1
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Mentzer AJ, Dilthey AT, Pollard M, Gurdasani D, Karakoc E, Carstensen T, Muhwezi A, Cutland C, Diarra A, da Silva Antunes R, Paul S, Smits G, Wareing S, Kim H, Pomilla C, Chong AY, Brandt DYC, Nielsen R, Neaves S, Timpson N, Crinklaw A, Lindestam Arlehamn CS, Rautanen A, Kizito D, Parks T, Auckland K, Elliott KE, Mills T, Ewer K, Edwards N, Fatumo S, Webb E, Peacock S, Jeffery K, van der Klis FRM, Kaleebu P, Vijayanand P, Peters B, Sette A, Cereb N, Sirima S, Madhi SA, Elliott AM, McVean G, Hill AVS, Sandhu MS. High-resolution African HLA resource uncovers HLA-DRB1 expression effects underlying vaccine response. Nat Med 2024:10.1038/s41591-024-02944-5. [PMID: 38740997 DOI: 10.1038/s41591-024-02944-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/25/2024] [Indexed: 05/16/2024]
Abstract
How human genetic variation contributes to vaccine effectiveness in infants is unclear, and data are limited on these relationships in populations with African ancestries. We undertook genetic analyses of vaccine antibody responses in infants from Uganda (n = 1391), Burkina Faso (n = 353) and South Africa (n = 755), identifying associations between human leukocyte antigen (HLA) and antibody response for five of eight tested antigens spanning pertussis, diphtheria and hepatitis B vaccines. In addition, through HLA typing 1,702 individuals from 11 populations of African ancestry derived predominantly from the 1000 Genomes Project, we constructed an imputation resource, fine-mapping class II HLA-DR and DQ associations explaining up to 10% of antibody response variance in our infant cohorts. We observed differences in the genetic architecture of pertussis antibody response between the cohorts with African ancestries and an independent cohort with European ancestry, but found no in silico evidence of differences in HLA peptide binding affinity or breadth. Using immune cell expression quantitative trait loci datasets derived from African-ancestry samples from the 1000 Genomes Project, we found evidence of differential HLA-DRB1 expression correlating with inferred protection from pertussis following vaccination. This work suggests that HLA-DRB1 expression may play a role in vaccine response and should be considered alongside peptide selection to improve vaccine design.
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Affiliation(s)
- Alexander J Mentzer
- Centre for Human Genetics, University of Oxford, Oxford, UK.
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
| | - Alexander T Dilthey
- Centre for Human Genetics, University of Oxford, Oxford, UK
- Institute of Medical Microbiology and Hospital Hygiene, University Hospital of Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | | | | | | | | | - Allan Muhwezi
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Clare Cutland
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Amidou Diarra
- Groupe de Recherche Action en Santé (GRAS) 06 BP 10248, Ouagadougou, Burkina Faso
| | | | - Sinu Paul
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Gaby Smits
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Susan Wareing
- Microbiology Department, John Radcliffe Hospital, Oxford University NHS Foundation Trust, Oxford, UK
| | | | | | - Amanda Y Chong
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Debora Y C Brandt
- Department of Integrative Biology, University of California at Berkeley, California, CA, USA
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California at Berkeley, California, CA, USA
| | - Samuel Neaves
- Avon Longitudinal Study of Parents and Children at University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Nicolas Timpson
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Austin Crinklaw
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Anna Rautanen
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Dennison Kizito
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Tom Parks
- Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Kate E Elliott
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Tara Mills
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Katie Ewer
- The Jenner Institute, University of Oxford, Oxford, UK
| | - Nick Edwards
- The Jenner Institute, University of Oxford, Oxford, UK
| | - Segun Fatumo
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- The Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine London, London, UK
| | - Emily Webb
- MRC International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine London, London, UK
| | - Sarah Peacock
- Tissue Typing Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Katie Jeffery
- Microbiology Department, John Radcliffe Hospital, Oxford University NHS Foundation Trust, Oxford, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | | | - Bjorn Peters
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Alessandro Sette
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | | | - Sodiomon Sirima
- Groupe de Recherche Action en Santé (GRAS) 06 BP 10248, Ouagadougou, Burkina Faso
| | - Shabir A Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Alison M Elliott
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- MRC International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine London, London, UK
| | - Gil McVean
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Adrian V S Hill
- Centre for Human Genetics, University of Oxford, Oxford, UK
- The Jenner Institute, University of Oxford, Oxford, UK
| | - Manjinder S Sandhu
- Department of Epidemiology & Biostatistics, School of Public Health, Imperial College London, London, UK.
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2
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Sohail M, Palma-Martínez MJ, Chong AY, Quinto-Cortés CD, Barberena-Jonas C, Medina-Muñoz SG, Ragsdale A, Delgado-Sánchez G, Cruz-Hervert LP, Ferreyra-Reyes L, Ferreira-Guerrero E, Mongua-Rodríguez N, Canizales-Quintero S, Jimenez-Kaufmann A, Moreno-Macías H, Aguilar-Salinas CA, Auckland K, Cortés A, Acuña-Alonzo V, Gignoux CR, Wojcik GL, Ioannidis AG, Fernández-Valverde SL, Hill AVS, Tusié-Luna MT, Mentzer AJ, Novembre J, García-García L, Moreno-Estrada A. Mexican Biobank advances population and medical genomics of diverse ancestries. Nature 2023; 622:775-783. [PMID: 37821706 PMCID: PMC10600006 DOI: 10.1038/s41586-023-06560-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/22/2023] [Indexed: 10/13/2023]
Abstract
Latin America continues to be severely underrepresented in genomics research, and fine-scale genetic histories and complex trait architectures remain hidden owing to insufficient data1. To fill this gap, the Mexican Biobank project genotyped 6,057 individuals from 898 rural and urban localities across all 32 states in Mexico at a resolution of 1.8 million genome-wide markers with linked complex trait and disease information creating a valuable nationwide genotype-phenotype database. Here, using ancestry deconvolution and inference of identity-by-descent segments, we inferred ancestral population sizes across Mesoamerican regions over time, unravelling Indigenous, colonial and postcolonial demographic dynamics2-6. We observed variation in runs of homozygosity among genomic regions with different ancestries reflecting distinct demographic histories and, in turn, different distributions of rare deleterious variants. We conducted genome-wide association studies (GWAS) for 22 complex traits and found that several traits are better predicted using the Mexican Biobank GWAS compared to the UK Biobank GWAS7,8. We identified genetic and environmental factors associating with trait variation, such as the length of the genome in runs of homozygosity as a predictor for body mass index, triglycerides, glucose and height. This study provides insights into the genetic histories of individuals in Mexico and dissects their complex trait architectures, both crucial for making precision and preventive medicine initiatives accessible worldwide.
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Affiliation(s)
- Mashaal Sohail
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (Cinvestav), Irapuato, Mexico.
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
- Centro de Ciencias Genómicas (CCG), Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Mexico.
| | - María J Palma-Martínez
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (Cinvestav), Irapuato, Mexico
| | - Amanda Y Chong
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Consuelo D Quinto-Cortés
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (Cinvestav), Irapuato, Mexico
| | - Carmina Barberena-Jonas
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (Cinvestav), Irapuato, Mexico
| | - Santiago G Medina-Muñoz
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (Cinvestav), Irapuato, Mexico
| | - Aaron Ragsdale
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (Cinvestav), Irapuato, Mexico
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Luis Pablo Cruz-Hervert
- Instituto Nacional de Salud Pública (INSP), Cuernavaca, Mexico
- División de Estudios de Posgrado e Investigación, Facultad de Odontología, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | | | | | | | | | - Andrés Jimenez-Kaufmann
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (Cinvestav), Irapuato, Mexico
| | - Hortensia Moreno-Macías
- Unidad de Biología Molecular y Medicina Genómica, Instituto de Investigaciones Biomédicas UNAM/Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- Universidad Autónoma Metropolitana, Mexico City, Mexico
| | - Carlos A Aguilar-Salinas
- Division de Nutrición, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Kathryn Auckland
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Adrián Cortés
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | | | - Christopher R Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Genevieve L Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Selene L Fernández-Valverde
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (Cinvestav), Irapuato, Mexico
- School of Biotechnology and Biomolecular Sciences and the RNA Institute, The University of New South Wales, Sydney, New South Wales, Australia
| | - Adrian V S Hill
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- The Jenner Institute, University of Oxford, Oxford, UK
| | - María Teresa Tusié-Luna
- Unidad de Biología Molecular y Medicina Genómica, Instituto de Investigaciones Biomédicas UNAM/Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Alexander J Mentzer
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | | | - Andrés Moreno-Estrada
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (Cinvestav), Irapuato, Mexico.
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3
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Butler-Laporte G, Auckland K, Noor Z, Kabir M, Alam M, Carstensen T, Wojcik GL, Chong AY, Pomilla C, Noble JA, McDevitt SL, Smits G, Wareing S, van der Klis FRM, Jeffery K, Kirkpatrick BD, Sirima S, Madhi S, Elliott A, Richards JB, Hill AVS, Duggal P, Sandhu MS, Haque R, Petri WA, Mentzer AJ. Targeting hepatitis B vaccine escape using immunogenetics in Bangladeshi infants. medRxiv 2023:2023.06.26.23291885. [PMID: 37425840 PMCID: PMC10327284 DOI: 10.1101/2023.06.26.23291885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Hepatitis B virus (HBV) vaccine escape mutants (VEM) are increasingly described, threatening progress in control of this virus worldwide. Here we studied the relationship between host genetic variation, vaccine immunogenicity and viral sequences implicating VEM emergence. In a cohort of 1,096 Bangladeshi children, we identified human leukocyte antigen (HLA) variants associated with response vaccine antigens. Using an HLA imputation panel with 9,448 south Asian individuals DPB1*04:01 was associated with higher HBV antibody responses (p=4.5×10-30). The underlying mechanism is a result of higher affinity binding of HBV surface antigen epitopes to DPB1*04:01 dimers. This is likely a result of evolutionary pressure at the HBV surface antigen 'a-determinant' segment incurring VEM specific to HBV. Prioritizing pre-S isoform HBV vaccines may tackle the rise of HBV vaccine evasion.
