisovans and Implications for Human Health and Response to Medications. Genome Biol Evol 2023; 15:evad222. [PMID: 38051947 PMCID: PMC10727477 DOI: 10.1093/gbe/evad222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 11/08/2023] [Accepted: 11/16/2023] [Indexed: 12/07/2023] Open
Abstract
Modern humans carry both Neanderthal and Denisovan (archaic) genome elements that are part of the human gene pool and affect the life and health of living individuals. The impact of archaic DNA may be particularly evident in pharmacogenes-genes responsible for the processing of exogenous substances such as food, pollutants, and medications-as these can relate to changing environmental effects, and beneficial variants may have been retained as modern humans encountered new environments. However, the health implications and contribution of archaic ancestry in pharmacogenes of modern humans remain understudied. Here, we explore 11 key cytochrome P450 genes (CYP450) involved in 75% of all drug metabolizing reactions in three Neanderthal and one Denisovan individuals and examine archaic introgression in modern human populations. We infer the metabolizing efficiency of these 11 CYP450 genes in archaic individuals and find important predicted phenotypic differences relative to modern human variants. We identify several single nucleotide variants shared between archaic and modern humans in each gene, including some potentially function-altering mutations in archaic CYP450 genes, which may result in altered metabolism in living people carrying these variants. We also identified several variants in the archaic CYP450 genes that are novel and unique to archaic humans as well as one gene, CYP2B6, that shows evidence for a gene duplication found only in Neanderthals and modern Africans. Finally, we highlight CYP2A6, CYP2C9, and CYP2J2, genes which show evidence for archaic introgression into modern humans and posit evolutionary hypotheses that explain their allele frequencies in modern populations.
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Affiliation(s)
- Tadeusz H Wroblewski
- Department of Biomedical Informatics, Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kelsey E Witt
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, South Carolina, USA
| | - Seung-been Lee
- Precision Medicine Institute, Macrogen Inc., Seoul, Republic of Korea
| | - Ripan S Malhi
- Department of Anthropology and Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Illinois, USA
| | - David Peede
- Department of Ecology, Evolution, and Organismal Biology and Center for Computational and Molecular Biology, Brown University, Providence, Rhode Island, USA
- Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, USA
| | - Emilia Huerta-Sánchez
- Department of Ecology, Evolution, and Organismal Biology and Center for Computational and Molecular Biology, Brown University, Providence, Rhode Island, USA
| | | | - Katrina G Claw
- Department of Biomedical Informatics, Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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19
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Lytras S, Wickenhagen A, Sugrue E, Stewart DG, Swingler S, Sims A, Jackson Ireland H, Davies EL, Ludlam EM, Li Z, Hughes J, Wilson SJ. Resurrection of 2'-5'-oligoadenylate synthetase 1 (OAS1) from the ancestor of modern horseshoe bats blocks SARS-CoV-2 replication. PLoS Biol 2023; 21:e3002398. [PMID: 38015855 PMCID: PMC10683996 DOI: 10.1371/journal.pbio.3002398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 10/20/2023] [Indexed: 11/30/2023] Open
Abstract
The prenylated form of the human 2'-5'-oligoadenylate synthetase 1 (OAS1) protein has been shown to potently inhibit the replication of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the virus responsible for the Coronavirus Disease 2019 (COVID-19) pandemic. However, the OAS1 orthologue in the horseshoe bats (superfamily Rhinolophoidea), the reservoir host of SARS-related coronaviruses (SARSr-CoVs), has lost the prenylation signal required for this antiviral activity. Herein, we used an ancestral state reconstruction approach to predict and reconstitute in vitro, the most likely OAS1 protein sequence expressed by the Rhinolophoidea common ancestor prior to its prenylation loss (RhinoCA OAS1). We exogenously expressed the ancient bat protein in vitro to show that, unlike its non-prenylated horseshoe bat descendants, RhinoCA OAS1 successfully blocks SARS-CoV-2 replication. Using protein structure predictions in combination with evolutionary hypothesis testing methods, we highlight sites under unique diversifying selection specific to OAS1's evolution in the Rhinolophoidea. These sites are located near the RNA-binding region and the C-terminal end of the protein where the prenylation signal would have been. Our results confirm that OAS1 prenylation loss at the base of the Rhinolophoidea clade ablated the ability of OAS1 to restrict SARSr-CoV replication and that subsequent evolution of the gene in these bats likely favoured an alternative function. These findings can advance our understanding of the tightly linked association between SARSr-CoVs and horseshoe bats.
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Affiliation(s)
- Spyros Lytras
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Arthur Wickenhagen
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Elena Sugrue
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Douglas G. Stewart
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Simon Swingler
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Anna Sims
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Hollie Jackson Ireland
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Emma L. Davies
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Eliza M. Ludlam
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Zhuonan Li
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Joseph Hughes
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Sam J. Wilson
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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20
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Torices S, Teglas T, Naranjo O, Fattakhov N, Frydlova K, Cabrera R, Osborne OM, Sun E, Kluttz A, Toborek M. Occludin Regulates HIV-1 Infection by Modulation of the Interferon Stimulated OAS Gene Family. Mol Neurobiol 2023; 60:4966-4982. [PMID: 37209263 PMCID: PMC10199280 DOI: 10.1007/s12035-023-03381-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 05/04/2023] [Indexed: 05/22/2023]
Abstract
HIV-1-associated blood brain barrier (BBB) alterations and neurocognitive disorders are frequent clinical manifestations in HIV-1 infected patients. The BBB is formed by cells of the neurovascular unit (NVU) and sealed together by tight junction proteins, such as occludin (ocln). Pericytes are a key cell type of NVU that can harbor HIV-1 infection via a mechanism that is regulated, at least in part, by ocln. After viral infection, the immune system starts the production of interferons, which induce the expression of the 2'-5'-oligoadenylate synthetase (OAS) family of interferon stimulated genes and activate the endoribonuclease RNaseL that provides antiviral protection by viral RNA degradation. The current study evaluated the involvement of the OAS genes in HIV-1 infection of cells of NVU and the role of ocln in controlling OAS antiviral signaling pathway. We identified that ocln modulates the expression levels of the OAS1, OAS2, OAS3, and OASL genes and proteins and, in turn, that the members of the OAS family can influence HIV replication in human brain pericytes. Mechanistically, this effect was regulated via the STAT signaling. HIV-1 infection of pericytes significantly upregulated expression of all OAS genes at the mRNA level but selectively OAS1, OAS2, and OAS3 at the protein level. Interestingly no changes were found in RNaseL after HIV-1 infection. Overall, these results contribute to a better understanding of the molecular mechanisms implicated in the regulation of HIV-1 infection in human brain pericytes and suggest a novel role for ocln in controlling of this process.
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Affiliation(s)
- Silvia Torices
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 528E Gautier Bldg. 1011 NW 15th Street, Miami, FL, 11336, USA.
| | - Timea Teglas
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 528E Gautier Bldg. 1011 NW 15th Street, Miami, FL, 11336, USA
| | - Oandy Naranjo
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 528E Gautier Bldg. 1011 NW 15th Street, Miami, FL, 11336, USA
| | - Nikolai Fattakhov
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 528E Gautier Bldg. 1011 NW 15th Street, Miami, FL, 11336, USA
| | - Kristyna Frydlova
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 528E Gautier Bldg. 1011 NW 15th Street, Miami, FL, 11336, USA
| | - Rosalba Cabrera
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 528E Gautier Bldg. 1011 NW 15th Street, Miami, FL, 11336, USA
| | - Olivia M Osborne
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 528E Gautier Bldg. 1011 NW 15th Street, Miami, FL, 11336, USA
| | - Enze Sun
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 528E Gautier Bldg. 1011 NW 15th Street, Miami, FL, 11336, USA
| | - Allan Kluttz
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 528E Gautier Bldg. 1011 NW 15th Street, Miami, FL, 11336, USA
| | - Michal Toborek
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 528E Gautier Bldg. 1011 NW 15th Street, Miami, FL, 11336, USA.
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21
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Aquino Y, Bisiaux A, Li Z, O'Neill M, Mendoza-Revilla J, Merkling SH, Kerner G, Hasan M, Libri V, Bondet V, Smith N, de Cevins C, Ménager M, Luca F, Pique-Regi R, Barba-Spaeth G, Pietropaoli S, Schwartz O, Leroux-Roels G, Lee CK, Leung K, Wu JT, Peiris M, Bruzzone R, Abel L, Casanova JL, Valkenburg SA, Duffy D, Patin E, Rotival M, Quintana-Murci L. Dissecting human population variation in single-cell responses to SARS-CoV-2. Nature 2023; 621:120-128. [PMID: 37558883 PMCID: PMC10482701 DOI: 10.1038/s41586-023-06422-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 07/11/2023] [Indexed: 08/11/2023]
Abstract
Humans display substantial interindividual clinical variability after SARS-CoV-2 infection1-3, the genetic and immunological basis of which has begun to be deciphered4. However, the extent and drivers of population differences in immune responses to SARS-CoV-2 remain unclear. Here we report single-cell RNA-sequencing data for peripheral blood mononuclear cells-from 222 healthy donors of diverse ancestries-that were stimulated with SARS-CoV-2 or influenza A virus. We show that SARS-CoV-2 induces weaker, but more heterogeneous, interferon-stimulated gene activity compared with influenza A virus, and a unique pro-inflammatory signature in myeloid cells. Transcriptional responses to viruses display marked population differences, primarily driven by changes in cell abundance including increased lymphoid differentiation associated with latent cytomegalovirus infection. Expression quantitative trait loci and mediation analyses reveal a broad effect of cell composition on population disparities in immune responses, with genetic variants exerting a strong effect on specific loci. Furthermore, we show that natural selection has increased population differences in immune responses, particularly for variants associated with SARS-CoV-2 response in East Asians, and document the cellular and molecular mechanisms by which Neanderthal introgression has altered immune functions, such as the response of myeloid cells to viruses. Finally, colocalization and transcriptome-wide association analyses reveal an overlap between the genetic basis of immune responses to SARS-CoV-2 and COVID-19 severity, providing insights into the factors contributing to current disparities in COVID-19 risk.
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Affiliation(s)
- Yann Aquino
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
- Collège Doctoral, Sorbonne Université, Paris, France
| | - Aurélie Bisiaux
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Zhi Li
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Mary O'Neill
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Javier Mendoza-Revilla
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Sarah Hélène Merkling
- Insect-Virus Interactions Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Gaspard Kerner
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Milena Hasan
- Cytometry and Biomarkers UTechS, Institut Pasteur, Université Paris Cité, Paris, France
| | - Valentina Libri
- Cytometry and Biomarkers UTechS, Institut Pasteur, Université Paris Cité, Paris, France
| | - Vincent Bondet
- Translational Immunology Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Nikaïa Smith
- Translational Immunology Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Camille de Cevins
- Université Paris Cité, Imagine Institute, Laboratory of Inflammatory Responses and Transcriptomic Networks in Diseases, Atip-Avenir Team, INSERM UMR1163, Paris, France
| | - Mickaël Ménager
- Université Paris Cité, Imagine Institute, Laboratory of Inflammatory Responses and Transcriptomic Networks in Diseases, Atip-Avenir Team, INSERM UMR1163, Paris, France
- Labtech Single-Cell@Imagine, Imagine Institute, INSERM UMR1163, Paris, France
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
| | - Giovanna Barba-Spaeth
- Structural Virology Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
| | - Stefano Pietropaoli
- Structural Virology Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
| | - Olivier Schwartz
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
| | | | - Cheuk-Kwong Lee
- Hong Kong Red Cross Blood Transfusion Service, Hospital Authority, Hong Kong SAR, China
| | - Kathy Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong SAR, China
| | - Joseph T Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong SAR, China
| | - Malik Peiris
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
- Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong SAR, China
| | - Roberto Bruzzone
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
- Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong SAR, China
| | - Laurent Abel
- St Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France
- Université Paris Cité, Imagine Institute, Paris, France
| | - Jean-Laurent Casanova
- St Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France
- Université Paris Cité, Imagine Institute, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, New York, NY, USA
| | - Sophie A Valkenburg
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Darragh Duffy
- Translational Immunology Unit, Institut Pasteur, Université Paris Cité, Paris, France
- Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong SAR, China
| | - Etienne Patin
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Maxime Rotival
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France.
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France.
- Chair Human Genomics and Evolution, Collège de France, Paris, France.
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22
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Ramasamy R. Overview of immunological & virological factors driving the evolution & global spread of SARS-CoV-2 variants. Indian J Med Res 2023; 158:257-268. [PMID: 37815068 PMCID: PMC10720969 DOI: 10.4103/ijmr.ijmr_2591_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Indexed: 10/11/2023] Open
Abstract
The SARS-CoV-2, a highly infectious positive strand RNA virus first identified in December 2019, has produced multiple genetic variants that have rapidly and sequentially spread worldwide during the coronavirus disease 2019 (COVID-19) pandemic. Genetic changes in SARS-CoV-2 for greater infectivity, replication and transmission were selected during the early stages of the pandemic. More recently, after widespread infection and vaccination, SARS-CoV-2 variants that evade antigen-specific adaptive immunity, have begun to be selected. This article provides an overview of the molecular immunological and virological factors underlying the origin and global spread of important SARS-CoV-2 variant lineages.
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23
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Aoki K, Takahata N, Oota H, Wakano JY, Feldman MW. Infectious diseases may have arrested the southward advance of microblades in Upper Palaeolithic East Asia. Proc Biol Sci 2023; 290:20231262. [PMID: 37644833 PMCID: PMC10465978 DOI: 10.1098/rspb.2023.1262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/01/2023] [Indexed: 08/31/2023] Open
Abstract
An unsolved archaeological puzzle of the East Asian Upper Palaeolithic is why the southward expansion of an innovative lithic technology represented by microblades stalled at the Qinling-Huaihe Line. It has been suggested that the southward migration of foragers with microblades stopped there, which is consistent with ancient DNA studies showing that populations to the north and south of this line had differentiated genetically by 19 000 years ago. Many infectious pathogens are believed to have been associated with hominins since the Palaeolithic, and zoonotic pathogens in particular are prevalent at lower latitudes, which may have produced a disease barrier. We propose a mathematical model to argue that mortality due to infectious diseases may have arrested the wave-of-advance of the technologically advantaged foragers from the north.
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Affiliation(s)
- Kenichi Aoki
- Graduate School of Science, University of Tokyo, Hongo, Tokyo 113-0033, Japan
| | - Naoyuki Takahata
- Graduate University for Advanced Studies, Hayama, Kanagawa 240-0116, Japan
| | - Hiroki Oota
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Tokyo 113-0033, Japan
| | - Joe Yuichiro Wakano
- School of Interdisciplinary Mathematical Sciences, Meiji University, Nakano, Tokyo 164-8525, Japan
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24
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Cobat A, Zhang Q, Abel L, Casanova JL, Fellay J. Human Genomics of COVID-19 Pneumonia: Contributions of Rare and Common Variants. Annu Rev Biomed Data Sci 2023; 6:465-486. [PMID: 37196358 PMCID: PMC10879986 DOI: 10.1146/annurev-biodatasci-020222-021705] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) infection is silent or benign in most infected individuals, but causes hypoxemic COVID-19 pneumonia in about 10% of cases. We review studies of the human genetics of life-threatening COVID-19 pneumonia, focusing on both rare and common variants. Large-scale genome-wide association studies have identified more than 20 common loci robustly associated with COVID-19 pneumonia with modest effect sizes, some implicating genes expressed in the lungs or leukocytes. The most robust association, on chromosome 3, concerns a haplotype inherited from Neanderthals. Sequencing studies focusing on rare variants with a strong effect have been particularly successful, identifying inborn errors of type I interferon (IFN) immunity in 1-5% of unvaccinated patients with critical pneumonia, and their autoimmune phenocopy, autoantibodies against type I IFN, in another 15-20% of cases. Our growing understanding of the impact of human genetic variation on immunity to SARS-CoV-2 is enabling health systems to improve protection for individuals and populations.
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Affiliation(s)
- Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France;
- Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA;
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France;
- Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA;
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France;
- Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA;
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France;
- Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA;
- Howard Hughes Medical Institute, New York, NY, USA
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland;
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Biomedical Data Science Center, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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25
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Pan-Hammarström Q, Casanova JL. Human genetic and immunological determinants of SARS-CoV-2 and Epstein-Barr virus diseases in childhood: Insightful contrasts. J Intern Med 2023; 294:127-144. [PMID: 36906905 DOI: 10.1111/joim.13628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
Abstract
There is growing evidence to suggest that severe disease in children infected with common viruses that are typically benign in other children can result from inborn errors of immunity or their phenocopies. Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a cytolytic respiratory RNA virus, can lead to acute hypoxemic COVID-19 pneumonia in children with inborn errors of type I interferon (IFN) immunity or autoantibodies against IFNs. These patients do not appear to be prone to severe disease during infection with Epstein-Barr virus (EBV), a leukocyte-tropic DNA virus that can establish latency. By contrast, various forms of severe EBV disease, ranging from acute hemophagocytosis to chronic or long-term illnesses, such as agammaglobulinemia and lymphoma, can manifest in children with inborn errors disrupting specific molecular bridges involved in the control of EBV-infected B cells by cytotoxic T cells. The patients with these disorders do not seem to be prone to severe COVID-19 pneumonia. These experiments of nature reveal surprising levels of redundancy of two different arms of immunity, with type I IFN being essential for host defense against SARS-CoV-2 in respiratory epithelial cells, and certain surface molecules on cytotoxic T cells essential for host defense against EBV in B lymphocytes.
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Affiliation(s)
| | - Jean-Laurent Casanova
- St Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, New York, USA
- Howard Hughes Medical Institute, New York, New York, USA
- Laboratory of Human Genetics of Infectious Diseases, Inserm, Paris, France
- Imagine Institute, Paris Cité University, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
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26
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Oláh E. Learning from cancer to address COVID-19. Biol Futur 2023:10.1007/s42977-023-00156-5. [PMID: 37410273 DOI: 10.1007/s42977-023-00156-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 02/24/2023] [Indexed: 07/07/2023]
Abstract
Patients with cancer have been disproportionately affected by the novel coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Knowledge collected during the last three decades of cancer research has helped the medical research community worldwide to respond to many of the challenges raised by COVID-19, during the pandemic. The review, briefly summarizes the underlying biology and risk factors of COVID-19 and cancer, and aims to present recent evidence on cellular and molecular relationship between the two diseases, with a focus on those that are related to the hallmarks of cancer and uncovered in the first less than three years of the pandemic (2020-2022). This may not only help answer the question "Why cancer patients are considered to be at a particularly high risk of developing severe COVID-19 illness?", but also helped treatments of patients during the COVID-19 pandemic. The last session highlights the pioneering mRNA studies and the breakthrough discovery on nucleoside-modifications of mRNA by Katalin Karikó, which led to the innovation and development of the mRNA-based SARSCoV-2 vaccines saving lives of millions and also opened the door for a new era of vaccines and a new class of therapeutics.
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Affiliation(s)
- Edit Oláh
- Department of Molecular Genetics, National Institute of Oncology, Ráth György u. 7-9, Budapest, 1122, Hungary.
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27
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Vaill M, Kawanishi K, Varki N, Gagneux P, Varki A. Comparative physiological anthropogeny: exploring molecular underpinnings of distinctly human phenotypes. Physiol Rev 2023; 103:2171-2229. [PMID: 36603157 PMCID: PMC10151058 DOI: 10.1152/physrev.00040.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023] Open
Abstract
Anthropogeny is a classic term encompassing transdisciplinary investigations of the origins of the human species. Comparative anthropogeny is a systematic comparison of humans and other living nonhuman hominids (so-called "great apes"), aiming to identify distinctly human features in health and disease, with the overall goal of explaining human origins. We begin with a historical perspective, briefly describing how the field progressed from the earliest evolutionary insights to the current emphasis on in-depth molecular and genomic investigations of "human-specific" biology and an increased appreciation for cultural impacts on human biology. While many such genetic differences between humans and other hominids have been revealed over the last two decades, this information remains insufficient to explain the most distinctive phenotypic traits distinguishing humans from other living hominids. Here we undertake a complementary approach of "comparative physiological anthropogeny," along the lines of the preclinical medical curriculum, i.e., beginning with anatomy and considering each physiological system and in each case considering genetic and molecular components that are relevant. What is ultimately needed is a systematic comparative approach at all levels from molecular to physiological to sociocultural, building networks of related information, drawing inferences, and generating testable hypotheses. The concluding section will touch on distinctive considerations in the study of human evolution, including the importance of gene-culture interactions.
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Affiliation(s)
- Michael Vaill
- Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California
| | - Kunio Kawanishi
- Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
- Department of Experimental Pathology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Nissi Varki
- Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California
- Department of Pathology, University of California, San Diego, La Jolla, California
| | - Pascal Gagneux
- Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California
- Department of Pathology, University of California, San Diego, La Jolla, California
| | - Ajit Varki
- Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California
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28
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Yazdanparast S, Bakhtiyaridovvombaygi M, Mikanik F, Ahmadi R, Ghorbani M, Mansoorian MR, Mansoorian M, Chegni H, Moshari J, Gharehbaghian A. Spotlight on contributory role of host immunogenetic profiling in SARS-CoV-2 infection: Susceptibility, severity, mortality, and vaccine effectiveness. Life Sci 2023:121907. [PMID: 37394094 DOI: 10.1016/j.lfs.2023.121907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 06/29/2023] [Accepted: 06/29/2023] [Indexed: 07/04/2023]
Abstract
BACKGROUND The SARS-CoV-2 virus has spread continuously worldwide, characterized by various clinical symptoms. The immune system responds to SARS-CoV-2 infection by producing Abs and secreting cytokines. Recently, numerous studies have highlighted that immunogenetic factors perform a putative role in COVID-19 pathogenesis and implicate vaccination effectiveness. AIM This review summarizes the relevant articles and evaluates the significance of mutation and polymorphism in immune-related genes regarding susceptibility, severity, mortality, and vaccination effectiveness of COVID-19. Furthermore, the correlation between host immunogenetic and SARS-CoV-2 reinfection is discussed. METHOD A comprehensive search was conducted to identify relevant articles using five databases until January 2023, which resulted in 105 total articles. KEY FINDINGS Taken to gather this review summarized that: (a) there is a plausible correlation between immune-related genes and COVID-19 outcomes, (b) the HLAs, cytokines, chemokines, and other immune-related genes expression profiles can be a prognostic factor in COVID-19-infected patients, and (c) polymorphisms in immune-related genes have been associated with the effectiveness of vaccination. SIGNIFICANCE Regarding the importance of mutation and polymorphisms in immune-related genes in COVID-19 outcomes, modulating candidate genes is expected to help clinical decisions, patient outcomes management, and innovative therapeutic approach development. In addition, the manipulation of host immunogenetics is hypothesized to induce more robust cellular and humoral immune responses, effectively increase the efficacy of vaccines, and subsequently reduce the incidence rates of reinfection-associated COVID-19.
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Affiliation(s)
- Somayeh Yazdanparast
- Student Research Committee, Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Bakhtiyaridovvombaygi
- Student Research Committee, Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Mikanik
- Student Research Committee, Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Reza Ahmadi
- Department of Infectious Diseases, School of Medicine, Infectious Diseases Center, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Mohammad Ghorbani
- Laboratory Hematology and Transfusion Medicine, Department of Pathology, Faculty Medicine, Gonabad University of Medical Sciences, Gonabad, Iran.
| | | | - Mozhgan Mansoorian
- Nursing Research Center, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Hamid Chegni
- Department of Immunology, School of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jalil Moshari
- School of Medicine, Gonabad University of Medical Science, Gonabad, Iran
| | - Ahmad Gharehbaghian
- Department of Hematology and Blood Bank, School of Allied Medical Science, Shahid Beheshti University of Medical Science, Tehran, Iran; Pediatric Congenital Hematologic Disorders Research Center, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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29
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Mocci S, Littera R, Chessa L, Campagna M, Melis M, Ottelio CM, Piras IS, Lai S, Firinu D, Tranquilli S, Mascia A, Vacca M, Schirru D, Lecca LI, Rassu S, Cannas F, Sanna C, Carta MG, Sedda F, Giuressi E, Cipri S, Miglianti M, Perra A, Giglio S. A review of the main genetic factors influencing the course of COVID-19 in Sardinia: the role of human leukocyte antigen-G. Front Immunol 2023; 14:1138559. [PMID: 37342325 PMCID: PMC10277491 DOI: 10.3389/fimmu.2023.1138559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 05/23/2023] [Indexed: 06/22/2023] Open
Abstract
Introduction A large number of risk and protective factors have been identified during the SARS-CoV-2 pandemic which may influence the outcome of COVID-19. Among these, recent studies have explored the role of HLA-G molecules and their immunomodulatory effects in COVID-19, but there are very few reports exploring the genetic basis of these manifestations. The present study aims to investigate how host genetic factors, including HLA-G gene polymorphisms and sHLA-G, can affect SARS-CoV-2 infection. Materials and Methods We compared the immune-genetic and phenotypic characteristics between COVID-19 patients (n = 381) with varying degrees of severity of the disease and 420 healthy controls from Sardinia (Italy). Results HLA-G locus analysis showed that the extended haplotype HLA-G*01:01:01:01/UTR-1 was more prevalent in both COVID-19 patients and controls. In particular, this extended haplotype was more common among patients with mild symptoms than those with severe symptoms [22.7% vs 15.7%, OR = 0.634 (95% CI 0.440 - 0.913); P = 0.016]. Furthermore, the most significant HLA-G 3'UTR polymorphism (rs371194629) shows that the HLA-G 3'UTR Del/Del genotype frequency decreases gradually from 27.6% in paucisymptomatic patients to 15.9% in patients with severe symptoms (X2 = 7.095, P = 0.029), reaching the lowest frequency (7.0%) in ICU patients (X2 = 11.257, P = 0.004). However, no significant differences were observed for the soluble HLA-G levels in patients and controls. Finally, we showed that SARS-CoV-2 infection in the Sardinian population is also influenced by other genetic factors such as β-thalassemia trait (rs11549407C>T in the HBB gene), KIR2DS2/HLA-C C1+ group combination and the HLA-B*58:01, C*07:01, DRB1*03:01 haplotype which exert a protective effect [P = 0.005, P = 0.001 and P = 0.026 respectively]. Conversely, the Neanderthal LZTFL1 gene variant (rs35044562A>G) shows a detrimental consequence on the disease course [P = 0.001]. However, by using a logistic regression model, HLA-G 3'UTR Del/Del genotype was independent from the other significant variables [ORM = 0.4 (95% CI 0.2 - 0.7), PM = 6.5 x 10-4]. Conclusion Our results reveal novel genetic variants which could potentially serve as biomarkers for disease prognosis and treatment, highlighting the importance of considering genetic factors in the management of COVID-19 patients.