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Affiliation(s)
- Guillaume Butler-Laporte
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Division of Infectious Diseases, McGill University Health Centre, Montréal, Québec, Canada
| | - Kathryn Auckland
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Zannatun Noor
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Mamun Kabir
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Masud Alam
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Tommy Carstensen
- Wellcome Trust Sanger Institute, University of Cambridge, Hinxton, United Kingdom
- Queen Mary University of London, London, United Kingdom
| | - Genevieve L Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Amanda Y Chong
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Cristina Pomilla
- Wellcome Trust Sanger Institute, University of Cambridge, Hinxton, United Kingdom
| | - Janelle A Noble
- Children’s Hospital Oakland Research Institute, Oakland, California, USA
- Department of Pediatrics, University of California, San Francisco, California, USA
| | | | - Gaby Smits
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Susan Wareing
- Microbiology Department, John Radcliffe Hospital, Oxford University NHS Foundation Trust, Oxford, UK
| | - Fiona RM van der Klis
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Katie Jeffery
- Microbiology Department, John Radcliffe Hospital, Oxford University NHS Foundation Trust, Oxford, UK
| | - Beth D Kirkpatrick
- Department of Microbiology and Molecular Genetics, Vaccine Testing Center, University of Vermont College of Medicine, Vermont, USA
| | - Sodiomon Sirima
- Groupe de Recherche Action en Santé (GRAS) 06 BP 10248 Ouagadougou, Burkina Faso
| | - Shabir Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Alison Elliott
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - J Brent Richards
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- 5 Prime Sciences Inc, Montreal, Quebec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
- Department of Twin Research, King’s College London, London, United Kingdom
| | - Adrian VS Hill
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | | | - Manjinder S Sandhu
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, United Kingdom
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - William A Petri
- Department of Medicine, Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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4
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Chen S, Cardinal RN, Auckland K, Gräf S, O'Brien JT, Underwood BR. Risk Factors for Longer-Term Mortality in Discharged Patients with Dementia and SARS-CoV-2 Infection: A Matched Case-Control Study. J Alzheimers Dis 2023; 92:295-309. [PMID: 36744344 DOI: 10.3233/jad-221093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND Persisting symptoms and increased mortality after SARS-CoV-2 infection has been described in COVID-19 survivors. OBJECTIVE We examined longer-term mortality in patients with dementia and SARS-CoV-2 infection. METHODS A retrospective matched case-control study of 165 patients with dementia who survived an acute hospital admission with COVID-19 infection, and 1325 patients with dementia who survived a hospital admission but without SARS-CoV-2 infection. Potential risk factors investigated included socio-demographic factors, clinical features, and results of investigations. Data were fitted using a Cox proportional hazard model. RESULTS Compared to patients with dementia but without SARS-CoV-2 infection, people with dementia and SARS-CoV-2 infection had a 4.4-fold risk of death (adjusted hazard ratio [aHR] = 4.44, 95% confidence interval [CI] 3.13-6.30) even beyond the acute phase of infection. This excess mortality could be seen up to 125 days after initial recovery but was not elevated beyond this time. Risk factors for COVID-19-associated mortality included prescription of antipsychotics (aHR = 3.06, 95% CI 1.40-6.69) and benzodiazepines (aHR = 3.00, 95% CI 1.28-7.03). Abnormalities on investigation associated with increased mortality included high white cell count (aHR = 1.21, 95% CI 1.04-1.39), higher absolute neutrophil count (aHR = 1.28, 95% CI 1.12-1.46), higher C-reactive protein (aHR = 1.01, 95% CI 1.00-1.02), higher serum sodium (aHR = 1.09, 95% CI 1.01-1.19), and higher ionized calcium (aHR = 1.03, 95% CI 1.00-1.06). The post-acute COVID mortality could be modeled for the first 120 days after recovery with a balanced accuracy of 87.2%. CONCLUSION We found an increased mortality in patients with dementia beyond the acute phase of illness. We identified several investigation results associated with increased mortality, and increased mortality in patients prescribed antipsychotics or benzodiazepines.
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Affiliation(s)
- Shanquan Chen
- Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Rudolf N Cardinal
- Department of Psychiatry, University of Cambridge, Cambridge, UK.,Cambridgeshire and Peterborough NHS Foundation Trust, UK
| | | | | | - Stefan Gräf
- Department of Medicine, University of Cambridge, Cambridge, UK.,Departmentof Haematology, University of Cambridge, Cambridge, UK.,NIHR BioResource for Translational Research, Cambridge, UK
| | - John T O'Brien
- Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Benjamin R Underwood
- Department of Psychiatry, University of Cambridge, Cambridge, UK.,Cambridgeshire and Peterborough NHS Foundation Trust, UK
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5
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Gilchrist JJ, Auckland K, Parks T, Mentzer AJ, Goldblatt L, Naranbhai V, Band G, Rockett KA, Toure OB, Konate S, Sissoko S, Djimdé AA, Thera MA, Doumbo OK, Sow S, Floyd S, Pönnighaus JM, Warndorff DK, Crampin AC, Fine PEM, Fairfax BP, Hill AVS. Genome-wide association study of leprosy in Malawi and Mali. PLoS Pathog 2022; 18:e1010312. [PMID: 36121873 PMCID: PMC9624411 DOI: 10.1371/journal.ppat.1010312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 11/01/2022] [Accepted: 07/12/2022] [Indexed: 11/28/2022] Open
Abstract
Leprosy is a chronic infection of the skin and peripheral nerves caused by Mycobacterium leprae. Despite recent improvements in disease control, leprosy remains an important cause of infectious disability globally. Large-scale genetic association studies in Chinese, Vietnamese and Indian populations have identified over 30 susceptibility loci for leprosy. There is a significant burden of leprosy in Africa, however it is uncertain whether the findings of published genetic association studies are generalizable to African populations. To address this, we conducted a genome-wide association study (GWAS) of leprosy in Malawian (327 cases, 436 controls) and Malian (247 cases, 368 controls) individuals. In that analysis, we replicated four risk loci previously reported in China, Vietnam and India; MHC Class I and II, LACC1 and SLC29A3. We further identified a novel leprosy susceptibility locus at 10q24 (rs2015583; combined p = 8.81 × 10-9; OR = 0.51 [95% CI 0.40 - 0.64]). Using publicly-available data we characterise regulatory activity at this locus, identifying ACTR1A as a candidate mediator of leprosy risk. This locus shows evidence of recent positive selection and demonstrates pleiotropy with established risk loci for inflammatory bowel disease and childhood-onset asthma. A shared genetic architecture for leprosy and inflammatory bowel disease has been previously described. We expand on this, strengthening the hypothesis that selection pressure driven by leprosy has shaped the evolution of autoimmune and atopic disease in modern populations. More broadly, our data highlights the importance of defining the genetic architecture of disease across genetically diverse populations, and that disease insights derived from GWAS in one population may not translate to all affected populations.
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Affiliation(s)
- James J. Gilchrist
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- MRC–Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail: (JJG); (AVSH)
| | - Kathryn Auckland
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Tom Parks
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Alexander J. Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Vivek Naranbhai
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Gavin Band
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Kirk A. Rockett
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Ousmane B. Toure
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Salimata Konate
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Sibiri Sissoko
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Abdoulaye A. Djimdé
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Mahamadou A. Thera
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Ogobara K. Doumbo
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Samba Sow
- Center for Vaccine Development, Bamako, Mali
| | - Sian Floyd
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Jörg M. Pönnighaus
- Malawi Epidemiology and Intervention Research Unit (formerly Karonga Prevention Study), Chilumba, Malawi
| | - David K. Warndorff
- Malawi Epidemiology and Intervention Research Unit (formerly Karonga Prevention Study), Chilumba, Malawi
| | - Amelia C. Crampin
- Malawi Epidemiology and Intervention Research Unit (formerly Karonga Prevention Study), Chilumba, Malawi
| | - Paul E. M. Fine
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Benjamin P. Fairfax
- MRC–Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Adrian V. S. Hill
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Jenner Institute, University of Oxford, Oxford, United Kingdom
- * E-mail: (JJG); (AVSH)
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6
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Liu YC, Hunter-Anderson R, Cheronet O, Eakin J, Camacho F, Pietrusewsky M, Rohland N, Ioannidis A, Athens JS, Douglas MT, Ikehara-Quebral RM, Bernardos R, Culleton BJ, Mah M, Adamski N, Broomandkhoshbacht N, Callan K, Lawson AM, Mandl K, Michel M, Oppenheimer J, Stewardson K, Zalzala F, Kidd K, Kidd J, Schurr TG, Auckland K, Hill AVS, Mentzer AJ, Quinto-Cortés CD, Robson K, Kennett DJ, Patterson N, Bustamante CD, Moreno-Estrada A, Spriggs M, Vilar M, Lipson M, Pinhasi R, Reich D. Ancient DNA reveals five streams of migration into Micronesia and matrilocality in early Pacific seafarers. Science 2022; 377:72-79. [PMID: 35771911 PMCID: PMC9983687 DOI: 10.1126/science.abm6536] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Micronesia began to be peopled earlier than other parts of Remote Oceania, but the origins of its inhabitants remain unclear. We generated genome-wide data from 164 ancient and 112 modern individuals. Analysis reveals five migratory streams into Micronesia. Three are East Asian related, one is Polynesian, and a fifth is a Papuan source related to mainland New Guineans that is different from the New Britain-related Papuan source for southwest Pacific populations but is similarly derived from male migrants ~2500 to 2000 years ago. People of the Mariana Archipelago may derive all of their precolonial ancestry from East Asian sources, making them the only Remote Oceanians without Papuan ancestry. Female-inherited mitochondrial DNA was highly differentiated across early Remote Oceanian communities but homogeneous within, implying matrilocal practices whereby women almost never raised their children in communities different from the ones in which they grew up.
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Affiliation(s)
- Yue-Chen Liu
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna 1030, Austria
| | - Joanne Eakin
- Independent Researcher, Albuquerque, NM 87107, USA
| | - Frank Camacho
- Department of Biology, University of Guam, Mangilao 96923, Guam
| | - Michael Pietrusewsky
- Department of Anthropology, University of Hawaiʻi at Mānoa, Honolulu, HI 96822, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexander Ioannidis
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA.,Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - J. Stephen Athens
- International Archaeological Research Institute, Inc., Honolulu, HI 96826, USA
| | | | | | - Rebecca Bernardos
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Brendan J. Culleton
- Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kirsten Mandl
- Department of Evolutionary Anthropology, University of Vienna, Vienna 1030, Austria
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kenneth Kidd
- Department of Genetics, Yale Medical School, New Haven, CT 06520, USA
| | - Judith Kidd
- Department of Genetics, Yale Medical School, New Haven, CT 06520, USA
| | - Theodore G. Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kathryn Auckland
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Adrian V. S. Hill
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK,The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Alexander J. Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK,Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, UK
| | - Consuelo D. Quinto-Cortés
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Unit of Advanced Genomics, CINVESTAV, Irapuato 36821, Mexico
| | - Kathryn Robson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Douglas J. Kennett
- Department of Anthropology, University of California, Santa Barbara, CA 93106, USA
| | - Nick Patterson
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carlos D. Bustamante
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA.,Center for Computational, Evolutionary and Human Genomics (CEHG), Stanford University, Stanford, CA 94305, USA,Current Address: Galatea Bio, Inc. 975 W 22nd St. Hialeah, FL 33010, USA
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Unit of Advanced Genomics, CINVESTAV, Irapuato 36821, Mexico
| | - Matthew Spriggs
- School of Archaeology and Anthropology, The Australian National University, Canberra, ACT 2601, Australia,Vanuatu National Museum, Vanuatu Culture Centre, P.O. Box 184, Port Vila, Vanuatu
| | - Miguel Vilar
- Department of Anthropology, University of Maryland, College Park, MD 20742, USA
| | - Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna 1030, Austria,Human Evolution and Archaeological Sciences, University of Vienna, Vienna 1030, Austria
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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7
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Ioannidis AG, Blanco-Portillo J, Sandoval K, Hagelberg E, Barberena-Jonas C, Hill AVS, Rodríguez-Rodríguez JE, Fox K, Robson K, Haoa-Cardinali S, Quinto-Cortés CD, Miquel-Poblete JF, Auckland K, Parks T, Sofro ASM, Ávila-Arcos MC, Sockell A, Homburger JR, Eng C, Huntsman S, Burchard EG, Gignoux CR, Verdugo RA, Moraga M, Bustamante CD, Mentzer AJ, Moreno-Estrada A. Paths and timings of the peopling of Polynesia inferred from genomic networks. Nature 2021; 597:522-526. [PMID: 34552258 PMCID: PMC9710236 DOI: 10.1038/s41586-021-03902-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 08/12/2021] [Indexed: 02/08/2023]
Abstract
Polynesia was settled in a series of extraordinary voyages across an ocean spanning one third of the Earth1, but the sequences of islands settled remain unknown and their timings disputed. Currently, several centuries separate the dates suggested by different archaeological surveys2-4. Here, using genome-wide data from merely 430 modern individuals from 21 key Pacific island populations and novel ancestry-specific computational analyses, we unravel the detailed genetic history of this vast, dispersed island network. Our reconstruction of the branching Polynesian migration sequence reveals a serial founder expansion, characterized by directional loss of variants, that originated in Samoa and spread first through the Cook Islands (Rarotonga), then to the Society (Tōtaiete mā) Islands (11th century), the western Austral (Tuha'a Pae) Islands and Tuāmotu Archipelago (12th century), and finally to the widely separated, but genetically connected, megalithic statue-building cultures of the Marquesas (Te Henua 'Enana) Islands in the north, Raivavae in the south, and Easter Island (Rapa Nui), the easternmost of the Polynesian islands, settled in approximately AD 1200 via Mangareva.