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Affiliation(s)
- Stefano Mocci
- Medical Genetics, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
- AART-ODV (Association for the Advancement of Research on Transplantation), Cagliari, Italy
| | - Roberto Littera
- AART-ODV (Association for the Advancement of Research on Transplantation), Cagliari, Italy
- Medical Genetics, R. Binaghi Hospital, Local Public Health and Social Care Unit (ASSL) of Cagliari, Cagliari, Italy
| | - Luchino Chessa
- AART-ODV (Association for the Advancement of Research on Transplantation), Cagliari, Italy
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
- Liver Unit, University Hospital, Cagliari, Italy
| | - Marcello Campagna
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Maurizio Melis
- AART-ODV (Association for the Advancement of Research on Transplantation), Cagliari, Italy
| | - Carla Maria Ottelio
- Anesthesia and Intensive Care Unit, R. Binaghi Hospital, Local Public Health and Social Care Unit (ASSL) of Cagliari, Cagliari, Italy
| | - Ignazio S. Piras
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, United States
| | - Sara Lai
- Medical Genetics, R. Binaghi Hospital, Local Public Health and Social Care Unit (ASSL) of Cagliari, Cagliari, Italy
| | - Davide Firinu
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Stefania Tranquilli
- Medical Genetics, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Alessia Mascia
- Medical Genetics, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Monica Vacca
- Medical Genetics, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Daniele Schirru
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Luigi Isaia Lecca
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Stefania Rassu
- Medical Genetics, R. Binaghi Hospital, Local Public Health and Social Care Unit (ASSL) of Cagliari, Cagliari, Italy
| | - Federica Cannas
- Medical Genetics, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Celeste Sanna
- Medical Genetics, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Mauro Giovanni Carta
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Francesca Sedda
- Section of Pathology, Oncology and Molecular Pathology Unit, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Erika Giuressi
- Medical Genetics, R. Binaghi Hospital, Local Public Health and Social Care Unit (ASSL) of Cagliari, Cagliari, Italy
| | - Selene Cipri
- GeneMos-APS (Association for Social Advancement), Reggio Calabria, Italy
| | - Michela Miglianti
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Andrea Perra
- AART-ODV (Association for the Advancement of Research on Transplantation), Cagliari, Italy
- Section of Pathology, Oncology and Molecular Pathology Unit, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Sabrina Giglio
- Medical Genetics, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
- Medical Genetics, R. Binaghi Hospital, Local Public Health and Social Care Unit (ASSL) of Cagliari, Cagliari, Italy
- Centre for Research University Services (CeSAR, Centro Servizi di Ateneo per la Ricerca), University of Cagliari, Monserrato, Italy
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30
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Su HC, Jing H, Zhang Y, Casanova JL. Interfering with Interferons: A Critical Mechanism for Critical COVID-19 Pneumonia. Annu Rev Immunol 2023; 41:561-585. [PMID: 37126418 DOI: 10.1146/annurev-immunol-101921-050835] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Infection with SARS-CoV-2 results in clinical outcomes ranging from silent or benign infection in most individuals to critical pneumonia and death in a few. Genetic studies in patients have established that critical cases can result from inborn errors of TLR3- or TLR7-dependent type I interferon immunity, or from preexisting autoantibodies neutralizing primarily IFN-α and/or IFN-ω. These findings are consistent with virological studies showing that multiple SARS-CoV-2 proteins interfere with pathways of induction of, or response to, type I interferons. They are also congruent with cellular studies and mouse models that found that type I interferons can limit SARS-CoV-2 replication in vitro and in vivo, while their absence or diminution unleashes viral growth. Collectively, these findings point to insufficient type I interferon during the first days of infection as a general mechanism underlying critical COVID-19 pneumonia, with implications for treatment and directions for future research.
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Affiliation(s)
- Helen C Su
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH; Bethesda, Maryland, USA;
| | - Huie Jing
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH; Bethesda, Maryland, USA;
| | - Yu Zhang
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH; Bethesda, Maryland, USA;
| | - Jean-Laurent Casanova
- Howard Hughes Medical Institute and St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Paris, France
- University of Paris Cité, Imagine Institute, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
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31
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Matuozzo D, Talouarn E, Marchal A, Zhang P, Manry J, Seeleuthner Y, Zhang Y, Bolze A, Chaldebas M, Milisavljevic B, Gervais A, Bastard P, Asano T, Bizien L, Barzaghi F, Abolhassani H, Abou Tayoun A, Aiuti A, Alavi Darazam I, Allende LM, Alonso-Arias R, Arias AA, Aytekin G, Bergman P, Bondesan S, Bryceson YT, Bustos IG, Cabrera-Marante O, Carcel S, Carrera P, Casari G, Chaïbi K, Colobran R, Condino-Neto A, Covill LE, Delmonte OM, El Zein L, Flores C, Gregersen PK, Gut M, Haerynck F, Halwani R, Hancerli S, Hammarström L, Hatipoğlu N, Karbuz A, Keles S, Kyheng C, Leon-Lopez R, Franco JL, Mansouri D, Martinez-Picado J, Metin Akcan O, Migeotte I, Morange PE, Morelle G, Martin-Nalda A, Novelli G, Novelli A, Ozcelik T, Palabiyik F, Pan-Hammarström Q, de Diego RP, Planas-Serra L, Pleguezuelo DE, Prando C, Pujol A, Reyes LF, Rivière JG, Rodriguez-Gallego C, Rojas J, Rovere-Querini P, Schlüter A, Shahrooei M, Sobh A, Soler-Palacin P, Tandjaoui-Lambiotte Y, Tipu I, Tresoldi C, Troya J, van de Beek D, Zatz M, Zawadzki P, Al-Muhsen SZ, Alosaimi MF, Alsohime FM, Baris-Feldman H, Butte MJ, Constantinescu SN, Cooper MA, Dalgard CL, Fellay J, Heath JR, Lau YL, Lifton RP, Maniatis T, Mogensen TH, von Bernuth H, Lermine A, Vidaud M, Boland A, Deleuze JF, Nussbaum R, Kahn-Kirby A, Mentre F, Tubiana S, Gorochov G, Tubach F, Hausfater P, Meyts I, Zhang SY, Puel A, Notarangelo LD, Boisson-Dupuis S, Su HC, Boisson B, Jouanguy E, Casanova JL, Zhang Q, Abel L, Cobat A. Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19. Genome Med 2023; 15:22. [PMID: 37020259 PMCID: PMC10074346 DOI: 10.1186/s13073-023-01173-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 03/10/2023] [Indexed: 04/07/2023] Open
Abstract
BACKGROUND We previously reported that impaired type I IFN activity, due to inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity or to autoantibodies against type I IFN, account for 15-20% of cases of life-threatening COVID-19 in unvaccinated patients. Therefore, the determinants of life-threatening COVID-19 remain to be identified in ~ 80% of cases. METHODS We report here a genome-wide rare variant burden association analysis in 3269 unvaccinated patients with life-threatening COVID-19, and 1373 unvaccinated SARS-CoV-2-infected individuals without pneumonia. Among the 928 patients tested for autoantibodies against type I IFN, a quarter (234) were positive and were excluded. RESULTS No gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants was TLR7, with an OR of 27.68 (95%CI 1.5-528.7, P = 1.1 × 10-4) for biochemically loss-of-function (bLOF) variants. We replicated the enrichment in rare predicted LOF (pLOF) variants at 13 influenza susceptibility loci involved in TLR3-dependent type I IFN immunity (OR = 3.70[95%CI 1.3-8.2], P = 2.1 × 10-4). This enrichment was further strengthened by (1) adding the recently reported TYK2 and TLR7 COVID-19 loci, particularly under a recessive model (OR = 19.65[95%CI 2.1-2635.4], P = 3.4 × 10-3), and (2) considering as pLOF branchpoint variants with potentially strong impacts on splicing among the 15 loci (OR = 4.40[9%CI 2.3-8.4], P = 7.7 × 10-8). Finally, the patients with pLOF/bLOF variants at these 15 loci were significantly younger (mean age [SD] = 43.3 [20.3] years) than the other patients (56.0 [17.3] years; P = 1.68 × 10-5). CONCLUSIONS Rare variants of TLR3- and TLR7-dependent type I IFN immunity genes can underlie life-threatening COVID-19, particularly with recessive inheritance, in patients under 60 years old.