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Affiliation(s)
- Alexander G Ioannidis
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA.
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico.
| | - Javier Blanco-Portillo
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Karla Sandoval
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico
| | | | - Carmina Barberena-Jonas
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Adrian V S Hill
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Juan Esteban Rodríguez-Rodríguez
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Keolu Fox
- Department of Anthropology, University of California San Diego, La Jolla, CA, USA
| | - Kathryn Robson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Consuelo D Quinto-Cortés
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico
| | | | - Kathryn Auckland
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Tom Parks
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Abdul Salam M Sofro
- Department of Biochemistry, Faculty of Medicine, Yayasan Rumah Sakit Islam (YARSI) University, Cempaka Putih, Jakarta, Indonesia
| | - María C Ávila-Arcos
- International Laboratory for Human Genome Research (LIIGH), UNAM Juriquilla, Queretaro, Mexico
| | - Alexandra Sockell
- Center for Computational, Evolutionary and Human Genomics (CEHG), Stanford University, Stanford, CA, USA
| | - Julian R Homburger
- Center for Computational, Evolutionary and Human Genomics (CEHG), Stanford University, Stanford, CA, USA
| | - Celeste Eng
- Program in Pharmaceutical Sciences and Pharmacogenomics, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Scott Huntsman
- Program in Pharmaceutical Sciences and Pharmacogenomics, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Esteban G Burchard
- Program in Pharmaceutical Sciences and Pharmacogenomics, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Christopher R Gignoux
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, CO, USA
| | - Ricardo A Verdugo
- Human Genetics Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
- Translational Oncology Department, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Mauricio Moraga
- Human Genetics Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
- Department of Anthropology, Faculty of Social Sciences, University of Chile, Santiago, Chile
| | - Carlos D Bustamante
- Center for Computational, Evolutionary and Human Genomics (CEHG), Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico.
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8
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Ainsworth M, Andersson M, Auckland K, Baillie JK, Barnes E, Beer S, Beveridge A, Bibi S, Blackwell L, Borak M, Bown A, Brooks T, Burgess-Brown NA, Camara S, Catton M, Chau KK, Christott T, Clutterbuck E, Coker J, Cornall RJ, Cox S, Crawford-Jones D, Crook DW, D'Arcangelo S, Dejnirattsai W, Dequaire JMM, Dimitriadis S, Dingle KE, Doherty G, Dold C, Dong T, Dunachie SJ, Ebner D, Emmenegger M, Espinosa A, Eyre DW, Fairhead R, Fassih S, Feehily C, Felle S, Fernandez-Cid A, Fernandez Mendoza M, Foord TH, Fordwoh T, Fox McKee D, Frater J, Gallardo Sanchez V, Gent N, Georgiou D, Groves CJ, Hallis B, Hammond PM, Hatch SB, Harvala HJ, Hill J, Hoosdally SJ, Horsington B, Howarth A, James T, Jeffery K, Jones E, Justice A, Karpe F, Kavanagh J, Kim DS, Kirton R, Klenerman P, Knight JC, Koukouflis L, Kwok A, Leuschner U, Levin R, Linder A, Lockett T, Lumley SF, Marinou S, Marsden BD, Martinez J, Martins Ferreira L, Mason L, Matthews PC, Mentzer AJ, Mobbs A, Mongkolsapaya J, Morrow J, Mukhopadhyay SMM, Neville MJ, Oakley S, Oliveira M, Otter A, Paddon K, Pascoe J, Peng Y, Perez E, Perumal PK, Peto TEA, Pickford H, Ploeg RJ, Pollard AJ, Richardson A, Ritter TG, Roberts DJ, Rodger G, Rollier CS, Rowe C, Rudkin JK, Screaton G, Semple MG, Sienkiewicz A, Silva-Reyes L, Skelly DT, Sobrino Diaz A, Stafford L, Stockdale L, Stoesser N, Street T, Stuart DI, Sweed A, Taylor A, Thraves H, Tsang HP, Verheul MK, Vipond R, Walker TM, Wareing S, Warren Y, Wells C, Wilson C, Withycombe K, Young RK. Performance characteristics of five immunoassays for SARS-CoV-2: a head-to-head benchmark comparison. Lancet Infect Dis 2020; 20:1390-1400. [PMID: 32979318 PMCID: PMC7511171 DOI: 10.1016/s1473-3099(20)30634-4] [Citation(s) in RCA: 260] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/29/2020] [Accepted: 08/03/2020] [Indexed: 01/19/2023]
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic in 2020. Testing is crucial for mitigating public health and economic effects. Serology is considered key to population-level surveillance and potentially individual-level risk assessment. However, immunoassay performance has not been compared on large, identical sample sets. We aimed to investigate the performance of four high-throughput commercial SARS-CoV-2 antibody immunoassays and a novel 384-well ELISA. METHODS We did a head-to-head assessment of SARS-CoV-2 IgG assay (Abbott, Chicago, IL, USA), LIAISON SARS-CoV-2 S1/S2 IgG assay (DiaSorin, Saluggia, Italy), Elecsys Anti-SARS-CoV-2 assay (Roche, Basel, Switzerland), SARS-CoV-2 Total assay (Siemens, Munich, Germany), and a novel 384-well ELISA (the Oxford immunoassay). We derived sensitivity and specificity from 976 pre-pandemic blood samples (collected between Sept 4, 2014, and Oct 4, 2016) and 536 blood samples from patients with laboratory-confirmed SARS-CoV-2 infection, collected at least 20 days post symptom onset (collected between Feb 1, 2020, and May 31, 2020). Receiver operating characteristic (ROC) curves were used to assess assay thresholds. FINDINGS At the manufacturers' thresholds, for the Abbott assay sensitivity was 92·7% (95% CI 90·2-94·8) and specificity was 99·9% (99·4-100%); for the DiaSorin assay sensitivity was 96·2% (94·2-97·7) and specificity was 98·9% (98·0-99·4); for the Oxford immunoassay sensitivity was 99·1% (97·8-99·7) and specificity was 99·0% (98·1-99·5); for the Roche assay sensitivity was 97·2% (95·4-98·4) and specificity was 99·8% (99·3-100); and for the Siemens assay sensitivity was 98·1% (96·6-99·1) and specificity was 99·9% (99·4-100%). All assays achieved a sensitivity of at least 98% with thresholds optimised to achieve a specificity of at least 98% on samples taken 30 days or more post symptom onset. INTERPRETATION Four commercial, widely available assays and a scalable 384-well ELISA can be used for SARS-CoV-2 serological testing to achieve sensitivity and specificity of at least 98%. The Siemens assay and Oxford immunoassay achieved these metrics without further optimisation. This benchmark study in immunoassay assessment should enable refinements of testing strategies and the best use of serological testing resource to benefit individuals and population health. FUNDING Public Health England and UK National Institute for Health Research.
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9
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Swietlik EM, Prapa M, Martin JM, Pandya D, Auckland K, Morrell NW, Gräf S. 'There and Back Again'-Forward Genetics and Reverse Phenotyping in Pulmonary Arterial Hypertension. Genes (Basel) 2020; 11:E1408. [PMID: 33256119 PMCID: PMC7760524 DOI: 10.3390/genes11121408] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/17/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023] Open
Abstract
Although the invention of right heart catheterisation in the 1950s enabled accurate clinical diagnosis of pulmonary arterial hypertension (PAH), it was not until 2000 when the landmark discovery of the causative role of bone morphogenetic protein receptor type II (BMPR2) mutations shed new light on the pathogenesis of PAH. Since then several genes have been discovered, which now account for around 25% of cases with the clinical diagnosis of idiopathic PAH. Despite the ongoing efforts, in the majority of patients the cause of the disease remains elusive, a phenomenon often referred to as "missing heritability". In this review, we discuss research approaches to uncover the genetic architecture of PAH starting with forward phenotyping, which in a research setting should focus on stable intermediate phenotypes, forward and reverse genetics, and finally reverse phenotyping. We then discuss potential sources of "missing heritability" and how functional genomics and multi-omics methods are employed to tackle this problem.
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Affiliation(s)
- Emilia M. Swietlik
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
- Royal Papworth Hospital NHS Foundation Trust, Cambridge CB2 0AY, UK
- Addenbrooke’s Hospital NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Matina Prapa
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
- Addenbrooke’s Hospital NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Jennifer M. Martin
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
| | - Divya Pandya
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
| | - Kathryn Auckland
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
| | - Nicholas W. Morrell
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
- Royal Papworth Hospital NHS Foundation Trust, Cambridge CB2 0AY, UK
- Addenbrooke’s Hospital NHS Foundation Trust, Cambridge CB2 0QQ, UK
- NIHR BioResource for Translational Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Stefan Gräf
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
- NIHR BioResource for Translational Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
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10
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Andersson MI, Arancibia-Carcamo CV, Auckland K, Baillie JK, Barnes E, Beneke T, Bibi S, Brooks T, Carroll M, Crook D, Dingle K, Dold C, Downs LO, Dunn L, Eyre DW, Gilbert Jaramillo J, Harvala H, Hoosdally S, Ijaz S, James T, James W, Jeffery K, Justice A, Klenerman P, Knight JC, Knight M, Liu X, Lumley SF, Matthews PC, McNaughton AL, Mentzer AJ, Mongkolsapaya J, Oakley S, Oliveira MS, Peto T, Ploeg RJ, Ratcliff J, Robbins MJ, Roberts DJ, Rudkin J, Russell RA, Screaton G, Semple MG, Skelly D, Simmonds P, Stoesser N, Turtle L, Wareing S, Zambon M. SARS-CoV-2 RNA detected in blood products from patients with COVID-19 is not associated with infectious virus. Wellcome Open Res 2020; 5:181. [PMID: 33283055 PMCID: PMC7689603 DOI: 10.12688/wellcomeopenres.16002.2] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2020] [Indexed: 12/19/2022] Open
Abstract
Background: Laboratory diagnosis of SARS-CoV-2 infection (the cause of COVID-19) uses PCR to detect viral RNA (vRNA) in respiratory samples. SARS-CoV-2 RNA has also been detected in other sample types, but there is limited understanding of the clinical or laboratory significance of its detection in blood. Methods: We undertook a systematic literature review to assimilate the evidence for the frequency of vRNA in blood, and to identify associated clinical characteristics. We performed RT-PCR in serum samples from a UK clinical cohort of acute and convalescent COVID-19 cases (n=212), together with convalescent plasma samples collected by NHS Blood and Transplant (NHSBT) (n=462 additional samples). To determine whether PCR-positive blood samples could pose an infection risk, we attempted virus isolation from a subset of RNA-positive samples. Results: We identified 28 relevant studies, reporting SARS-CoV-2 RNA in 0-76% of blood samples; pooled estimate 10% (95%CI 5-18%). Among serum samples from our clinical cohort, 27/212 (12.7%) had SARS-CoV-2 RNA detected by RT-PCR. RNA detection occurred in samples up to day 20 post symptom onset, and was associated with more severe disease (multivariable odds ratio 7.5). Across all samples collected ≥28 days post symptom onset, 0/494 (0%, 95%CI 0-0.7%) had vRNA detected. Among our PCR-positive samples, cycle threshold (ct) values were high (range 33.5-44.8), suggesting low vRNA copy numbers. PCR-positive sera inoculated into cell culture did not produce any cytopathic effect or yield an increase in detectable SARS-CoV-2 RNA. There was a relationship between RT-PCR negativity and the presence of total SARS-CoV-2 antibody (p=0.02). Conclusions: vRNA was detectable at low viral loads in a minority of serum samples collected in acute infection, but was not associated with infectious SARS-CoV-2 (within the limitations of the assays used). This work helps to inform biosafety precautions for handling blood products from patients with current or previous COVID-19.
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Affiliation(s)
- Monique I. Andersson
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Carolina V. Arancibia-Carcamo
- Translational Gastroenterology Unit, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre (BRC), John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Kathryn Auckland
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - J. Kenneth Baillie
- Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Eleanor Barnes
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre (BRC), John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Tom Beneke
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Sagida Bibi
- Department of Paediatrics, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Tim Brooks
- Porton Down, Public Health England, Manor Farm Road, Porton Down, Salisbury, SP4 0JG, UK
| | - Miles Carroll
- Porton Down, Public Health England, Manor Farm Road, Porton Down, Salisbury, SP4 0JG, UK
| | - Derrick Crook
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre (BRC), John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Kate Dingle
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Christina Dold
- Department of Paediatrics, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Louise O. Downs
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Laura Dunn
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - David W. Eyre
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre (BRC), John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Big Data Institute, Roosevelt Drive, Old Road Campus, Headington, Oxford, OX3 7LF, UK
| | - Javier Gilbert Jaramillo
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Heli Harvala
- NHS Blood and Transfusion, 26 Margaret St, Marylebone, London, W1W 8NB, UK
- University College London, Gower St, Bloomsbury, London, WC1E 6BT, UK
| | - Sarah Hoosdally
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Samreen Ijaz
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - Tim James
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - William James
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Katie Jeffery
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Anita Justice
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Julian C. Knight
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Michael Knight
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Xu Liu
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Sheila F. Lumley
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Philippa C. Matthews
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre (BRC), John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Anna L. McNaughton
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Alexander J. Mentzer
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | | | - Sarah Oakley
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Marta S. Oliveira
- NHS Blood and Transplant, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Timothy Peto
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre (BRC), John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Rutger J. Ploeg
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Jeremy Ratcliff
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Melanie J. Robbins
- Component Development Laboratory, NHS Blood and Transplant, Cambridge Donor Centre, Cambridge, CB2 0PT, UK
| | - David J. Roberts
- NHS Blood and Transplant, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Justine Rudkin
- Big Data Institute, Roosevelt Drive, Old Road Campus, Headington, Oxford, OX3 7LF, UK
- Nuffield Department of Population Health, University Oxford Richard Doll Building, Old Road Campus, Headington, Oxford, OX3 7LF, UK
| | - Rebecca A. Russell
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Gavin Screaton
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Malcolm G. Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 3BX, UK
| | - Donal Skelly
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Peter Simmonds
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Nicole Stoesser
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 3BX, UK
| | - Susan Wareing
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Maria Zambon
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
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11
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Lumley SF, Eyre DW, McNaughton AL, Howarth A, Hoosdally S, Hatch SB, Kavanagh J, Chau KK, Downs LO, Cox S, Dunn L, Justice A, Wareing S, Dingle K, Rudkin J, Auckland K, Fyfe A, Bolton J, Paton R, Mentzer AJ, Jeffery K, Andersson MI, James T, Peto TEA, Marsden BD, Screaton G, Cornall RJ, Klenerman P, Ebner D, Stuart DI, Crook DW, Stoesser N, Kennedy SH, Thompson C, Gupta S, Matthews PC. SARS-CoV-2 antibody prevalence, titres and neutralising activity in an antenatal cohort, United Kingdom, 14 April to 15 June 2020. Euro Surveill 2020; 25:2001721. [PMID: 33094717 PMCID: PMC7651878 DOI: 10.2807/1560-7917.es.2020.25.41.2001721] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 10/22/2020] [Indexed: 12/29/2022] Open
Abstract
SARS-CoV-2 IgG screening of 1,000 antenatal serum samples in the Oxford area, United Kingdom, between 14 April and 15 June 2020, yielded a 5.3% seroprevalence, mirroring contemporaneous regional data. Among the 53 positive samples, 39 showed in vitro neutralisation activity, correlating with IgG titre (Pearson's correlation p<0.0001). While SARS-CoV-2 seroprevalence in pregnancy cohorts could potentially inform population surveillance, clinical correlates of infection and immunity in pregnancy, and antenatal epidemiology evolution over time need further study.
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Affiliation(s)
- Sheila F Lumley
- Nuffield Department of Medicine, University of Oxford, Medawar Building, South Parks Road, Oxford, United Kingdom
- Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
- These authors contributed equally to this work
| | - David W Eyre
- Nuffield Department of Medicine, University of Oxford, Medawar Building, South Parks Road, Oxford, United Kingdom
- Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
- These authors contributed equally to this work
- Nuffield Department of Population Health, University of Oxford, Big Data Institute, Old Road Campus, Oxford, United Kingdom
| | - Anna L McNaughton
- Nuffield Department of Medicine, University of Oxford, Medawar Building, South Parks Road, Oxford, United Kingdom
- These authors contributed equally to this work
| | - Alison Howarth
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Sarah Hoosdally
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Stephanie B Hatch
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Big Data Institute, Old Road Campus, Oxford, United Kingdom
| | - James Kavanagh
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Kevin K Chau
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Louise O Downs
- Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Stuart Cox
- Department of Clinical Biochemistry, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Laura Dunn
- Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Anita Justice
- Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Susan Wareing
- Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Kate Dingle
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Justine Rudkin
- Nuffield Department of Population Health, University of Oxford, Big Data Institute, Old Road Campus, Oxford, United Kingdom
| | - Kathryn Auckland
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Alexander Fyfe
- Department of Zoology, University of Oxford, Medawar Building, South Parks Road, Oxford, United Kingdom
| | - Jai Bolton
- Department of Zoology, University of Oxford, Medawar Building, South Parks Road, Oxford, United Kingdom
| | - Robert Paton
- Department of Zoology, University of Oxford, Medawar Building, South Parks Road, Oxford, United Kingdom
| | - Alexander J Mentzer
- Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Katie Jeffery
- Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Monique I Andersson
- Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Tim James
- Department of Clinical Biochemistry, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Tim E A Peto
- Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Brian D Marsden
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, United Kingdom
- The Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Henry Wellcome Building, Roosevelt Dr, Headington, Oxford, United Kingdom
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, Oxford, United Kingdom
| | - Gavin Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, Roosevelt Drive, Headington, Oxford, United Kingdom
| | - Richard J Cornall
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, Roosevelt Drive, Headington, Oxford, United Kingdom
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, Medawar Building, South Parks Road, Oxford, United Kingdom
- Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Daniel Ebner
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Big Data Institute, Old Road Campus, Oxford, United Kingdom
| | - David I Stuart
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, United Kingdom
- The Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Henry Wellcome Building, Roosevelt Dr, Headington, Oxford, United Kingdom
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Big Data Institute, Old Road Campus, Oxford, United Kingdom
| | - Derrick W Crook
- Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Nicole Stoesser
- Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Stephen H Kennedy
- Nuffield Department of Women's & Reproductive Health, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Craig Thompson
- Department of Zoology, University of Oxford, Medawar Building, South Parks Road, Oxford, United Kingdom
| | - Sunetra Gupta
- Department of Zoology, University of Oxford, Medawar Building, South Parks Road, Oxford, United Kingdom
| | - Philippa C Matthews
- Nuffield Department of Medicine, University of Oxford, Medawar Building, South Parks Road, Oxford, United Kingdom
- Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
- These authors contributed equally to this work
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
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12
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Rodriguez OL, Gibson WS, Parks T, Emery M, Powell J, Strahl M, Deikus G, Auckland K, Eichler EE, Marasco WA, Sebra R, Sharp AJ, Smith ML, Bashir A, Watson CT. A Novel Framework for Characterizing Genomic Haplotype Diversity in the Human Immunoglobulin Heavy Chain Locus. Front Immunol 2020; 11:2136. [PMID: 33072076 PMCID: PMC7539625 DOI: 10.3389/fimmu.2020.02136] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/06/2020] [Indexed: 02/06/2023] Open
Abstract
An incomplete ascertainment of genetic variation within the highly polymorphic immunoglobulin heavy chain locus (IGH) has hindered our ability to define genetic factors that influence antibody-mediated processes. Due to locus complexity, standard high-throughput approaches have failed to accurately and comprehensively capture IGH polymorphism. As a result, the locus has only been fully characterized two times, severely limiting our knowledge of human IGH diversity. Here, we combine targeted long-read sequencing with a novel bioinformatics tool, IGenotyper, to fully characterize IGH variation in a haplotype-specific manner. We apply this approach to eight human samples, including a haploid cell line and two mother-father-child trios, and demonstrate the ability to generate high-quality assemblies (>98% complete and >99% accurate), genotypes, and gene annotations, identifying 2 novel structural variants and 15 novel IGH alleles. We show multiplexing allows for scaling of the approach without impacting data quality, and that our genotype call sets are more accurate than short-read (>35% increase in true positives and >97% decrease in false-positives) and array/imputation-based datasets. This framework establishes a desperately needed foundation for leveraging IG genomic data to study population-level variation in antibody-mediated immunity, critical for bettering our understanding of disease risk, and responses to vaccines and therapeutics.