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Affiliation(s)
- Daniela Matuozzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Estelle Talouarn
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Astrid Marchal
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jeremy Manry
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, Bethesda, MD, USA
| | | | - Matthieu Chaldebas
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Baptiste Milisavljevic
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Adrian Gervais
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Pediatric Hematology-Immunology and Rheumatology Unit, Necker Hospital for Sick Children, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Takaki Asano
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Lucy Bizien
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Federica Barzaghi
- Department of Paediatric Immunohematology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Hassan Abolhassani
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran, Iran
| | - Ahmad Abou Tayoun
- Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai, United Arab Emirates
- Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Ilad Alavi Darazam
- Infectious Diseases and Tropical Medicine Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Infectious Diseases and Tropical Medicine, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Luis M Allende
- Immunology Department, University Hospital 12 de Octubre, Research Institute imas12 and Complutense University, Madrid, Spain
| | - Rebeca Alonso-Arias
- Immunology Department, Hospital Universitario Central de Asturias; Health Research Institute of Principality of Asturias, Oviedo, Spain
| | - Andrés Augusto Arias
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Department of Microbiology and Parasitology, Primary Immunodeficiencies Group, School of Medicine, University of Antioquia UdeA, 050010, Medellin, Colombia
- School of Microbiology, University of Antioquia UdeA, 050010, Medellin, Colombia
| | - Gokhan Aytekin
- Deparment of Internal Medicine, Division of Allergy and Immunology, Konya City Hospital, Konya, Turkey
| | - Peter Bergman
- Department of Infectious Diseases, The Immunodeficiency Unit, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Division of Clinical Immunology, Stockholm, Sweden
| | - Simone Bondesan
- Clinical Genomics, IRCSS San Raffaele Scientific Institute, Milan, Italy
| | - Yenan T Bryceson
- Department of Medicine, Centre for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | | | - Oscar Cabrera-Marante
- Institute of Biomedical Research of IdiPAZ, University Hospital "La Paz", Madrid, Spain
| | - Sheila Carcel
- Unidad de Gestión Clínica de Cuidados Intensivos, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba (UCO), Córdoba, Spain
| | - Paola Carrera
- Clinical Genomics, IRCSS San Raffaele Scientific Institute, Milan, Italy
| | - Giorgio Casari
- Division of Genetics and Cell Biology, Genome-Phenome Relationship, San Raffaele Hospital, Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
| | - Khalil Chaïbi
- Intensive Care Unit Department, Avicenne Hospital, Assistance Publique-Hôpitaux de Paris, Bobigny, France
- Common and Rare Kidney Diseases, Sorbonne University, INSERM UMR-S 1155, Paris, France
| | - Roger Colobran
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Translational Immunology Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
- Genetics Department, Immunology Division, Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona (UAB), Barcelona, Catalonia, Spain
| | - Antonio Condino-Neto
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Laura E Covill
- Department of Medicine, Centre for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, Bethesda, MD, USA
| | - Loubna El Zein
- Biology Department, Lebanese University, Beirut, Lebanon
| | - Carlos Flores
- Genomics Division, Institute of Technology and Renewable Energies (ITER), Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Carlos III Health Institute, Madrid, Spain
- Research Unit, University Hospital of Ntra. Sra. de Candelaria, Santa Cruz de Tenerife, Spain
- Faculty of Health Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Peter K Gregersen
- Feinstein Institute for Medical Research, Northwell Health USA, Manhasset, NY, USA
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Filomeen Haerynck
- Department of Internal Diseases and Pediatrics, Primary Immune Deficiency Research Laboratory, Centre for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Centre, Ghent, Belgium
| | - Rabih Halwani
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Selda Hancerli
- Department of Pediatrics (Infectious Diseases), Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Lennart Hammarström
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
| | - Nevin Hatipoğlu
- Pediatric Infectious Diseases Unit, Bakirkoy Dr Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Adem Karbuz
- Department of Pediatric Infectious Disease, Dr. Cemil Tascioglu City Hospital, Istanbul, Turkey
| | - Sevgi Keles
- Meram Medical Faculty, Pediatric Infectious Diseases Department, Necmettin Erbakan University, Konya, Turkey
| | - Christèle Kyheng
- Department of General Paediatrics, Hôpital Bicêtre, Assistance Publique-Hôpitaux de Paris, University of Paris Saclay, Le Kremlin-Bicêtre, France
| | - Rafael Leon-Lopez
- Unidad de Gestión Clínica de Cuidados Intensivos, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba (UCO), Córdoba, Spain
| | - Jose Luis Franco
- Primary Immunodeficiencies Group, Department of Microbiology and Parasitology, School of Medicine, University of Antioquia UDEA, Medellin, 050010, Colombia
| | - Davood Mansouri
- The Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Clinical Immunology and Infectious Diseases, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Pediatric Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute and Institute for Health Science Research Germans Trias I Pujol (IGTP), Badalona, Spain
- Institute for Health Science Research Germans Trias I Pujol (IGTP), Badalona, Spain
- Department of Infectious Diseases and Immunity, University of Vic-Central University of Catalonia, Vic, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- Consorcio Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Ozge Metin Akcan
- Meram Medical Faculty, Pediatric Infectious Diseases Department, Necmettin Erbakan University, Konya, Turkey
| | - Isabelle Migeotte
- Centre de Génétique Humaine de L'Université Libre de Bruxelles, Hôpital Erasme, Brussels, Belgium
| | - Pierre-Emmanuel Morange
- Laboratory of Haematology, La Timone Hospital, Marseille, France
- C2VN, INSERM, INRAE, Aix-Marseille University, Marseille, France
| | - Guillaume Morelle
- Department of General Paediatrics, Hôpital Bicêtre, Assistance Publique-Hôpitaux de Paris, University of Paris Saclay, Le Kremlin-Bicêtre, France
| | - Andrea Martin-Nalda
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona (UAB), Barcelona, Catalonia, Spain
- Infection and Immunity in Pediatric Patients Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, Rome, Italy
- IRCCS Neuromed, Pozzilli, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Tayfun Ozcelik
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Figen Palabiyik
- Pediatric Infectious Diseases Unit, Bakirkoy Dr Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | | | - Rebeca Pérez de Diego
- Laboratory of Immunogenetics of Human Diseases, IdiPAZ Institute for Health Research, University Hospital "La Paz", Madrid, Spain
| | - Laura Planas-Serra
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Center for Biomedical Research On Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Daniel E Pleguezuelo
- Immunology Department, University Hospital 12 de Octubre, Research Institute imas12 and Complutense University, Madrid, Spain
| | - Carolina Prando
- Faculdades Pequeno Príncipe, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Brazil
| | - Aurora Pujol
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Center for Biomedical Research On Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | | | - Jacques G Rivière
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona (UAB), Barcelona, Catalonia, Spain
- Infection and Immunity in Pediatric Patients Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Carlos Rodriguez-Gallego
- Department of Immunology, University Hospital of Gran Canaria Dr. Negrin, Canarian Health System, Las Palmas de Gran Canaria, Spain
- Department of Clinical Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Julian Rojas
- Primary Immunodeficiencies Group, Department of Microbiology and Parasitology, School of Medicine, University of Antioquia UDEA, Medellin, 050010, Colombia
| | - Patrizia Rovere-Querini
- Vita-Salute San Raffaele University, Milan, Italy
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Agatha Schlüter
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Center for Biomedical Research On Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Mohammad Shahrooei
- Specialized Immunology Laboratory of Dr Shahrooei, Sina Medical Complex, Ahvaz, Iran
- Department of Microbiology and Immunology, Clinical and Diagnostic Immunology, KU Leuven, Leuven, Belgium
| | - Ali Sobh
- Department of Pediatrics, Mansoura University Children's Hospital, Mansoura University Faculty of Medicine, Mansoura, Egypt
| | - Pere Soler-Palacin
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona (UAB), Barcelona, Catalonia, Spain
- Infection and Immunity in Pediatric Patients Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Yacine Tandjaoui-Lambiotte
- Hypoxia and Lung, INSERM U1272, Avicenne Hospital, Assistance Publique-Hôpitaux de Paris, Bobigny, France
| | - Imran Tipu
- Department of Life Sciences, School of Science, University of Management and Technology, Lahore, Pakistan
| | - Cristina Tresoldi
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Jesus Troya
- Department of Internal Medicine, Infanta Leonor University Hospital, Madrid, Spain
| | - Diederik van de Beek
- Department of Neurology, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Mayana Zatz
- Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Pawel Zawadzki
- Gordion Bioscience Inc, Cambridge, MA, USA
- Faculty of Physics, Adam Mickiewicz University, Poznan, Poland
| | - Saleh Zaid Al-Muhsen
- Department of Pediatrics, Immunology Research Laboratory, College of Medicine and King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Faraj Alosaimi
- Department of Pediatrics, Immunology Research Laboratory, College of Medicine and King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Fahad M Alsohime
- Department of Pediatrics, Immunology Research Laboratory, College of Medicine and King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Hagit Baris-Feldman
- The Genetics Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Manish J Butte
- Departments of Pediatrics and Microbiology, Immunology, and Molecular Genetics, Division of Immunology, Allergy, and Rheumatology, University of California Los Angeles, Los Angeles, CA, USA
| | - Stefan N Constantinescu
- Ludwig Institute for Cancer Research, Brussels, Belgium
- SIGN Unit, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
- WELBIO (Walloon Excellence in Life Sciences and Biotechnology), Brussels, Belgium
- Nuffield Department of Medicine, Ludwig Institute for Cancer Research, Oxford University, Oxford, UK
| | - Megan A Cooper
- Department of Pediatrics, Division of Rheumatology/Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Clifton L Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, USA
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | | | - Yu-Lung Lau
- Department of Paediatrics and Adolescent Medicine, Queen Mary Hospital, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Richard P Lifton
- Laboratory of Genetics and Genomics, The Rockefeller University, New York, NY, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for Genome Analysis, Yale School of Medicine, New Haven, CT, USA
| | - Tom Maniatis
- Zukerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Trine H Mogensen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Horst von Bernuth
- Department of Paediatric Respiratory Medicine, Immunology, and Critical Care Medicine, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Alban Lermine
- Laboratoire de Biologie Médicale Multisites Seqoia, MG2025, MG2025, Paris, France
| | - Michel Vidaud
- Laboratoire de Biologie Médicale Multisites Seqoia, MG2025, MG2025, Paris, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | | | | | - France Mentre
- Unité de Recherche Clinique, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Sarah Tubiana
- Centre d'Investigation Clinique, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Guy Gorochov
- Sorbonne Université, INSERM Centre d'Immunologie et des Maladies Infectieuses, CIMI-Paris, Département d'immunologie Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Florence Tubach
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié Salpêtrière, Département de Santé Publique, Unité de Recherche Clinique PSL-CFX , CIC-1901, Paris, France
| | - Pierre Hausfater
- Emergency Department, Hôpital Pitié-Salpêtrière, APHP-Sorbonne Université, Paris, France
- GRC-14 BIOFAST Sorbonn Université, UMR INSERM 1135, CIMI, Sorbonne Université, Paris, France
| | - Isabelle Meyts
- Department of Microbiology, Immunology and Transplantation, Laboratory for Inborn Errors of Immunity, KU Leuven, Leuven, Belgium
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Luigi D Notarangelo
- Laboratory of Host Defenses, NIAID, National Institutes of Health, Bethesda, MA, USA
| | - Stephanie Boisson-Dupuis
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Helen C Su
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, Bethesda, MD, USA
| | - Bertrand Boisson
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Emmanuelle Jouanguy
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.
- University Paris Cité, Imagine Institute, Paris, France.
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, New York, NY, USA.
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.
- University Paris Cité, Imagine Institute, Paris, France.
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.
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Affiliation(s)
- Gaspard Kerner
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, Centre National de la Recherche Scientifique (CNRS) UMR, 2000, Paris, France
| | - Jeremy Choin
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, Centre National de la Recherche Scientifique (CNRS) UMR, 2000, Paris, France. .,Chair of Human Genomics and Evolution, Collège de France, Paris, France.
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Turner MD. Possible Causes of Hypertrophic Osteoarthropathy in the La Ferrassie 1 Neanderthal. Cureus 2023; 15:e35721. [PMID: 37016656 PMCID: PMC10066876 DOI: 10.7759/cureus.35721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2023] [Indexed: 03/06/2023] Open
Abstract
For over a century, researchers have been perplexed by the unique osteological findings on La Ferrassie 1 (LF1), one of the most complete Neanderthal remains ever found. In 1997, Fennel and Trinkaus proposed that LF1 suffered from hypertrophic osteoarthropathy (HOA), likely secondary to chronic thoracic infection or pulmonary malignancy. This disease process can have many etiologies, and no study has fully explored the possible origin of LF1's HOA. Ultimately, it is most likely that LF1's HOA etiology arose from one of the many infectious diseases that prehistoric Neanderthals were exposed to, specifically a chronic pulmonary RNA virus.
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Pomeroy E. Review: The different adaptive trajectories in Neanderthals and Homo sapiens and their implications for contemporary human physiological variation. Comp Biochem Physiol A Mol Integr Physiol 2023; 280:111420. [PMID: 37001690 DOI: 10.1016/j.cbpa.2023.111420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023]
Abstract
Neanderthals are our one of our closest evolutionary cousins, but while they evolved in Eurasia, we (anatomically modern humans, AMH) originated in Africa. This contrasting evolutionary history has led to morphological and genetic distinctions between our species. Neanderthals are characterised by a relatively stocky build, high body mass, proportionally wide bodies and shorter limbs, a bell-shaped ribcage with a wide pelvis, and a long, low cranial vault compared with AMH. Classic readings of Neanderthal morphology link many of these traits to cold climate adaptations, however these interpretations have been questioned and alternative hypotheses including behavioural factors, dietary adaptations, locomotor specialisations, evolutionary history and neutral evolutionary processes have been invoked. Compared with AMH, Neanderthals may have been adapted for strength and power rather than endurance and may have consumed a diet high in animal products. However, reviewing these hypotheses highlights a number of limitations in our understanding of contemporary human physiology and metabolism, including the relationship between climate and morphology in AMH and Neanderthals, physiological limits on protein consumption, and the relationship between gut morphology and diet. As various relevant factors are clearly linked (e.g. diet, behaviour, metabolism, morphology, activity), ultimately a more integrated approach may be needed to fully understand Neanderthal biology. Variation among contemporary AMHs may offer, with caveats, a useful model for understanding the evolution of both Neanderthal and modern human characteristics, which in turn may further deepen our understanding of variability within and between contemporary humans. Neanderthals; Anatomically modern humans; morphology; climate adaptation; power adaptations; metabolism; diet; physiology; endurance running.
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Gazeau S, Deng X, Ooi HK, Mostefai F, Hussin J, Heffernan J, Jenner AL, Craig M. The race to understand immunopathology in COVID-19: Perspectives on the impact of quantitative approaches to understand within-host interactions. IMMUNOINFORMATICS (AMSTERDAM, NETHERLANDS) 2023; 9:100021. [PMID: 36643886 PMCID: PMC9826539 DOI: 10.1016/j.immuno.2023.100021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/16/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023]
Abstract
The COVID-19 pandemic has revealed the need for the increased integration of modelling and data analysis to public health, experimental, and clinical studies. Throughout the first two years of the pandemic, there has been a concerted effort to improve our understanding of the within-host immune response to the SARS-CoV-2 virus to provide better predictions of COVID-19 severity, treatment and vaccine development questions, and insights into viral evolution and the impacts of variants on immunopathology. Here we provide perspectives on what has been accomplished using quantitative methods, including predictive modelling, population genetics, machine learning, and dimensionality reduction techniques, in the first 26 months of the COVID-19 pandemic approaches, and where we go from here to improve our responses to this and future pandemics.