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Affiliation(s)
- Oscar L Rodriguez
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - William S Gibson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
| | - Tom Parks
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Matthew Emery
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - James Powell
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Maya Strahl
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Gintaras Deikus
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Kathryn Auckland
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States.,Howard Hughes Medical Institute, University of Washington, Seattle, WA, United States
| | - Wayne A Marasco
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Icahn Institute of Data Science and Genomic Technology, New York, NY, United States
| | - Andrew J Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Melissa L Smith
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States.,Icahn Institute of Data Science and Genomic Technology, New York, NY, United States
| | - Ali Bashir
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
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13
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Andersson MI, Arancibia-Carcamo CV, Auckland K, Baillie JK, Barnes E, Beneke T, Bibi S, Brooks T, Carroll M, Crook D, Dingle K, Dold C, Downs LO, Dunn L, Eyre DW, Gilbert Jaramillo J, Harvala H, Hoosdally S, Ijaz S, James T, James W, Jeffery K, Justice A, Klenerman P, Knight JC, Knight M, Liu X, Lumley SF, Matthews PC, McNaughton AL, Mentzer AJ, Mongkolsapaya J, Oakley S, Oliveira MS, Peto T, Ploeg RJ, Ratcliff J, Robbins MJ, Roberts DJ, Rudkin J, Russell RA, Screaton G, Semple MG, Skelly D, Simmonds P, Stoesser N, Turtle L, Wareing S, Zambon M. SARS-CoV-2 RNA detected in blood products from patients with COVID-19 is not associated with infectious virus. Wellcome Open Res 2020; 5:181. [PMID: 33283055 PMCID: PMC7689603 DOI: 10.12688/wellcomeopenres.16002.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2020] [Indexed: 11/13/2023] Open
Abstract
Background: Laboratory diagnosis of SARS-CoV-2 infection (the cause of COVID-19) uses PCR to detect viral RNA (vRNA) in respiratory samples. SARS-CoV-2 RNA has also been detected in other sample types, but there is limited understanding of the clinical or laboratory significance of its detection in blood. Methods: We undertook a systematic literature review to assimilate the evidence for the frequency of vRNA in blood, and to identify associated clinical characteristics. We performed RT-PCR in serum samples from a UK clinical cohort of acute and convalescent COVID-19 cases (n=212), together with convalescent plasma samples collected by NHS Blood and Transplant (NHSBT) (n=462 additional samples). To determine whether PCR-positive blood samples could pose an infection risk, we attempted virus isolation from a subset of RNA-positive samples. Results: We identified 28 relevant studies, reporting SARS-CoV-2 RNA in 0-76% of blood samples; pooled estimate 10% (95%CI 5-18%). Among serum samples from our clinical cohort, 27/212 (12.7%) had SARS-CoV-2 RNA detected by RT-PCR. RNA detection occurred in samples up to day 20 post symptom onset, and was associated with more severe disease (multivariable odds ratio 7.5). Across all samples collected ≥28 days post symptom onset, 0/494 (0%, 95%CI 0-0.7%) had vRNA detected. Among our PCR-positive samples, cycle threshold (ct) values were high (range 33.5-44.8), suggesting low vRNA copy numbers. PCR-positive sera inoculated into cell culture did not produce any cytopathic effect or yield an increase in detectable SARS-CoV-2 RNA. Conclusions: vRNA was detectable at low viral loads in a minority of serum samples collected in acute infection, but was not associated with infectious SARS-CoV-2 (within the limitations of the assays used). This work helps to inform biosafety precautions for handling blood products from patients with current or previous COVID-19.
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Affiliation(s)
- Monique I. Andersson
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Carolina V. Arancibia-Carcamo
- Translational Gastroenterology Unit, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre (BRC), John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Kathryn Auckland
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - J. Kenneth Baillie
- Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Eleanor Barnes
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre (BRC), John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Tom Beneke
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Sagida Bibi
- Department of Paediatrics, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Tim Brooks
- Porton Down, Public Health England, Manor Farm Road, Porton Down, Salisbury, SP4 0JG, UK
| | - Miles Carroll
- Porton Down, Public Health England, Manor Farm Road, Porton Down, Salisbury, SP4 0JG, UK
| | - Derrick Crook
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre (BRC), John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Kate Dingle
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Christina Dold
- Department of Paediatrics, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Louise O. Downs
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Laura Dunn
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - David W. Eyre
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre (BRC), John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Big Data Institute, Roosevelt Drive, Old Road Campus, Headington, Oxford, OX3 7LF, UK
| | - Javier Gilbert Jaramillo
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Heli Harvala
- NHS Blood and Transfusion, 26 Margaret St, Marylebone, London, W1W 8NB, UK
- University College London, Gower St, Bloomsbury, London, WC1E 6BT, UK
| | - Sarah Hoosdally
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Samreen Ijaz
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - Tim James
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - William James
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Katie Jeffery
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Anita Justice
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Julian C. Knight
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Michael Knight
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Xu Liu
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Sheila F. Lumley
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Philippa C. Matthews
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre (BRC), John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Anna L. McNaughton
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Alexander J. Mentzer
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | | | - Sarah Oakley
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Marta S. Oliveira
- NHS Blood and Transplant, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Timothy Peto
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre (BRC), John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Rutger J. Ploeg
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Jeremy Ratcliff
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Melanie J. Robbins
- Component Development Laboratory, NHS Blood and Transplant, Cambridge Donor Centre, Cambridge, CB2 0PT, UK
| | - David J. Roberts
- NHS Blood and Transplant, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Justine Rudkin
- Big Data Institute, Roosevelt Drive, Old Road Campus, Headington, Oxford, OX3 7LF, UK
- Nuffield Department of Population Health, University Oxford Richard Doll Building, Old Road Campus, Headington, Oxford, OX3 7LF, UK
| | - Rebecca A. Russell
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Gavin Screaton
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Malcolm G. Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 3BX, UK
| | - Donal Skelly
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Peter Simmonds
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Nicole Stoesser
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 3BX, UK
| | - Susan Wareing
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Maria Zambon
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
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14
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Adams ER, Ainsworth M, Anand R, Andersson MI, Auckland K, Baillie JK, Barnes E, Beer S, Bell JI, Berry T, Bibi S, Carroll M, Chinnakannan SK, Clutterbuck E, Cornall RJ, Crook DW, de Silva T, Dejnirattisai W, Dingle KE, Dold C, Espinosa A, Eyre DW, Farmer H, Fernandez Mendoza M, Georgiou D, Hoosdally SJ, Hunter A, Jefferey K, Kelly DF, Klenerman P, Knight J, Knowles C, Kwok AJ, Leuschner U, Levin R, Liu C, López-Camacho C, Martinez J, Matthews PC, McGivern H, Mentzer AJ, Milton J, Mongkolsapaya J, Moore SC, Oliveira MS, Pereira F, Perez E, Peto T, Ploeg RJ, Pollard A, Prince T, Roberts DJ, Rudkin JK, Sanchez V, Screaton GR, Semple MG, Slon-Campos J, Skelly DT, Smith EN, Sobrinodiaz A, Staves J, Stuart DI, Supasa P, Surik T, Thraves H, Tsang P, Turtle L, Walker AS, Wang B, Washington C, Watkins N, Whitehouse J. Antibody testing for COVID-19: A report from the National COVID Scientific Advisory Panel. Wellcome Open Res 2020; 5:139. [PMID: 33748431 PMCID: PMC7941096 DOI: 10.12688/wellcomeopenres.15927.1] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2020] [Indexed: 01/26/2023] Open
Abstract
Background: The COVID-19 pandemic caused >1 million infections during January-March 2020. There is an urgent need for reliable antibody detection approaches to support diagnosis, vaccine development, safe release of individuals from quarantine, and population lock-down exit strategies. We set out to evaluate the performance of ELISA and lateral flow immunoassay (LFIA) devices. Methods: We tested plasma for COVID (severe acute respiratory syndrome coronavirus 2; SARS-CoV-2) IgM and IgG antibodies by ELISA and using nine different LFIA devices. We used a panel of plasma samples from individuals who have had confirmed COVID infection based on a PCR result (n=40), and pre-pandemic negative control samples banked in the UK prior to December-2019 (n=142). Results: ELISA detected IgM or IgG in 34/40 individuals with a confirmed history of COVID infection (sensitivity 85%, 95%CI 70-94%), vs. 0/50 pre-pandemic controls (specificity 100% [95%CI 93-100%]). IgG levels were detected in 31/31 COVID-positive individuals tested ≥10 days after symptom onset (sensitivity 100%, 95%CI 89-100%). IgG titres rose during the 3 weeks post symptom onset and began to fall by 8 weeks, but remained above the detection threshold. Point estimates for the sensitivity of LFIA devices ranged from 55-70% versus RT-PCR and 65-85% versus ELISA, with specificity 95-100% and 93-100% respectively. Within the limits of the study size, the performance of most LFIA devices was similar. Conclusions: Currently available commercial LFIA devices do not perform sufficiently well for individual patient applications. However, ELISA can be calibrated to be specific for detecting and quantifying SARS-CoV-2 IgM and IgG and is highly sensitive for IgG from 10 days following first symptoms.
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Affiliation(s)
- Emily R. Adams
- Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Mark Ainsworth
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Rekha Anand
- NHS Blood and Transplant Birmingham, Vincent Drive, Birmingham, B15 2SG, UK
| | | | - Kathryn Auckland
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | | | - Eleanor Barnes
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Sally Beer
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - John I. Bell
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Tamsin Berry
- Department of Health and Social Care, UK Government, London, UK
| | - Sagida Bibi
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, OX3 7LE, UK
| | - Miles Carroll
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
- Public Health England, Porton Down, Salisbury, SP4 0JG, UK
| | - Senthil K. Chinnakannan
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Elizabeth Clutterbuck
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, OX3 7LE, UK
| | - Richard J. Cornall
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Derrick W. Crook
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Thushan de Silva
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, S10 2RX, UK
| | - Wanwisa Dejnirattisai
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Kate E. Dingle
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Christina Dold
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, OX3 7LE, UK
| | - Alexis Espinosa
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - David W. Eyre
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Helen Farmer
- Department of Health and Social Care, UK Government, London, UK
| | | | | | - Sarah J. Hoosdally
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Alastair Hunter
- NHS Blood and Transplant Basildon, Burnt Mills Industrial Estate, Basildon, SS13 1FH, UK
| | - Katie Jefferey
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Dominic F. Kelly
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, OX3 7LE, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Julian Knight
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Clarice Knowles
- Department of Health and Social Care, UK Government, London, UK
| | - Andrew J. Kwok
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Ullrich Leuschner
- NHS Blood and Transplant Oxford, John Radcliffe Hospital, Oxford, UK
| | | | - Chang Liu
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - César López-Camacho
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Jose Martinez
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Philippa C. Matthews
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Hannah McGivern
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Alexander J. Mentzer
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Jonathan Milton
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Juthathip Mongkolsapaya
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Shona C. Moore
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Marta S. Oliveira
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 9DU, UK
| | | | - Elena Perez
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Timothy Peto
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Rutger J. Ploeg
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Andrew Pollard
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, OX3 7LE, UK
| | - Tessa Prince
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - David J. Roberts
- NHS Blood and Transplant Oxford, John Radcliffe Hospital, Oxford, UK
| | - Justine K. Rudkin
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Veronica Sanchez
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Gavin R. Screaton
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Malcolm G. Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Alder Hey Children's Hospital, Liverpool, UK
| | - Jose Slon-Campos
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Donal T. Skelly
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | | | | | - Julie Staves
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - David I. Stuart
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 ODE, UK
| | - Piyada Supasa
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Tomas Surik
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Hannah Thraves
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Pat Tsang
- NHS Blood and Transplant Oxford, John Radcliffe Hospital, Oxford, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Tropical & Infectious Disease Unit, Royal Liverpool University Hospital (member of Liverpool Health Partners), Liverpool, L7 8XP, UK
| | - A. Sarah Walker
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Beibei Wang
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | | | - Nicholas Watkins
- NHS Blood and Transplant Cambridge, Long Road, Cambridge, CB2 0PT, UK
| | | | - National COVID Testing Scientific Advisory Panel
- Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- NHS Blood and Transplant Birmingham, Vincent Drive, Birmingham, B15 2SG, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
- Roslin Institute, University of Edinburgh, Edinburgh, EH25 9RJ, UK
- Department of Health and Social Care, UK Government, London, UK
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, OX3 7LE, UK
- Public Health England, Porton Down, Salisbury, SP4 0JG, UK
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, S10 2RX, UK
- NHS Blood and Transplant Basildon, Burnt Mills Industrial Estate, Basildon, SS13 1FH, UK
- NHS Blood and Transplant Oxford, John Radcliffe Hospital, Oxford, UK
- Worthing Hospital, Worthing, BN11 2DH, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 9DU, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Imperial College London, London, SW7 2AZ, UK
- Alder Hey Children's Hospital, Liverpool, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 ODE, UK
- Tropical & Infectious Disease Unit, Royal Liverpool University Hospital (member of Liverpool Health Partners), Liverpool, L7 8XP, UK
- NHS Blood and Transplant Cambridge, Long Road, Cambridge, CB2 0PT, UK
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15
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Auckland K, Mittal B, Cairns BJ, Garg N, Kumar S, Mentzer AJ, Kado J, Perman ML, Steer AC, Hill AVS, Parks T. The Human Leukocyte Antigen Locus and Rheumatic Heart Disease Susceptibility in South Asians and Europeans. Sci Rep 2020; 10:9004. [PMID: 32488134 PMCID: PMC7265443 DOI: 10.1038/s41598-020-65855-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 05/07/2020] [Indexed: 12/28/2022] Open
Abstract
Rheumatic heart disease (RHD), an autoinflammatory heart disease, was recently declared a global health priority by the World Health Organization. Here we report a genome-wide association study (GWAS) of RHD susceptibility in 1,163 South Asians (672 cases; 491 controls) recruited in India and Fiji. We analysed directly obtained and imputed genotypes, and followed-up associated loci in 1,459 Europeans (150 cases; 1,309 controls) from the UK Biobank study. We identify a novel susceptibility signal in the class III region of the human leukocyte antigen (HLA) complex in the South Asian dataset that clearly replicates in the Europeans (rs201026476; combined odds ratio 1.81, 95% confidence intervals 1.51-2.18, P = 3.48×10-10). Importantly, this signal remains despite conditioning on the lead class I and class II variants (P = 0.00033). These findings suggest the class III region is a key determinant of RHD susceptibility offering important new insight into pathogenesis while partly explaining the inconsistency of earlier reports.