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Affiliation(s)
- Sonia Gazeau
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Canada
- Sainte-Justine University Hospital Research Centre, Montréal, Canada
| | - Xiaoyan Deng
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Canada
- Sainte-Justine University Hospital Research Centre, Montréal, Canada
| | - Hsu Kiang Ooi
- Digital Technologies Research Centre, National Research Council Canada, Toronto, Canada
| | - Fatima Mostefai
- Montréal Heart Institute Research Centre, Montréal, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, Canada
| | - Julie Hussin
- Montréal Heart Institute Research Centre, Montréal, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, Canada
| | - Jane Heffernan
- Modelling Infection and Immunity Lab, Mathematics Statistics, York University, Toronto, Canada
- Centre for Disease Modelling (CDM), Mathematics Statistics, York University, Toronto, Canada
| | - Adrianne L Jenner
- School of Mathematical Sciences, Queensland University of Technology, Brisbane Australia
| | - Morgan Craig
- Department of Mathematics and Statistics, Université de Montréal, Montréal, Canada
- Sainte-Justine University Hospital Research Centre, Montréal, Canada
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Natterson-Horowitz B, Aktipis A, Fox M, Gluckman PD, Low FM, Mace R, Read A, Turner PE, Blumstein DT. The future of evolutionary medicine: sparking innovation in biomedicine and public health. FRONTIERS IN SCIENCE 2023; 1:997136. [PMID: 37869257 PMCID: PMC10590274 DOI: 10.3389/fsci.2023.997136] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
Evolutionary medicine - i.e. the application of insights from evolution and ecology to biomedicine - has tremendous untapped potential to spark transformational innovation in biomedical research, clinical care and public health. Fundamentally, a systematic mapping across the full diversity of life is required to identify animal model systems for disease vulnerability, resistance, and counter-resistance that could lead to novel clinical treatments. Evolutionary dynamics should guide novel therapeutic approaches that target the development of treatment resistance in cancers (e.g., via adaptive or extinction therapy) and antimicrobial resistance (e.g., via innovations in chemistry, antimicrobial usage, and phage therapy). With respect to public health, the insight that many modern human pathologies (e.g., obesity) result from mismatches between the ecologies in which we evolved and our modern environments has important implications for disease prevention. Life-history evolution can also shed important light on patterns of disease burden, for example in reproductive health. Experience during the COVID-19 (SARS-CoV-2) pandemic has underlined the critical role of evolutionary dynamics (e.g., with respect to virulence and transmissibility) in predicting and managing this and future pandemics, and in using evolutionary principles to understand and address aspects of human behavior that impede biomedical innovation and public health (e.g., unhealthy behaviors and vaccine hesitancy). In conclusion, greater interdisciplinary collaboration is vital to systematically leverage the insight-generating power of evolutionary medicine to better understand, prevent, and treat existing and emerging threats to human, animal, and planetary health.
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Affiliation(s)
- B. Natterson-Horowitz
- Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Athena Aktipis
- Department of Psychology, Arizona State University, Tempe, AZ, United States
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, United States
| | - Molly Fox
- Department of Anthropology, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, United States
| | - Peter D. Gluckman
- Koi Tū: The Centre for Informed Futures, University of Auckland, Auckland, New Zealand
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Felicia M. Low
- Koi Tū: The Centre for Informed Futures, University of Auckland, Auckland, New Zealand
| | - Ruth Mace
- Department of Anthropology, University College London, London, United Kingdom
| | - Andrew Read
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, State College, PA, United States
- Department of Entomology, The Pennsylvania State University, State College, PA, United States
- Huck Institutes of the Life Sciences, The Pennsylvania State University, State College, PA, United States
| | - Paul E. Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
- Program in Microbiology, Yale School of Medicine, New Haven, CT, United States
| | - Daniel T. Blumstein
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
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Takahata N, Sugawara H. Role of error catastrophe in transmission ability of virus. Genes Genet Syst 2023; 97:237-246. [PMID: 36709980 DOI: 10.1266/ggs.22-00096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The role played by error catastrophe is explicitly taken into account in a mathematical formulation to analyze COVID-19 data. The idea is to combine the mathematical genetics formalism of the error catastrophe of mutations in virus gene loci with the standard model of epidemics, which lacks the explicit incorporation of the effect of mutation on the spreading of viruses. We apply this formalism to the case of SARS-CoV-2 virus. We assume the universality of the error catastrophe in the process of analyzing the data. This means that some basic parameter to describe the error catastrophe is independent of which group (country or city) we deal with. Concretely, we analyze Omicron variant data from South Africa and then analyze cases from Japan using the same value of the basic parameter derived in the South Africa analysis. The excellent fit between the two sets of data, one from South Africa and the other from Japan, using the common values of genetic parameters, justifies our assumption of the universality of these parameters.
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Gokul A, Arumugam T, Ramsuran V. Genetic Ethnic Differences in Human 2'-5'-Oligoadenylate Synthetase and Disease Associations: A Systematic Review. Genes (Basel) 2023; 14:527. [PMID: 36833454 PMCID: PMC9956131 DOI: 10.3390/genes14020527] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Recently, several studies have highlighted a skewed prevalence of infectious diseases within the African continent. Furthermore, a growing number of studies have demonstrated unique genetic variants found within the African genome are one of the contributing factors to the disease severity of infectious diseases within Africa. Understanding the host genetic mechanisms that offer protection against infectious diseases provides an opportunity to develop unique therapeutic interventions. Over the past two decades, several studies have linked the 2'-5'-oligoadenylate synthetase (OAS) family with a range of infectious diseases. More recently, the OAS-1 gene has also been associated with disease severity caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which led to a global pandemic. The OAS family serves as an antiviral factor through the interaction with Ribonuclease-Latent (RNase-L). This review explores the genetic variants observed within the OAS genes and the associations with various viral infections and how previously reported ethnic-specific polymorphisms drive clinical significance. This review provides an overview of OAS genetic association studies with a particular focus on viral diseases affecting individuals of African descent.
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Affiliation(s)
- Anmol Gokul
- School of Laboratory Medicine and Medical Sciences, College of Health Science, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Thilona Arumugam
- School of Laboratory Medicine and Medical Sciences, College of Health Science, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Veron Ramsuran
- School of Laboratory Medicine and Medical Sciences, College of Health Science, University of KwaZulu-Natal, Durban 4041, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban 4001, South Africa
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39
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Carlsson M, Wittsten J, Söderberg-Nauclér C. A note on variable susceptibility, the herd-immunity threshold and modeling of infectious diseases. PLoS One 2023; 18:e0279454. [PMID: 36791079 PMCID: PMC9931097 DOI: 10.1371/journal.pone.0279454] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 12/07/2022] [Indexed: 02/16/2023] Open
Abstract
The unfolding of the COVID-19 pandemic has been very difficult to predict using mathematical models for infectious diseases. While it has been demonstrated that variations in susceptibility have a damping effect on key quantities such as the incidence peak, the herd-immunity threshold and the final size of the pandemic, this complex phenomenon is almost impossible to measure or quantify, and it remains unclear how to incorporate it for modeling and prediction. In this work we show that, from a modeling perspective, variability in susceptibility on an individual level is equivalent with a fraction θ of the population having an "artificial" sterilizing immunity. We also derive novel formulas for the herd-immunity threshold and the final size of the pandemic, and show that these values are substantially lower than predicted by the classical formulas, in the presence of variable susceptibility. In the particular case of SARS-CoV-2, there is by now undoubtedly variable susceptibility due to waning immunity from both vaccines and previous infections, and our findings may be used to greatly simplify models. If such variations were also present prior to the first wave, as indicated by a number of studies, these findings can help explain why the magnitude of the initial waves of SARS-CoV-2 was relatively low, compared to what one may have expected based on standard models.
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Affiliation(s)
- Marcus Carlsson
- Centre for Mathematical Sciences, Lund University, Lund, Sweden
- * E-mail:
| | - Jens Wittsten
- Department of Engineering, University of Borås, Borås, Sweden
| | - Cecilia Söderberg-Nauclér
- Department of Medicine, BioClinicum, Karolinska Institutet, Solna, Sweden
- Department of Neurology, Karolinska University Hospital, Stockholm, Sweden
- Institute of Biomedicine, MediCity Research Laboratory, University of Turku, Turku, Finland
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40
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Lee D, Le Pen J, Yatim A, Dong B, Aquino Y, Ogishi M, Pescarmona R, Talouarn E, Rinchai D, Zhang P, Perret M, Liu Z, Jordan I, Elmas Bozdemir S, Bayhan GI, Beaufils C, Bizien L, Bisiaux A, Lei W, Hasan M, Chen J, Gaughan C, Asthana A, Libri V, Luna JM, Jaffré F, Hoffmann HH, Michailidis E, Moreews M, Seeleuthner Y, Bilguvar K, Mane S, Flores C, Zhang Y, Arias AA, Bailey R, Schlüter A, Milisavljevic B, Bigio B, Le Voyer T, Materna M, Gervais A, Moncada-Velez M, Pala F, Lazarov T, Levy R, Neehus AL, Rosain J, Peel J, Chan YH, Morin MP, Pino-Ramirez RM, Belkaya S, Lorenzo L, Anton J, Delafontaine S, Toubiana J, Bajolle F, Fumadó V, DeDiego ML, Fidouh N, Rozenberg F, Pérez-Tur J, Chen S, Evans T, Geissmann F, Lebon P, Weiss SR, Bonnet D, Duval X, Pan-Hammarström Q, Planas AM, Meyts I, Haerynck F, Pujol A, Sancho-Shimizu V, Dalgard CL, Bustamante J, Puel A, Boisson-Dupuis S, Boisson B, Maniatis T, Zhang Q, Bastard P, Notarangelo L, Béziat V, Perez de Diego R, Rodriguez-Gallego C, Su HC, Lifton RP, Jouanguy E, Cobat A, Alsina L, Keles S, Haddad E, Abel L, Belot A, Quintana-Murci L, Rice CM, Silverman RH, Zhang SY, Casanova JL. Inborn errors of OAS-RNase L in SARS-CoV-2-related multisystem inflammatory syndrome in children. Science 2023; 379:eabo3627. [PMID: 36538032 PMCID: PMC10451000 DOI: 10.1126/science.abo3627] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 08/16/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
Multisystem inflammatory syndrome in children (MIS-C) is a rare and severe condition that follows benign COVID-19. We report autosomal recessive deficiencies of OAS1, OAS2, or RNASEL in five unrelated children with MIS-C. The cytosolic double-stranded RNA (dsRNA)-sensing OAS1 and OAS2 generate 2'-5'-linked oligoadenylates (2-5A) that activate the single-stranded RNA-degrading ribonuclease L (RNase L). Monocytic cell lines and primary myeloid cells with OAS1, OAS2, or RNase L deficiencies produce excessive amounts of inflammatory cytokines upon dsRNA or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) stimulation. Exogenous 2-5A suppresses cytokine production in OAS1-deficient but not RNase L-deficient cells. Cytokine production in RNase L-deficient cells is impaired by MDA5 or RIG-I deficiency and abolished by mitochondrial antiviral-signaling protein (MAVS) deficiency. Recessive OAS-RNase L deficiencies in these patients unleash the production of SARS-CoV-2-triggered, MAVS-mediated inflammatory cytokines by mononuclear phagocytes, thereby underlying MIS-C.