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Affiliation(s)
- Kathryn Auckland
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, OX3 7BN, UK
| | - Balraj Mittal
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, 226025, Uttar Pradesh, India
| | - Benjamin J Cairns
- MRC Population Health Research Unit, Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, Oxfordshire, OX3 7LF, UK
| | - Naveen Garg
- Department of Cardiology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, 226014, Uttar Pradesh, India
| | - Surendra Kumar
- Department of Cytogenetics/Anatomy, All India Institute of Medical Sciences, New Delhi, 110029, Delhi, India
| | - Alexander J Mentzer
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, OX3 7BN, UK
| | - Joseph Kado
- Department of Medical Science, Fiji National University, Suva, PO Box 7222, Viti Levu, Fiji
| | - Mai Ling Perman
- Department of Medical Science, Fiji National University, Suva, PO Box 7222, Viti Levu, Fiji
| | - Andrew C Steer
- Tropical Infectious Diseases, Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia
| | - Adrian V S Hill
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, OX3 7BN, UK
| | - Tom Parks
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, OX3 7BN, UK.
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, Greater London, WC1E 7HT, UK.
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16
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Adams ER, Ainsworth M, Anand R, Andersson MI, Auckland K, Baillie JK, Barnes E, Beer S, Bell JI, Berry T, Bibi S, Carroll M, Chinnakannan SK, Clutterbuck E, Cornall RJ, Crook DW, de Silva T, Dejnirattisai W, Dingle KE, Dold C, Espinosa A, Eyre DW, Farmer H, Fernandez Mendoza M, Georgiou D, Hoosdally SJ, Hunter A, Jefferey K, Kelly DF, Klenerman P, Knight J, Knowles C, Kwok AJ, Leuschner U, Levin R, Liu C, López-Camacho C, Martinez J, Matthews PC, McGivern H, Mentzer AJ, Milton J, Mongkolsapaya J, Moore SC, Oliveira MS, Pereira F, Perez E, Peto T, Ploeg RJ, Pollard A, Prince T, Roberts DJ, Rudkin JK, Sanchez V, Screaton GR, Semple MG, Slon-Campos J, Skelly DT, Smith EN, Sobrinodiaz A, Staves J, Stuart DI, Supasa P, Surik T, Thraves H, Tsang P, Turtle L, Walker AS, Wang B, Washington C, Watkins N, Whitehouse J. Antibody testing for COVID-19: A report from the National COVID Scientific Advisory Panel. Wellcome Open Res 2020. [PMID: 33748431 DOI: 10.12688/wellcomeopenres10.12688/wellcomeopenres.15927.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2023] Open
Abstract
Background: The COVID-19 pandemic caused >1 million infections during January-March 2020. There is an urgent need for reliable antibody detection approaches to support diagnosis, vaccine development, safe release of individuals from quarantine, and population lock-down exit strategies. We set out to evaluate the performance of ELISA and lateral flow immunoassay (LFIA) devices. Methods: We tested plasma for COVID (severe acute respiratory syndrome coronavirus 2; SARS-CoV-2) IgM and IgG antibodies by ELISA and using nine different LFIA devices. We used a panel of plasma samples from individuals who have had confirmed COVID infection based on a PCR result (n=40), and pre-pandemic negative control samples banked in the UK prior to December-2019 (n=142). Results: ELISA detected IgM or IgG in 34/40 individuals with a confirmed history of COVID infection (sensitivity 85%, 95%CI 70-94%), vs. 0/50 pre-pandemic controls (specificity 100% [95%CI 93-100%]). IgG levels were detected in 31/31 COVID-positive individuals tested ≥10 days after symptom onset (sensitivity 100%, 95%CI 89-100%). IgG titres rose during the 3 weeks post symptom onset and began to fall by 8 weeks, but remained above the detection threshold. Point estimates for the sensitivity of LFIA devices ranged from 55-70% versus RT-PCR and 65-85% versus ELISA, with specificity 95-100% and 93-100% respectively. Within the limits of the study size, the performance of most LFIA devices was similar. Conclusions: Currently available commercial LFIA devices do not perform sufficiently well for individual patient applications. However, ELISA can be calibrated to be specific for detecting and quantifying SARS-CoV-2 IgM and IgG and is highly sensitive for IgG from 10 days following first symptoms.
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Affiliation(s)
- Emily R Adams
- Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Mark Ainsworth
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Rekha Anand
- NHS Blood and Transplant Birmingham, Vincent Drive, Birmingham, B15 2SG, UK
| | | | - Kathryn Auckland
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | | | - Eleanor Barnes
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Sally Beer
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - John I Bell
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Tamsin Berry
- Department of Health and Social Care, UK Government, London, UK
| | - Sagida Bibi
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, OX3 7LE, UK
| | - Miles Carroll
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
- Public Health England, Porton Down, Salisbury, SP4 0JG, UK
| | - Senthil K Chinnakannan
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Elizabeth Clutterbuck
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, OX3 7LE, UK
| | - Richard J Cornall
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Derrick W Crook
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Thushan de Silva
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, S10 2RX, UK
| | - Wanwisa Dejnirattisai
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Kate E Dingle
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Christina Dold
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, OX3 7LE, UK
| | - Alexis Espinosa
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - David W Eyre
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Helen Farmer
- Department of Health and Social Care, UK Government, London, UK
| | | | | | - Sarah J Hoosdally
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Alastair Hunter
- NHS Blood and Transplant Basildon, Burnt Mills Industrial Estate, Basildon, SS13 1FH, UK
| | - Katie Jefferey
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Dominic F Kelly
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, OX3 7LE, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Julian Knight
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Clarice Knowles
- Department of Health and Social Care, UK Government, London, UK
| | - Andrew J Kwok
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Ullrich Leuschner
- NHS Blood and Transplant Oxford, John Radcliffe Hospital, Oxford, UK
| | | | - Chang Liu
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - César López-Camacho
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Jose Martinez
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Philippa C Matthews
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Hannah McGivern
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Alexander J Mentzer
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Jonathan Milton
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Juthathip Mongkolsapaya
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Shona C Moore
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Marta S Oliveira
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 9DU, UK
| | | | - Elena Perez
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Timothy Peto
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Rutger J Ploeg
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Andrew Pollard
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, OX3 7LE, UK
| | - Tessa Prince
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - David J Roberts
- NHS Blood and Transplant Oxford, John Radcliffe Hospital, Oxford, UK
| | - Justine K Rudkin
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Veronica Sanchez
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Gavin R Screaton
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Alder Hey Children's Hospital, Liverpool, UK
| | - Jose Slon-Campos
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Donal T Skelly
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | | | | | - Julie Staves
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - David I Stuart
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 ODE, UK
| | - Piyada Supasa
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Tomas Surik
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Hannah Thraves
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Pat Tsang
- NHS Blood and Transplant Oxford, John Radcliffe Hospital, Oxford, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Tropical & Infectious Disease Unit, Royal Liverpool University Hospital (member of Liverpool Health Partners), Liverpool, L7 8XP, UK
| | - A Sarah Walker
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Beibei Wang
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | | | - Nicholas Watkins
- NHS Blood and Transplant Cambridge, Long Road, Cambridge, CB2 0PT, UK
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17
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Chauhan A, Lalor T, Watson S, Adams D, Farrah TE, Anand A, Kimmitt R, Mills NL, Webb DJ, Dhaun N, Kalla R, Adams A, Vatn S, Bonfliglio F, Nimmo E, Kennedy N, Ventham N, Vatn M, Ricanek P, Halfvarson J, Soderhollm J, Pierik M, Torkvist L, Gomollon F, Gut I, Jahnsen J, Satsangi J, Body R, Almashali M, McDowell G, Taylor P, Lacey A, Rees A, Dayan C, Lazarus J, Nelson S, Okosieme O, Corcoran D, Young R, Ciadella P, McCartney P, Bajrangee A, Hennigan B, Collison D, Carrick D, Shaukat A, Good R, Watkins S, McEntegart M, Watt J, Welsh P, Sattar N, McConnachie A, Oldroyd K, Berry C, Parks T, Auckland K, Mentzer AJ, Kado J, Mirabel MM, Kauwe JK, Robson KJ, Mittal B, Steer AC, Hill AVS, Akbar M, Forrester M, Virlan AT, Gilmour A, Wallace C, Paterson C, Reid D, Siebert S, Porter D, Liversidge J, McInnes I, Goodyear C, Athwal V, Pritchett J, Zaitoun A, Irving W, Guha IN, Hanley NA, Hanley KP, Briggs T, Reynolds J, Rice G, Bondet V, Bruce E, Crow Y, Duffy D, Parker B, Bruce I, Martin K, Pritchett J, Aoibheann Mullan M, Llewellyn J, Athwal V, Zeef L, Farrow S, Streuli C, Henderson N, Friedman S, Hanley N, Hanley KP. Scientific Business Abstracts of the 112th Annual Meeting of the Association of Physicians of Great Britain and Ireland. QJM 2018; 111:920-924. [PMID: 31222346 DOI: 10.1093/qjmed/hcy193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - T Lalor
- From the University of Birmingham
| | - S Watson
- From the University of Birmingham
| | - D Adams
- From the University of Birmingham
| | - T E Farrah
- From the University/British Heart Foundation Centre of Research Excellence, University of Edinburgh
| | - A Anand
- From the University/British Heart Foundation Centre of Research Excellence, University of Edinburgh
| | - R Kimmitt
- From the University/British Heart Foundation Centre of Research Excellence, University of Edinburgh
| | - N L Mills
- From the University/British Heart Foundation Centre of Research Excellence, University of Edinburgh
| | - D J Webb
- From the University/British Heart Foundation Centre of Research Excellence, University of Edinburgh
| | - N Dhaun
- From the University/British Heart Foundation Centre of Research Excellence, University of Edinburgh
| | - R Kalla
- From the University of Edinburgh
| | - A Adams
- From the University of Edinburgh
| | - S Vatn