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Affiliation(s)
- Danyel Lee
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Jérémie Le Pen
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Ahmad Yatim
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Beihua Dong
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Yann Aquino
- Human Evolutionary Genetics Unit, Institut Pasteur, Paris City University, CNRS UMR 2000, Paris, France
- Doctoral College, Sorbonne University, Paris, France
| | - Masato Ogishi
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | | | - Estelle Talouarn
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Darawan Rinchai
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Magali Perret
- Laboratory of Immunology, Lyon Sud Hospital, Lyon, France
| | - Zhiyong Liu
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Iolanda Jordan
- Pediatric Intensive Care Department, Hospital Sant Joan de Déu, Barcelona, Spain
- Kids Corona Platform, Barcelona, Spain
- Center for Biomedical Network Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- Department of Surgery and Surgical Specializations, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
- Respiratory and Immunological Dysfunction in Pediatric Critically Ill Patients, Institute of Recerca Sant Joan de Déu, Barcelona, Spain
| | | | | | - Camille Beaufils
- Immunology and Rheumatology Division, Department of Pediatrics, University of Montreal, CHU Sainte-Justine, Montreal, QC, Canada
| | - Lucy Bizien
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Aurelie Bisiaux
- Human Evolutionary Genetics Unit, Institut Pasteur, Paris City University, CNRS UMR 2000, Paris, France
| | - Weite Lei
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Milena Hasan
- Center for Translational Research, Institut Pasteur, Paris City University, Paris, France
| | - Jie Chen
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Christina Gaughan
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Abhishek Asthana
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Valentina Libri
- Center for Translational Research, Institut Pasteur, Paris City University, Paris, France
| | - Joseph M. Luna
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
- Department of Biochemistry and Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH, USA
| | - Fabrice Jaffré
- Department of Surgery, Weill Cornell Medical College, New York, NY, USA
| | - H.-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Eleftherios Michailidis
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Marion Moreews
- International Center of Infectiology Research (CIRI), University of Lyon, INSERM U1111, Claude Bernard University, Lyon 1, CNRS, UMR5308, ENS of Lyon, Lyon, France
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Kaya Bilguvar
- Departments of Neurosurgery and Genetics and Yale Center for Genome Analysis, Yale School of Medicine, New Haven, CT, USA
- Department of Medical Genetics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Shrikant Mane
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Carlos Flores
- Research Unit, Nuestra Señora de la Candelaria University Hospital, Santa Cruz de Tenerife, Spain
- Genomics Division, Institute of Technology and Renewable Energies (ITER), Granadilla de Abona, Spain
- CIBERES, ISCIII, Madrid, Spain
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
- NIAID Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
| | - Andrés A. Arias
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Primary Immunodeficiencies Group, University of Antioquia (UdeA), Medellin, Colombia
- School of Microbiology, University of Antioquia (UdeA), Medellin, Colombia
| | - Rasheed Bailey
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Agatha Schlüter
- Neurometabolic Diseases Laboratory, IDIBELL–Hospital Duran I Reynals, CIBERER U759, ISIiii, Madrid, Spain
| | - Baptiste Milisavljevic
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Benedetta Bigio
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Tom Le Voyer
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Marie Materna
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Adrian Gervais
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Marcela Moncada-Velez
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Francesca Pala
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
| | - Tomi Lazarov
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Romain Levy
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Anna-Lena Neehus
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Jérémie Rosain
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Jessica Peel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Yi-Hao Chan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Marie-Paule Morin
- Immunology and Rheumatology Division, Department of Pediatrics, University of Montreal, CHU Sainte-Justine, Montreal, QC, Canada
| | | | - Serkan Belkaya
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Lazaro Lorenzo
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jordi Anton
- Department of Surgery and Surgical Specializations, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
- Pediatric Rheumatology Division, Hospital Sant Joan de Déu, Barcelona, Spain
- Study Group for Immune Dysfunction Diseases in Children (GEMDIP), Institute of Recerca Sant Joan de Déu, Barcelona, Spain
| | | | - Julie Toubiana
- Department of General Pediatrics and Pediatric Infectious Diseases, Necker Hospital for Sick Children, Assistance Publique–Hôpitaux de Paris (AP-HP), Paris City University, Paris, France
- Biodiversity and Epidemiology of Bacterial Pathogens, Pasteur Institute, Paris, France
| | - Fanny Bajolle
- Department of Pediatric Cardiology, Necker Hospital for Sick Children, AP-HP, Paris City University, Paris, France
| | - Victoria Fumadó
- Kids Corona Platform, Barcelona, Spain
- Department of Surgery and Surgical Specializations, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
- Pediatrics Infectious Diseases Division, Hospital Sant Joan de Déu, Barcelona, Spain
- Infectious Diseases and Microbiome, Institute of Recerca Sant Joan de Déu, Barcelona, Spain
| | - Marta L. DeDiego
- Department of Molecular and Cellular Biology, National Center for Biotechnology (CNB-CSIC), Madrid, Spain
| | - Nadhira Fidouh
- Laboratory of Virology, Bichat–Claude Bernard Hospital, Paris, France
| | - Flore Rozenberg
- Laboratory of Virology, AP-HP, Cochin Hospital, Paris, France
| | - Jordi Pérez-Tur
- Molecular Genetics Unit, Institute of Biomedicine of Valencia (IBV-CSIC), Valencia, Spain
- CIBERNED, ISCIII, Madrid, Spain
- Joint Research Unit in Neurology and Molecular Genetics, Institut of Investigation Sanitaria La Fe, Valencia, Spain
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medical College, New York, NY, USA
| | - Todd Evans
- Department of Surgery, Weill Cornell Medical College, New York, NY, USA
| | - Frédéric Geissmann
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pierre Lebon
- Medical School, Paris City University, Paris, France
| | - Susan R. Weiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Damien Bonnet
- Department of Pediatric Cardiology, Necker Hospital for Sick Children, AP-HP, Paris City University, Paris, France
| | - Xavier Duval
- Bichat–Claude Bernard Hospital, Paris, France
- University Paris Diderot, Paris 7, UFR of Médecine-Bichat, Paris, France
- IAME, INSERM, UMRS1137, Paris City University, Paris, France
- Infectious and Tropical Diseases Department, AP-HP, Bichat–Claude Bernard Hospital, Paris, France
| | - CoV-Contact Cohort§
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Human Evolutionary Genetics Unit, Institut Pasteur, Paris City University, CNRS UMR 2000, Paris, France
- Doctoral College, Sorbonne University, Paris, France
- Laboratory of Immunology, Lyon Sud Hospital, Lyon, France
- Pediatric Intensive Care Department, Hospital Sant Joan de Déu, Barcelona, Spain
- Kids Corona Platform, Barcelona, Spain
- Center for Biomedical Network Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- Department of Surgery and Surgical Specializations, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
- Respiratory and Immunological Dysfunction in Pediatric Critically Ill Patients, Institute of Recerca Sant Joan de Déu, Barcelona, Spain
- Bursa City Hospital, Bursa, Turkey
- Ankara City Hospital, Yildirim Beyazit University, Ankara, Turkey
- Immunology and Rheumatology Division, Department of Pediatrics, University of Montreal, CHU Sainte-Justine, Montreal, QC, Canada
- Center for Translational Research, Institut Pasteur, Paris City University, Paris, France
- Department of Biochemistry and Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH, USA
- Department of Surgery, Weill Cornell Medical College, New York, NY, USA
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
- International Center of Infectiology Research (CIRI), University of Lyon, INSERM U1111, Claude Bernard University, Lyon 1, CNRS, UMR5308, ENS of Lyon, Lyon, France
- Departments of Neurosurgery and Genetics and Yale Center for Genome Analysis, Yale School of Medicine, New Haven, CT, USA
- Department of Medical Genetics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Research Unit, Nuestra Señora de la Candelaria University Hospital, Santa Cruz de Tenerife, Spain
- Genomics Division, Institute of Technology and Renewable Energies (ITER), Granadilla de Abona, Spain
- CIBERES, ISCIII, Madrid, Spain
- Department of Clinical Sciences, University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
- NIAID Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
- Primary Immunodeficiencies Group, University of Antioquia (UdeA), Medellin, Colombia
- School of Microbiology, University of Antioquia (UdeA), Medellin, Colombia
- Neurometabolic Diseases Laboratory, IDIBELL–Hospital Duran I Reynals, CIBERER U759, ISIiii, Madrid, Spain
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Pediatrics Department, Hospital Sant Joan de Déu, Barcelona, Spain
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
- Pediatric Rheumatology Division, Hospital Sant Joan de Déu, Barcelona, Spain
- Study Group for Immune Dysfunction Diseases in Children (GEMDIP), Institute of Recerca Sant Joan de Déu, Barcelona, Spain
- Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
- Department of General Pediatrics and Pediatric Infectious Diseases, Necker Hospital for Sick Children, Assistance Publique–Hôpitaux de Paris (AP-HP), Paris City University, Paris, France
- Biodiversity and Epidemiology of Bacterial Pathogens, Pasteur Institute, Paris, France
- Department of Pediatric Cardiology, Necker Hospital for Sick Children, AP-HP, Paris City University, Paris, France
- Pediatrics Infectious Diseases Division, Hospital Sant Joan de Déu, Barcelona, Spain
- Infectious Diseases and Microbiome, Institute of Recerca Sant Joan de Déu, Barcelona, Spain
- Department of Molecular and Cellular Biology, National Center for Biotechnology (CNB-CSIC), Madrid, Spain
- Laboratory of Virology, Bichat–Claude Bernard Hospital, Paris, France
- Laboratory of Virology, AP-HP, Cochin Hospital, Paris, France
- Molecular Genetics Unit, Institute of Biomedicine of Valencia (IBV-CSIC), Valencia, Spain
- CIBERNED, ISCIII, Madrid, Spain
- Joint Research Unit in Neurology and Molecular Genetics, Institut of Investigation Sanitaria La Fe, Valencia, Spain
- Medical School, Paris City University, Paris, France
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Bichat–Claude Bernard Hospital, Paris, France
- University Paris Diderot, Paris 7, UFR of Médecine-Bichat, Paris, France
- IAME, INSERM, UMRS1137, Paris City University, Paris, France
- Infectious and Tropical Diseases Department, AP-HP, Bichat–Claude Bernard Hospital, Paris, France
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Department of Neuroscience and Experimental Therapeutics, Institute for Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC), Barcelona, Spain
- Institute for Biomedical Investigations August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Department of Pediatrics, University Hospitals Leuven and Laboratory for Inborn Errors of Immunity, KU Leuven, Leuven, Belgium
- Primary Immunodeficiency Research Laboratory, Center for Primary Immunodeficiency Ghent, Ghent University Hospital, Ghent, Belgium
- Neurometabolic Diseases Laboratory, IDIBELL–Hospital Duran I Reynals; and Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
- CIBERER U759, ISCiii, Madrid, Spain
- Department of Paediatric Infectious Diseases and Virology, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, UK
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Department of Anatomy, Physiology, and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, AP-HP, Paris, France
- New York Genome Center, New York, NY, USA
- Pediatric Hematology-Immunology and Rheumatology Unit, Necker Hospital for Sick Children, AP-HP, Paris, France
- Laboratory of Immunogenetics of Human Diseases, Innate Immunity Group, IdiPAZ Institute for Health Research, La Paz Hospital, Madrid, Spain
- Interdepartmental Group of Immunodeficiencies, Madrid, Spain
- Department of Immunology, University Hospital of Gran Canaria Dr. Negrín, Canarian Health System, Las Palmas de Gran Canaria, Spain
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
- Clinical Immunology and Primary Immunodeficiencies Unit, Pediatric Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Barcelona, Spain
- Necmettin Erbakan University, Konya, Turkey
- Department of Pediatrics, Department of Microbiology, Immunology and Infectious Diseases, University of Montreal and Immunology and Rheumatology Division, CHU Sainte-Justine, Montreal, QC, Canada
- National Reference Center for Rheumatic, Autoimmune and Systemic Diseases in Children (RAISE), Pediatric Nephrology, Rheumatology, Dermatology Unit, Hospital of Mother and Child, Hospices Civils of Lyon, Lyon, France
- Human Genomics and Evolution, Collège de France, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - COVID Human Genetic Effort¶
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Human Evolutionary Genetics Unit, Institut Pasteur, Paris City University, CNRS UMR 2000, Paris, France
- Doctoral College, Sorbonne University, Paris, France
- Laboratory of Immunology, Lyon Sud Hospital, Lyon, France
- Pediatric Intensive Care Department, Hospital Sant Joan de Déu, Barcelona, Spain
- Kids Corona Platform, Barcelona, Spain
- Center for Biomedical Network Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- Department of Surgery and Surgical Specializations, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
- Respiratory and Immunological Dysfunction in Pediatric Critically Ill Patients, Institute of Recerca Sant Joan de Déu, Barcelona, Spain
- Bursa City Hospital, Bursa, Turkey
- Ankara City Hospital, Yildirim Beyazit University, Ankara, Turkey
- Immunology and Rheumatology Division, Department of Pediatrics, University of Montreal, CHU Sainte-Justine, Montreal, QC, Canada
- Center for Translational Research, Institut Pasteur, Paris City University, Paris, France
- Department of Biochemistry and Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH, USA
- Department of Surgery, Weill Cornell Medical College, New York, NY, USA
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
- International Center of Infectiology Research (CIRI), University of Lyon, INSERM U1111, Claude Bernard University, Lyon 1, CNRS, UMR5308, ENS of Lyon, Lyon, France
- Departments of Neurosurgery and Genetics and Yale Center for Genome Analysis, Yale School of Medicine, New Haven, CT, USA
- Department of Medical Genetics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Research Unit, Nuestra Señora de la Candelaria University Hospital, Santa Cruz de Tenerife, Spain
- Genomics Division, Institute of Technology and Renewable Energies (ITER), Granadilla de Abona, Spain
- CIBERES, ISCIII, Madrid, Spain
- Department of Clinical Sciences, University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
- NIAID Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
- Primary Immunodeficiencies Group, University of Antioquia (UdeA), Medellin, Colombia
- School of Microbiology, University of Antioquia (UdeA), Medellin, Colombia
- Neurometabolic Diseases Laboratory, IDIBELL–Hospital Duran I Reynals, CIBERER U759, ISIiii, Madrid, Spain
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Pediatrics Department, Hospital Sant Joan de Déu, Barcelona, Spain