- Akerhshus University Hospital
| | | | - E Nimmo
- From the University of Edinburgh
| | | | | | | | | | | | | | - M Pierik
- Maastricht University Medical Centre
| | | | | | | | | | | | - R Body
- From the University of Manchester
| | - M Almashali
- Manchester University Hospitals Foundation NHS Trust
| | | | | | | | - A Rees
- From the Cardiff University
| | | | | | | | | | - D Corcoran
- From the British Heart Foundation (BHF), Glasgow Cardiovascular Research Centre, University of Glasgow
| | - R Young
- Robertson Centre for Biostatistics, University of Glasgow
| | - P Ciadella
- West of Scotland Heart and Lung Centre, Golden Jubilee National Hospital
| | - P McCartney
- From the British Heart Foundation (BHF), Glasgow Cardiovascular Research Centre, University of Glasgow
| | - A Bajrangee
- West of Scotland Heart and Lung Centre, Golden Jubilee National Hospital
| | - B Hennigan
- West of Scotland Heart and Lung Centre, Golden Jubilee National Hospital
| | - D Collison
- West of Scotland Heart and Lung Centre, Golden Jubilee National Hospital
| | - D Carrick
- West of Scotland Heart and Lung Centre, Golden Jubilee National Hospital
| | - A Shaukat
- West of Scotland Heart and Lung Centre, Golden Jubilee National Hospital
| | - R Good
- West of Scotland Heart and Lung Centre, Golden Jubilee National Hospital
| | - S Watkins
- West of Scotland Heart and Lung Centre, Golden Jubilee National Hospital
| | - M McEntegart
- West of Scotland Heart and Lung Centre, Golden Jubilee National Hospital
| | - J Watt
- West of Scotland Heart and Lung Centre, Golden Jubilee National Hospital
| | - P Welsh
- From the British Heart Foundation (BHF), Glasgow Cardiovascular Research Centre, University of Glasgow
| | - N Sattar
- From the British Heart Foundation (BHF), Glasgow Cardiovascular Research Centre, University of Glasgow
| | - A McConnachie
- Robertson Centre for Biostatistics, University of Glasgow
| | - K Oldroyd
- West of Scotland Heart and Lung Centre, Golden Jubilee National Hospital
| | - C Berry
- From the British Heart Foundation (BHF), Glasgow Cardiovascular Research Centre, University of Glasgow
| | - T Parks
- From the London School of Hygiene and Tropical Medicine
- University of Oxford
| | | | | | - J Kado
- Fiji Islands Ministry of Health and Medical Services
| | - M M Mirabel
- French National Institute of Health and Medical Research
| | | | | | - B Mittal
- Babasaheb Bhimrao Ambedkar University
| | - A C Steer
- Murdoch Children's Research Institute
| | | | - M Akbar
- From the Institute of Infection, Immunity & Inflammation, University of Glasgow
| | - M Forrester
- Division of Applied Medicine, School of Medicine and Dentistry, University of Aberdeen
| | - A T Virlan
- From the Institute of Infection, Immunity & Inflammation, University of Glasgow
| | - A Gilmour
- From the Institute of Infection, Immunity & Inflammation, University of Glasgow
| | - C Wallace
- Division of Applied Medicine, School of Medicine and Dentistry, University of Aberdeen
| | - C Paterson
- From the Institute of Infection, Immunity & Inflammation, University of Glasgow
| | - D Reid
- Division of Applied Medicine, School of Medicine and Dentistry, University of Aberdeen
| | - S Siebert
- From the Institute of Infection, Immunity & Inflammation, University of Glasgow
| | - D Porter
- From the Institute of Infection, Immunity & Inflammation, University of Glasgow
| | - J Liversidge
- Division of Applied Medicine, School of Medicine and Dentistry, University of Aberdeen
| | - I McInnes
- From the Institute of Infection, Immunity & Inflammation, University of Glasgow
| | - C Goodyear
- From the Institute of Infection, Immunity & Inflammation, University of Glasgow
| | - V Athwal
- From the Manchester University Foundation NHS Trust
- University of Manchester
| | | | | | | | | | - N A Hanley
- From the Manchester University Foundation NHS Trust
- University of Manchester
| | | | - T Briggs
- From the Manchester Centre of Genomic Medicine, University of Manchester
| | - J Reynolds
- Division of Musculoskeletal & Dermatological Sciences, University of Manchester
| | - G Rice
- From the Manchester Centre of Genomic Medicine, University of Manchester
| | - V Bondet
- Immunobiology of Dendritic Cells, Institut Pasteur
| | - E Bruce
- Division of Musculoskeletal & Dermatological Sciences, University of Manchester
| | - Y Crow
- Laboratory of Neurogenetics and Neuroinflammation, INSERM UMR1163, Institut Imagine
| | - D Duffy
- Immunobiology of Dendritic Cells, Institut Pasteur
| | - B Parker
- Division of Musculoskeletal & Dermatological Sciences, University of Manchester
| | - I Bruce
- Division of Musculoskeletal & Dermatological Sciences, University of Manchester
| | - K Martin
- From the University of Manchester
| | | | | | | | - V Athwal
- From the University of Manchester
| | - L Zeef
- From the University of Manchester
| | - S Farrow
- From the University of Manchester
- Respiratory Therapy Area, GlaxoSmithKline
| | | | | | | | - N Hanley
- From the University of Manchester
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18
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Posth C, Nägele K, Colleran H, Valentin F, Bedford S, Kami KW, Shing R, Buckley H, Kinaston R, Walworth M, Clark GR, Reepmeyer C, Flexner J, Maric T, Moser J, Gresky J, Kiko L, Robson KJ, Auckland K, Oppenheimer SJ, Hill AVS, Mentzer AJ, Zech J, Petchey F, Roberts P, Jeong C, Gray RD, Krause J, Powell A. Language continuity despite population replacement in Remote Oceania. Nat Ecol Evol 2018; 2:731-740. [PMID: 29487365 PMCID: PMC5868730 DOI: 10.1038/s41559-018-0498-2] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 02/12/2018] [Indexed: 01/01/2023]
Abstract
Recent genomic analyses show that the earliest peoples reaching Remote Oceania-associated with Austronesian-speaking Lapita culture-were almost completely East Asian, without detectable Papuan ancestry. However, Papuan-related genetic ancestry is found across present-day Pacific populations, indicating that peoples from Near Oceania have played a significant, but largely unknown, ancestral role. Here, new genome-wide data from 19 ancient South Pacific individuals provide direct evidence of a so-far undescribed Papuan expansion into Remote Oceania starting ~2,500 yr BP, far earlier than previously estimated and supporting a model from historical linguistics. New genome-wide data from 27 contemporary ni-Vanuatu demonstrate a subsequent and almost complete replacement of Lapita-Austronesian by Near Oceanian ancestry. Despite this massive demographic change, incoming Papuan languages did not replace Austronesian languages. Population replacement with language continuity is extremely rare-if not unprecedented-in human history. Our analyses show that rather than one large-scale event, the process was incremental and complex, with repeated migrations and sex-biased admixture with peoples from the Bismarck Archipelago.
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Affiliation(s)
- Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Kathrin Nägele
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Heidi Colleran
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Frédérique Valentin
- Maison de l'Archéologie et de l'Ethnologie, CNRS, UMR 7041, Nanterre, France
| | - Stuart Bedford
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany
- School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Kaitip W Kami
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany
- Vanuatu Cultural Centre, Port-Vila, Vanuatu
| | | | - Hallie Buckley
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Rebecca Kinaston
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Mary Walworth
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Geoffrey R Clark
- Archaeology and Natural History, College of Asia and the Pacific, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Christian Reepmeyer
- College of Arts, Society and Education, James Cook University, Cairns, Queensland, Australia
| | - James Flexner
- Department of Archaeology, University of Sydney, Sydney, New South Wales, Australia
| | - Tamara Maric
- Service de la Culture et du Patrimoine, Punaauia, Tahiti, French Polynesia
| | - Johannes Moser
- Commission for Archaeology of Non-European Cultures, German Archaeological Institute, Bonn, Germany
| | - Julia Gresky
- Department of Natural Sciences, German Archaeological Institute, Berlin, Germany
| | - Lawrence Kiko
- Solomon Islands National Museum, Honiara, Solomon Islands
| | - Kathryn J Robson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Kathryn Auckland
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Adrian V S Hill
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Jana Zech
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Fiona Petchey
- Waikato Radiocarbon Dating Laboratory, The University of Waikato , Hamilton, New Zealand
| | - Patrick Roberts
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Choongwon Jeong
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Russell D Gray
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Adam Powell
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany.
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19
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Lipson M, Skoglund P, Spriggs M, Valentin F, Bedford S, Shing R, Buckley H, Phillip I, Ward GK, Mallick S, Rohland N, Broomandkhoshbacht N, Cheronet O, Ferry M, Harper TK, Michel M, Oppenheimer J, Sirak K, Stewardson K, Auckland K, Hill AVS, Maitland K, Oppenheimer SJ, Parks T, Robson K, Williams TN, Kennett DJ, Mentzer AJ, Pinhasi R, Reich D. Population Turnover in Remote Oceania Shortly after Initial Settlement. Curr Biol 2018; 28:1157-1165.e7. [PMID: 29501328 DOI: 10.1016/j.cub.2018.02.051] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 02/19/2018] [Accepted: 02/19/2018] [Indexed: 01/08/2023]
Abstract
Ancient DNA from Vanuatu and Tonga dating to about 2,900-2,600 years ago (before present, BP) has revealed that the "First Remote Oceanians" associated with the Lapita archaeological culture were directly descended from the population that, beginning around 5000 BP, spread Austronesian languages from Taiwan to the Philippines, western Melanesia, and eventually Remote Oceania. Thus, ancestors of the First Remote Oceanians must have passed by the Papuan-ancestry populations they encountered in New Guinea, the Bismarck Archipelago, and the Solomon Islands with minimal admixture [1]. However, all present-day populations in Near and Remote Oceania harbor >25% Papuan ancestry, implying that additional eastward migration must have occurred. We generated genome-wide data for 14 ancient individuals from Efate and Epi Islands in Vanuatu from 2900-150 BP, as well as 185 present-day individuals from 18 islands. We find that people of almost entirely Papuan ancestry arrived in Vanuatu by around 2300 BP, most likely reflecting migrations a few hundred years earlier at the end of the Lapita period, when there is also evidence of changes in skeletal morphology and cessation of long-distance trade between Near and Remote Oceania [2, 3]. Papuan ancestry was subsequently diluted through admixture but remains at least 80%-90% in most islands. Through a fine-grained analysis of ancestry profiles, we show that the Papuan ancestry in Vanuatu derives from the Bismarck Archipelago rather than the geographically closer Solomon Islands. However, the Papuan ancestry in Polynesia-the most remote Pacific islands-derives from different sources, documenting a third stream of migration from Near to Remote Oceania.
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Affiliation(s)
- Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
| | - Pontus Skoglund
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; The Francis Crick Institute, London NW1 1AT, UK
| | - Matthew Spriggs
- School of Archaeology and Anthropology, College of Arts and Social Sciences, The Australian National University, Canberra, ACT 2601, Australia; Vanuatu National Museum, Vanuatu Cultural Centre, P.O. Box 184, Port Vila, Vanuatu
| | - Frederique Valentin
- Maison de l'Archéologie et de l'Ethnologie, CNRS, UMR 7041, 92023 Nanterre, France
| | - Stuart Bedford
- Vanuatu National Museum, Vanuatu Cultural Centre, P.O. Box 184, Port Vila, Vanuatu; Department of Archaeology and Natural History, College of Asia-Pacific, The Australian National University, Canberra, ACT 2601, Australia
| | - Richard Shing
- Vanuatu National Museum, Vanuatu Cultural Centre, P.O. Box 184, Port Vila, Vanuatu
| | - Hallie Buckley
- Department of Anatomy, Otago Global Health Institute, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Iarawai Phillip
- Vanuatu National Museum, Vanuatu Cultural Centre, P.O. Box 184, Port Vila, Vanuatu
| | - Graeme K Ward
- Department of Archaeology and Natural History, College of Asia-Pacific, The Australian National University, Canberra, ACT 2601, Australia
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA; Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Olivia Cheronet
- Department of Anthropology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria; Earth Institute, University College Dublin, Dublin 4, Ireland
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Thomas K Harper
- Department of Anthropology and Institute for Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Kendra Sirak
- Earth Institute, University College Dublin, Dublin 4, Ireland; Department of Anthropology, Emory University, Atlanta, GA, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Kathryn Auckland
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Adrian V S Hill
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Kathryn Maitland
- Department of Paediatrics, Faculty of Medicine, Imperial College, St Mary's Hospital, Norfolk Place, Paddington, London W2 1PG, UK
| | - Stephen J Oppenheimer
- School of Anthropology and Museum Ethnography, University of Oxford, Oxford OX2 6PE, UK
| | - Tom Parks
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Kathryn Robson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Thomas N Williams
- Department of Paediatrics, Faculty of Medicine, Imperial College, St Mary's Hospital, Norfolk Place, Paddington, London W2 1PG, UK
| | - Douglas J Kennett
- Department of Anthropology and Institute for Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Ron Pinhasi
- Department of Anthropology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria; Earth Institute, University College Dublin, Dublin 4, Ireland
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA; Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, MA 02138, USA.
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20
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Bergström A, Oppenheimer SJ, Mentzer AJ, Auckland K, Robson K, Attenborough R, Alpers MP, Koki G, Pomat W, Siba P, Xue Y, Sandhu MS, Tyler-Smith C. A Neolithic expansion, but strong genetic structure, in the independent history of New Guinea. Science 2017; 357:1160-1163. [PMID: 28912245 PMCID: PMC5802383 DOI: 10.1126/science.aan3842] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 08/22/2017] [Indexed: 12/27/2022]
Abstract
New Guinea shows human occupation since ~50 thousand years ago (ka), independent adoption of plant cultivation ~10 ka, and great cultural and linguistic diversity today. We performed genome-wide single-nucleotide polymorphism genotyping on 381 individuals from 85 language groups in Papua New Guinea and find a sharp divide originating 10 to 20 ka between lowland and highland groups and a lack of non-New Guinean admixture in the latter. All highlanders share ancestry within the last 10 thousand years, with major population growth in the same period, suggesting population structure was reshaped following the Neolithic lifestyle transition. However, genetic differentiation between groups in Papua New Guinea is much stronger than in comparable regions in Eurasia, demonstrating that such a transition does not necessarily limit the genetic and linguistic diversity of human societies.
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Affiliation(s)
- Anders Bergström
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
| | - Stephen J Oppenheimer
- School of Anthropology and Museum Ethnography, University of Oxford, Oxford OX2 6PE, UK
| | - Alexander J Mentzer
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Kathryn Auckland
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Kathryn Robson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Robert Attenborough
- Biological Anthropology, Department of Archaeology and Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
- School of Archaeology and Anthropology, Australian National University, Canberra, ACT 2601, Australia
| | - Michael P Alpers
- International Health Research, Curtin University, Perth, WA 6845, Australia
- Papua New Guinea Institute of Medical Research, Post Office Box 60, Goroka, Papua New Guinea
| | - George Koki
- Papua New Guinea Institute of Medical Research, Post Office Box 60, Goroka, Papua New Guinea
| | - William Pomat
- Papua New Guinea Institute of Medical Research, Post Office Box 60, Goroka, Papua New Guinea
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, Post Office Box 60, Goroka, Papua New Guinea
| | - Yali Xue
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Manjinder S Sandhu
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
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21
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Parks T, Mirabel MM, Kado J, Auckland K, Nowak J, Rautanen A, Mentzer AJ, Marijon E, Jouven X, Perman ML, Cua T, Kauwe JK, Allen JB, Taylor H, Robson KJ, Deane CM, Steer AC, Hill AVS. Association between a common immunoglobulin heavy chain allele and rheumatic heart disease risk in Oceania. Nat Commun 2017; 8:14946. [PMID: 28492228 PMCID: PMC5437274 DOI: 10.1038/ncomms14946] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 02/15/2017] [Indexed: 12/19/2022] Open
Abstract
The indigenous populations of the South Pacific experience a high burden of rheumatic heart disease (RHD). Here we report a genome-wide association study (GWAS) of RHD susceptibility in 2,852 individuals recruited in eight Oceanian countries. Stratifying by ancestry, we analysed genotyped and imputed variants in Melanesians (607 cases and 1,229 controls) before follow-up of suggestive loci in three further ancestral groups: Polynesians, South Asians and Mixed or other populations (totalling 399 cases and 617 controls). We identify a novel susceptibility signal in the immunoglobulin heavy chain (IGH) locus centring on a haplotype of nonsynonymous variants in the IGHV4-61 gene segment corresponding to the IGHV4-61*02 allele. We show each copy of IGHV4-61*02 is associated with a 1.4-fold increase in the risk of RHD (odds ratio 1.43, 95% confidence intervals 1.27–1.61, P=4.1 × 10−9). These findings provide new insight into the role of germline variation in the IGH locus in disease susceptibility. Rheumatic heart disease (RHD) is a chronic auto-inflammatory reaction to group A streptococcal infection, and frequently occurs in individuals from the South Pacific. This study finds a novel association between an immunoglobulin heavy chain allele and risk of RHD in Pacific Islanders and South Asians.
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Affiliation(s)
- Tom Parks
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Mariana M Mirabel
- Paris Centre de Recherche Cardiovasculaire, Institut National de la Santé et de la Recherche Médicale, Hôpital Européen Georges Pompidou, 56, rue Leblanc, 75908 Paris, France
| | - Joseph Kado
- Department of Paediatrics, Ministry of Health and Medical Services, Colonial War Memorial Hospital, Brown Street, Suva, Fiji.,College of Medicine, Nursing &Health Sciences, Fiji National University, Brown Street, Suva, Fiji
| | - Kathryn Auckland
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Jaroslaw Nowak
- Department of Statistics, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford OX1 3S, UK
| | - Anna Rautanen
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Alexander J Mentzer
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Eloi Marijon
- Paris Centre de Recherche Cardiovasculaire, Institut National de la Santé et de la Recherche Médicale, Hôpital Européen Georges Pompidou, 56, rue Leblanc, 75908 Paris, France.,Faculté de Médecine Paris Descartes, Université Paris Descartes, 15, rue de l'école de medicine, 75006 Paris, France
| | - Xavier Jouven
- Paris Centre de Recherche Cardiovasculaire, Institut National de la Santé et de la Recherche Médicale, Hôpital Européen Georges Pompidou, 56, rue Leblanc, 75908 Paris, France.,Faculté de Médecine Paris Descartes, Université Paris Descartes, 15, rue de l'école de medicine, 75006 Paris, France
| | - Mai Ling Perman
- College of Medicine, Nursing &Health Sciences, Fiji National University, Brown Street, Suva, Fiji
| | - Tuliana Cua
- Rheumatic Heart Disease Control Programme, Ministry of Health and Medical Services, Colonial War Memorial Hospital, Brown Street, Suva, Fiji
| | - John K Kauwe
- College of Life Sciences, Brigham Young University, 4146 Life Sciences Building, Provo, Utah 84602, USA
| | - John B Allen
- College of Life Sciences, Brigham Young University, 4146 Life Sciences Building, Provo, Utah 84602, USA
| | - Henry Taylor
- Rheumatic Heart Disease Control Programme, Samoa Ministry of Health, Moto'otua, Ifiifi Street, Apia, Samoa
| | - Kathryn J Robson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Charlotte M Deane
- Department of Statistics, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford OX1 3S, UK
| | - Andrew C Steer
- Centre for International Child Health, University of Melbourne, 50 Flemington Road, Parkville, Melbourne Victoria 3052, Australia.,Murdoch Children's Research Institute, 50 Flemington Road, Parkville, Melbourne, Victoria 3052, Australia
| | - Adrian V S Hill
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
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Parks T, Mirabel M, Kado J, Auckland K, Rautanen A, Kauwe K, Ward B, Steer A, Hill A. OC02_07 Genome-Wide Association Study of Susceptibility to Rheumatic Heart Disease in Oceania: Preliminary Results. Glob Heart 2016. [DOI: 10.1016/j.gheart.2016.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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23
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Othen LS, Bellem AC, Gartley CJ, Auckland K, King WA, Liptrap RM, Goodrowe KL. Hormonal control of estrous cyclicity and attempted superovulation in wood bison (Bison bison athabascae). Theriogenology 1999; 52:313-23. [PMID: 10734397 DOI: 10.1016/s0093-691x(99)00131-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
The wood bison (Bison bison athabascae) is a threatened Canadian species that has faced extinction twice in the last 100 yr. Development of assisted reproductive technologies could help ensure the long-term propagation and genetic management of this species. The objectives of this study were to refine estrus synchronization techniques and evaluate superovulatory responses after FSH or eCG administration. In Experiment 1, females were fitted with Syncro-mate B (SMB) implants for 9 d and received an injection of either estradiol valerate (E2V; n = 9) or cloprostenol (PGF; n = 9) at implant insertion (Day-9). In Experiment 2, estrus was synchronized with SMB implants and a PGF injection of Day-9, and superovulation was attempted on Day-2 with either 2500 IU eCG (n = 5) or 400 mg Folltropin-V (n = 5). In each experiment, biosin were examined daily for estrual behavior. Ultrasonography was used during the luteal phase to detect ovulation and assess ovarian status; feces were analyzed by ELISA for immunoreactive progestogens (P) to study ovarian endocrine responses. In Experiment 1, a closer synchrony of estrus was observed between Days 2 to 4 among the PGF-treated (77.8%) than the E2V-treated (66.7%) females. Corpora lutea (CL) were detected in 55% of E2V- and PGF-treated females. In Experiment 2, neither treatment successfully induced superovulation, with only a single female per treatment producing > or = 1 CL. In both experiments, progestogen profiles were similar for each treatment (P < 0.05).
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Affiliation(s)
- L S Othen
- Toronto Zoo, Scarborough, Ontario, Canada
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Abstract
The medical history in a young man who developed varicose veins and venous insufficiency secondary to an acquired arteriovenous fistula in the thigh is presented. The radiological and clinical findings are discussed. The disease process in the development of varicose veins is not fully understood and cannot be satisfactorily explained as a consequence of arterial pressure within the venous system or a defect in the venous valves alone. The widespread ectatic changes seen within the venous system in our patient suggests the activation of an unknown, possibly humoral factor, resulting in morphological modifications in the vein wall.
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Affiliation(s)
- J V Psaila
- Department of Vascular Surgery & Radiology, University Hospital of South Manchester, United Kingdom
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