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
- Pediatric Rheumatology Division, Hospital Sant Joan de Déu, Barcelona, Spain
- Study Group for Immune Dysfunction Diseases in Children (GEMDIP), Institute of Recerca Sant Joan de Déu, Barcelona, Spain
- Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
- Department of General Pediatrics and Pediatric Infectious Diseases, Necker Hospital for Sick Children, Assistance Publique–Hôpitaux de Paris (AP-HP), Paris City University, Paris, France
- Biodiversity and Epidemiology of Bacterial Pathogens, Pasteur Institute, Paris, France
- Department of Pediatric Cardiology, Necker Hospital for Sick Children, AP-HP, Paris City University, Paris, France
- Pediatrics Infectious Diseases Division, Hospital Sant Joan de Déu, Barcelona, Spain
- Infectious Diseases and Microbiome, Institute of Recerca Sant Joan de Déu, Barcelona, Spain
- Department of Molecular and Cellular Biology, National Center for Biotechnology (CNB-CSIC), Madrid, Spain
- Laboratory of Virology, Bichat–Claude Bernard Hospital, Paris, France
- Laboratory of Virology, AP-HP, Cochin Hospital, Paris, France
- Molecular Genetics Unit, Institute of Biomedicine of Valencia (IBV-CSIC), Valencia, Spain
- CIBERNED, ISCIII, Madrid, Spain
- Joint Research Unit in Neurology and Molecular Genetics, Institut of Investigation Sanitaria La Fe, Valencia, Spain
- Medical School, Paris City University, Paris, France
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Bichat–Claude Bernard Hospital, Paris, France
- University Paris Diderot, Paris 7, UFR of Médecine-Bichat, Paris, France
- IAME, INSERM, UMRS1137, Paris City University, Paris, France
- Infectious and Tropical Diseases Department, AP-HP, Bichat–Claude Bernard Hospital, Paris, France
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Department of Neuroscience and Experimental Therapeutics, Institute for Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC), Barcelona, Spain
- Institute for Biomedical Investigations August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Department of Pediatrics, University Hospitals Leuven and Laboratory for Inborn Errors of Immunity, KU Leuven, Leuven, Belgium
- Primary Immunodeficiency Research Laboratory, Center for Primary Immunodeficiency Ghent, Ghent University Hospital, Ghent, Belgium
- Neurometabolic Diseases Laboratory, IDIBELL–Hospital Duran I Reynals; and Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
- CIBERER U759, ISCiii, Madrid, Spain
- Department of Paediatric Infectious Diseases and Virology, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, UK
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Department of Anatomy, Physiology, and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, AP-HP, Paris, France
- New York Genome Center, New York, NY, USA
- Pediatric Hematology-Immunology and Rheumatology Unit, Necker Hospital for Sick Children, AP-HP, Paris, France
- Laboratory of Immunogenetics of Human Diseases, Innate Immunity Group, IdiPAZ Institute for Health Research, La Paz Hospital, Madrid, Spain
- Interdepartmental Group of Immunodeficiencies, Madrid, Spain
- Department of Immunology, University Hospital of Gran Canaria Dr. Negrín, Canarian Health System, Las Palmas de Gran Canaria, Spain
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
- Clinical Immunology and Primary Immunodeficiencies Unit, Pediatric Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Barcelona, Spain
- Necmettin Erbakan University, Konya, Turkey
- Department of Pediatrics, Department of Microbiology, Immunology and Infectious Diseases, University of Montreal and Immunology and Rheumatology Division, CHU Sainte-Justine, Montreal, QC, Canada
- National Reference Center for Rheumatic, Autoimmune and Systemic Diseases in Children (RAISE), Pediatric Nephrology, Rheumatology, Dermatology Unit, Hospital of Mother and Child, Hospices Civils of Lyon, Lyon, France
- Human Genomics and Evolution, Collège de France, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | | | - Anna M. Planas
- Department of Neuroscience and Experimental Therapeutics, Institute for Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC), Barcelona, Spain
- Institute for Biomedical Investigations August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Isabelle Meyts
- Department of Pediatrics, University Hospitals Leuven and Laboratory for Inborn Errors of Immunity, KU Leuven, Leuven, Belgium
| | - Filomeen Haerynck
- Primary Immunodeficiency Research Laboratory, Center for Primary Immunodeficiency Ghent, Ghent University Hospital, Ghent, Belgium
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, IDIBELL–Hospital Duran I Reynals; and Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
- CIBERER U759, ISCiii, Madrid, Spain
| | - Vanessa Sancho-Shimizu
- Department of Paediatric Infectious Diseases and Virology, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, UK
| | - Clifford L. Dalgard
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Department of Anatomy, Physiology, and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jacinta Bustamante
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
- Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, AP-HP, Paris, France
| | - Anne Puel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Stéphanie Boisson-Dupuis
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | | | - Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Paul Bastard
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
- Pediatric Hematology-Immunology and Rheumatology Unit, Necker Hospital for Sick Children, AP-HP, Paris, France
| | - Luigi Notarangelo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
| | - Vivien Béziat
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Rebeca Perez de Diego
- Laboratory of Immunogenetics of Human Diseases, Innate Immunity Group, IdiPAZ Institute for Health Research, La Paz Hospital, Madrid, Spain
- Interdepartmental Group of Immunodeficiencies, Madrid, Spain
| | - Carlos Rodriguez-Gallego
- Department of Clinical Sciences, University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
- Department of Immunology, University Hospital of Gran Canaria Dr. Negrín, Canarian Health System, Las Palmas de Gran Canaria, Spain
| | - Helen C. Su
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
- NIAID Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
| | - Richard P. Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Emmanuelle Jouanguy
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Aurélie Cobat
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Laia Alsina
- Kids Corona Platform, Barcelona, Spain
- Department of Surgery and Surgical Specializations, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
- Study Group for Immune Dysfunction Diseases in Children (GEMDIP), Institute of Recerca Sant Joan de Déu, Barcelona, Spain
- Clinical Immunology and Primary Immunodeficiencies Unit, Pediatric Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Barcelona, Spain
| | | | - Elie Haddad
- Department of Pediatrics, Department of Microbiology, Immunology and Infectious Diseases, University of Montreal and Immunology and Rheumatology Division, CHU Sainte-Justine, Montreal, QC, Canada
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Alexandre Belot
- International Center of Infectiology Research (CIRI), University of Lyon, INSERM U1111, Claude Bernard University, Lyon 1, CNRS, UMR5308, ENS of Lyon, Lyon, France
- National Reference Center for Rheumatic, Autoimmune and Systemic Diseases in Children (RAISE), Pediatric Nephrology, Rheumatology, Dermatology Unit, Hospital of Mother and Child, Hospices Civils of Lyon, Lyon, France
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, Paris City University, CNRS UMR 2000, Paris, France
- Human Genomics and Evolution, Collège de France, Paris, France
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Robert H. Silverman
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
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41
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Kerner G, Neehus AL, Philippot Q, Bohlen J, Rinchai D, Kerrouche N, Puel A, Zhang SY, Boisson-Dupuis S, Abel L, Casanova JL, Patin E, Laval G, Quintana-Murci L. Genetic adaptation to pathogens and increased risk of inflammatory disorders in post-Neolithic Europe. CELL GENOMICS 2023; 3:100248. [PMID: 36819665 PMCID: PMC9932995 DOI: 10.1016/j.xgen.2022.100248] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 10/24/2022] [Accepted: 12/14/2022] [Indexed: 01/15/2023]
Abstract
Ancient genomics can directly detect human genetic adaptation to environmental cues. However, it remains unclear how pathogens have exerted selective pressures on human genome diversity across different epochs and affected present-day inflammatory disease risk. Here, we use an ancestry-aware approximate Bayesian computation framework to estimate the nature, strength, and time of onset of selection acting on 2,879 ancient and modern European genomes from the last 10,000 years. We found that the bulk of genetic adaptation occurred after the start of the Bronze Age, <4,500 years ago, and was enriched in genes relating to host-pathogen interactions. Furthermore, we detected directional selection acting on specific leukocytic lineages and experimentally demonstrated that the strongest negatively selected candidate variant in immunity genes, lipopolysaccharide-binding protein (LBP) D283G, is hypomorphic. Finally, our analyses suggest that the risk of inflammatory disorders has increased in post-Neolithic Europeans, possibly because of antagonistic pleiotropy following genetic adaptation to pathogens.
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Affiliation(s)
- Gaspard Kerner
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, 75015 Paris, France
| | - Anna-Lena Neehus
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University Paris Cité, Imagine Institute, 75015 Paris, France
| | - Quentin Philippot
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University Paris Cité, Imagine Institute, 75015 Paris, France
| | - Jonathan Bohlen
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University Paris Cité, Imagine Institute, 75015 Paris, France
| | - Darawan Rinchai
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Nacim Kerrouche
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University Paris Cité, Imagine Institute, 75015 Paris, France
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University Paris Cité, Imagine Institute, 75015 Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Stéphanie Boisson-Dupuis
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University Paris Cité, Imagine Institute, 75015 Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University Paris Cité, Imagine Institute, 75015 Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University Paris Cité, Imagine Institute, 75015 Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute, New York, NY 10065, USA
- Department of Pediatrics, Necker Hospital for Sick Children, 75015 Paris, France
| | - Etienne Patin
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, 75015 Paris, France
| | - Guillaume Laval
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, 75015 Paris, France
| | - Lluis Quintana-Murci
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, 75015 Paris, France
- Collège de France, Chair of Human Genomics and Evolution, 75005 Paris, France
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42
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Słomian D, Szyda J, Dobosz P, Stojak J, Michalska-Foryszewska A, Sypniewski M, Liu J, Kotlarz K, Suchocki T, Mroczek M, Stępień M, Sztromwasser P, Król ZJ. Better safe than sorry-Whole-genome sequencing indicates that missense variants are significant in susceptibility to COVID-19. PLoS One 2023; 18:e0279356. [PMID: 36662838 PMCID: PMC9858061 DOI: 10.1371/journal.pone.0279356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 12/06/2022] [Indexed: 01/22/2023] Open
Abstract
Undoubtedly, genetic factors play an important role in susceptibility and resistance to COVID-19. In this study, we conducted the GWAS analysis. Out of 15,489,173 SNPs, we identified 18,191 significant SNPs for severe and 11,799 SNPs for resistant phenotype, showing that a great number of loci were significant in different COVID-19 representations. The majority of variants were synonymous (60.56% for severe, 58.46% for resistant phenotype) or located in introns (55.77% for severe, 59.83% for resistant phenotype). We identified the most significant SNPs for a severe outcome (in AJAP1 intron) and for COVID resistance (in FIG4 intron). We found no missense variants with a potential causal function on resistance to COVID-19; however, two missense variants were determined as significant a severe phenotype (in PM20D1 and LRP4 exons). None of the aforementioned SNPs and missense variants found in this study have been previously associated with COVID-19.
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Affiliation(s)
- Dawid Słomian
- National Research Institute of Animal Production, Balice, Poland
| | - Joanna Szyda
- National Research Institute of Animal Production, Balice, Poland
- Department of Genetics, Biostatistics Group, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Paula Dobosz
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
- Department of Haematology, Transplantation and Internal Medicine, University Clinical Centre of the Medical University of Warsaw, Warsaw, Poland
| | - Joanna Stojak
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
- Department of Experimental Embryology, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Magdalenka, Poland
| | | | - Mateusz Sypniewski
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
- Department of Genetics and Animal Breedings, Poznan University of Life Sciences, Poznan, Poland
| | - Jakub Liu
- Department of Genetics, Biostatistics Group, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Krzysztof Kotlarz
- Department of Genetics, Biostatistics Group, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Tomasz Suchocki
- National Research Institute of Animal Production, Balice, Poland
- Department of Genetics, Biostatistics Group, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Magdalena Mroczek
- Center for Cardiovascular Genetics & Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich, Switzerland
| | - Maria Stępień
- Department of Infectious Diseases, Doctoral School, Medical University of Lublin, Lublin, Poland
| | | | - Zbigniew J. Król
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
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43
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Pushparaj P, Nicoletto A, Sheward DJ, Das H, Castro Dopico X, Perez Vidakovics L, Hanke L, Chernyshev M, Narang S, Kim S, Fischbach J, Ekström S, McInerney G, Hällberg BM, Murrell B, Corcoran M, Karlsson Hedestam GB. Immunoglobulin germline gene polymorphisms influence the function of SARS-CoV-2 neutralizing antibodies. Immunity 2023; 56:193-206.e7. [PMID: 36574772 PMCID: PMC9742198 DOI: 10.1016/j.immuni.2022.12.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/23/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Abstract
The human immunoglobulin heavy-chain (IGH) locus is exceptionally polymorphic, with high levels of allelic and structural variation. Thus, germline IGH genotypes are personal, which may influence responses to infection and vaccination. For an improved understanding of inter-individual differences in antibody responses, we isolated SARS-CoV-2 spike-specific monoclonal antibodies from convalescent health care workers, focusing on the IGHV1-69 gene, which has the highest level of allelic variation of all IGHV genes. The IGHV1-69∗20-using CAB-I47 antibody and two similar antibodies isolated from an independent donor were critically dependent on allele usage. Neutralization was retained when reverting the V region to the germline IGHV1-69∗20 allele but lost when reverting to other IGHV1-69 alleles. Structural data confirmed that two germline-encoded polymorphisms, R50 and F55, in the IGHV1-69 gene were required for high-affinity receptor-binding domain interaction. These results demonstrate that polymorphisms in IGH genes can influence the function of SARS-CoV-2 neutralizing antibodies.
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Affiliation(s)
- Pradeepa Pushparaj
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Andrea Nicoletto
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Hrishikesh Das
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Xaquin Castro Dopico
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Laura Perez Vidakovics
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Mark Chernyshev
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Sanjana Narang
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Sungyong Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Julian Fischbach
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Simon Ekström
- Department of Biomedical Engineering, Lund University, 221 84 Lund, Sweden
| | - Gerald McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
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44
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Zsichla L, Müller V. Risk Factors of Severe COVID-19: A Review of Host, Viral and Environmental Factors. Viruses 2023; 15:175. [PMID: 36680215 PMCID: PMC9863423 DOI: 10.3390/v15010175] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
The clinical course and outcome of COVID-19 are highly variable, ranging from asymptomatic infections to severe disease and death. Understanding the risk factors of severe COVID-19 is relevant both in the clinical setting and at the epidemiological level. Here, we provide an overview of host, viral and environmental factors that have been shown or (in some cases) hypothesized to be associated with severe clinical outcomes. The factors considered in detail include the age and frailty, genetic polymorphisms, biological sex (and pregnancy), co- and superinfections, non-communicable comorbidities, immunological history, microbiota, and lifestyle of the patient; viral genetic variation and infecting dose; socioeconomic factors; and air pollution. For each category, we compile (sometimes conflicting) evidence for the association of the factor with COVID-19 outcomes (including the strength of the effect) and outline possible action mechanisms. We also discuss the complex interactions between the various risk factors.
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Affiliation(s)
- Levente Zsichla
- Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary
- National Laboratory for Health Security, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Viktor Müller
- Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary
- National Laboratory for Health Security, Eötvös Loránd University, 1117 Budapest, Hungary
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45
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Hagymási K. The Nobel prize in physiology and medicine - 2022. Struct Chem 2023; 34:733-736. [PMID: 36776693 PMCID: PMC9903259 DOI: 10.1007/s11224-023-02124-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 01/04/2023] [Indexed: 02/09/2023]
Abstract
The Nobel Assembly at Karolinska Institutet awarded the 2022 Nobel Prize in Physiology or Medicine to a Swedish geneticist, Svante Pääbo, for his discoveries concerning the genomes of extinct hominins and human evolution, for the sequencing of the genome of the Neanderthal, the discovery of a previously unknown hominin, Denisova, and the establishment of a new scientific discipline, paleogenomics.
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Affiliation(s)
- Krisztina Hagymási
- Department of Surgery, Transplantation and Gastroenterology, Semmelweis University, Budapest, Hungary
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46
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Barmania F, Mellet J, Holborn MA, Pepper MS. Genetic Associations with Coronavirus Susceptibility and Disease Severity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1412:119-140. [PMID: 37378764 DOI: 10.1007/978-3-031-28012-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the coronavirus disease 2019 (COVID-19) global public health emergency, and the disease it causes is highly variable in its clinical presentation. Host genetic factors are increasingly recognised as a determinant of infection susceptibility and disease severity. Several initiatives and groups have been established to analyse and review host genetic epidemiology associated with COVID-19 outcomes. Here, we review the genetic loci associated with COVID-19 susceptibility and severity focusing on the common variants identified in genome-wide association studies.
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Affiliation(s)
- Fatima Barmania
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Juanita Mellet
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Megan A Holborn
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Michael S Pepper
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.
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Ma Y, Xiang F. Discovery of genomes of Neanderthal, Denisova and its impact on modern human. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-1134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Tardiveau C, Monneret G, Lukaszewicz AC, Cheynet V, Cerrato E, Imhoff K, Peronnet E, Bodinier M, Kreitmann L, Blein S, Llitjos JF, Conti F, Gossez M, Buisson M, Yonis H, Cour M, Argaud L, Delignette MC, Wallet F, Dailler F, Monard C, Brengel-Pesce K, Venet F. A 9-mRNA signature measured from whole blood by a prototype PCR panel predicts 28-day mortality upon admission of critically ill COVID-19 patients. Front Immunol 2022; 13:1022750. [DOI: 10.3389/fimmu.2022.1022750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022] Open
Abstract
Immune responses affiliated with COVID-19 severity have been characterized and associated with deleterious outcomes. These approaches were mainly based on research tools not usable in routine clinical practice at the bedside. We observed that a multiplex transcriptomic panel prototype termed Immune Profiling Panel (IPP) could capture the dysregulation of immune responses of ICU COVID-19 patients at admission. Nine transcripts were associated with mortality in univariate analysis and this 9-mRNA signature remained significantly associated with mortality in a multivariate analysis that included age, SOFA and Charlson scores. Using a machine learning model with these 9 mRNA, we could predict the 28-day survival status with an Area Under the Receiver Operating Curve (AUROC) of 0.764. Interestingly, adding patients’ age to the model resulted in increased performance to predict the 28-day mortality (AUROC reaching 0.839). This prototype IPP demonstrated that such a tool, upon clinical/analytical validation and clearance by regulatory agencies could be used in clinical routine settings to quickly identify patients with higher risk of death requiring thus early aggressive intensive care.
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Matuozzo D, Talouarn E, Marchal A, Manry J, Seeleuthner Y, Zhang Y, Bolze A, Chaldebas M, Milisavljevic B, Zhang P, Gervais A, Bastard P, Asano T, Bizien L, Barzaghi F, Abolhassani H, Tayoun AA, Aiuti A, Darazam IA, Allende LM, Alonso-Arias R, Arias AA, Aytekin G, Bergman P, Bondesan S, Bryceson YT, Bustos IG, Cabrera-Marante O, Carcel S, Carrera P, Casari G, Chaïbi K, Colobran R, Condino-Neto A, Covill LE, El Zein L, Flores C, Gregersen PK, Gut M, Haerynck F, Halwani R, Hancerli S, Hammarström L, Hatipoğlu N, Karbuz A, Keles S, Kyheng C, Leon-Lopez R, Franco JL, Mansouri D, Martinez-Picado J, Akcan OM, Migeotte I, Morange PE, Morelle G, Martin-Nalda A, Novelli G, Novelli A, Ozcelik T, Palabiyik F, Pan-Hammarström Q, Pérez de Diego R, Planas-Serra L, Pleguezuelo DE, Prando C, Pujol A, Reyes LF, Rivière JG, Rodriguez-Gallego C, Rojas J, Rovere-Querini P, Schlüter A, Shahrooei M, Sobh A, Soler-Palacin P, Tandjaoui-Lambiotte Y, Tipu I, Tresoldi C, Troya J, van de Beek D, Zatz M, Zawadzki P, Al-Muhsen SZ, Baris-Feldman H, Butte MJ, Constantinescu SN, Cooper MA, Dalgard CL, Fellay J, Heath JR, Lau YL, Lifton RP, Maniatis T, Mogensen TH, von Bernuth H, Lermine A, Vidaud M, Boland A, Deleuze JF, Nussbaum R, Kahn-Kirby A, Mentre F, Tubiana S, Gorochov G, Tubach F, Hausfater P, Meyts I, Zhang SY, Puel A, Notarangelo LD, Boisson-Dupuis S, Su HC, Boisson B, Jouanguy E, Casanova JL, Zhang Q, Abel L, Cobat A. Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.10.22.22281221. [PMID: 36324795 PMCID: PMC9628204 DOI: 10.1101/2022.10.22.22281221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Background We previously reported inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity in 1-5% of unvaccinated patients with life-threatening COVID-19, and auto-antibodies against type I IFN in another 15-20% of cases. Methods We report here a genome-wide rare variant burden association analysis in 3,269 unvaccinated patients with life-threatening COVID-19 (1,301 previously reported and 1,968 new patients), and 1,373 unvaccinated SARS-CoV-2-infected individuals without pneumonia. A quarter of the patients tested had antibodies against type I IFN (234 of 928) and were excluded from the analysis. Results No gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants was TLR7 , with an OR of 27.68 (95%CI:1.5-528.7, P= 1.1×10 -4 ), in analyses restricted to biochemically loss-of-function (bLOF) variants. We replicated the enrichment in rare predicted LOF (pLOF) variants at 13 influenza susceptibility loci involved in TLR3-dependent type I IFN immunity (OR=3.70 [95%CI:1.3-8.2], P= 2.1×10 -4 ). Adding the recently reported TYK2 COVID-19 locus strengthened this enrichment, particularly under a recessive model (OR=19.65 [95%CI:2.1-2635.4]; P= 3.4×10 -3 ). When these 14 loci and TLR7 were considered, all individuals hemizygous ( n =20) or homozygous ( n =5) for pLOF or bLOF variants were patients (OR=39.19 [95%CI:5.2-5037.0], P =4.7×10 -7 ), who also showed an enrichment in heterozygous variants (OR=2.36 [95%CI:1.0-5.9], P =0.02). Finally, the patients with pLOF or bLOF variants at these 15 loci were significantly younger (mean age [SD]=43.3 [20.3] years) than the other patients (56.0 [17.3] years; P= 1.68×10 -5 ). Conclusions Rare variants of TLR3- and TLR7-dependent type I IFN immunity genes can underlie life-threatening COVID-19, particularly with recessive inheritance, in patients under 60 years old.
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Dagilis AJ, Peede D, Coughlan JM, Jofre GI, D'Agostino ERR, Mavengere H, Tate AD, Matute DR. A need for standardized reporting of introgression: Insights from studies across eukaryotes. Evol Lett 2022; 6:344-357. [PMID: 36254258 PMCID: PMC9554761 DOI: 10.1002/evl3.294] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/04/2022] [Accepted: 06/12/2022] [Indexed: 01/04/2023] Open
Abstract
With the rise of affordable next-generation sequencing technology, introgression-or the exchange of genetic materials between taxa-has become widely perceived to be a ubiquitous phenomenon in nature. Although this claim is supported by several keystone studies, no thorough assessment of the frequency of introgression across eukaryotes in nature has been performed to date. In this manuscript, we aim to address this knowledge gap by examining patterns of introgression across eukaryotes. We collated a single statistic, Patterson's D, which can be used as a test for introgression across 123 studies to further assess how taxonomic group, divergence time, and sequencing technology influence reports of introgression. Overall, introgression has mostly been measured in plants and vertebrates, with less attention given to the rest of the Eukaryotes. We find that the most frequently used metrics to detect introgression are difficult to compare across studies and even more so across biological systems due to differences in study effort, reporting standards, and methodology. Nonetheless, our analyses reveal several intriguing patterns, including the observation that differences in sequencing technologies may bias values of Patterson's D and that introgression may differ throughout the course of the speciation process. Together, these results suggest the need for a unified approach to quantifying introgression in natural communities and highlight important areas of future research that can be better assessed once this unified approach is met.
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Affiliation(s)
| | - David Peede
- Biology DepartmentUniversity of North CarolinaChapel HillNCUSA
- Department of Ecology, Evolution, and Organismal BiologyBrown UniversityProvidenceRIUSA
- Center for Computational Molecular BiologyBrown UniversityProvidenceRIUSA
| | - Jenn M. Coughlan
- Biology DepartmentUniversity of North CarolinaChapel HillNCUSA
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
| | - Gaston I. Jofre
- Biology DepartmentUniversity of North CarolinaChapel HillNCUSA
| | - Emmanuel R. R. D'Agostino
- Biology DepartmentUniversity of North CarolinaChapel HillNCUSA
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNJUSA
| | - Heidi Mavengere
- Biology DepartmentUniversity of North CarolinaChapel HillNCUSA
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