CERP - Center of Excellence in Respiratory Pathogens
Presentation
The Center of Excellence in Respiratory Pathogens (CERP) was created in January 2023 as a partnership between the Hospices Civils de Lyon, the Université Claude Bernard Lyon 1, under the CIRI, and Sanofi.
The CERP develops evidence generating research to support decision making related to respiratory pathogens. The CERP’s main objectives are: to create excellence in multi-disciplinary research combining virology, epidemiology, analytics, biocomputing and modeling; to ensure a continuum from data collection (surveillance & capacity building) to data use for policy making (analytic, modeling, and external engagement); to be a convener for major international stakeholders working on this thematic and to develop public-private instruments to ensure synergies.
Team members
NUNES MartaDirector, Chargée de mission marta.nunes@chu-lyon.fr
|
CHAUVEL CecileSenior Biostatistician/Data scientist cecile.chauvel@univ-lyon1.fr |
HASSENBOEHLER JulietteProject manager juliette.hassenboehler@chu-lyon.fr
|
ABOU-CHAKRA Claire NourSenior Epidemiologist claire.abou-chakra@chu-lyon.fr
|
VANHEMS PhilippeProfessor philippe.vanhems@chu-lyon.fr
|
DANANCHÉ CédricSenior Epidemiologist cedric.dananche@chu-lyon.fr
|
MYINT Aung PonePhD student @univ-lyon1.fr
|
PAUTONNIER JoannaMaster student @univ-lyon1.fr
|
Publications
(Publications by a team member in the last 2 years)
Abifadel M, Ahmmed K, Banu S, Camara I, Chowdhury F, Coulibaly D, Dabar G, Dananché C, Daw R, Hassan Z, Hervé M, Islam A, Komurian-Pradel F, Kouamé JP, Kouriba B, Najjar-Pellet J, Rakotonaivo A, Ranaivo-Rabetokotany F, Rasamoelina M, Rasolofoarison T, Riachi M, Saadatian-Elahi M, Samison L, Sanchez Picot V, Savané S, Thera I, Touré A, Vanhems P. Characteristics of Hospitalized COVID-19 Patients at Admission and Factors Associated with Clinical Severity in Low- and Middle-Income Countries: An Observational Study. Am J Trop Med Hyg. 2024:tpmd230456.
Tomasicchio M, Jaumdally S, Wilson L, Kotze A, Semple L, Meier S, Pooran A, Esmail A, Pillay K, Roberts R, Kriel R, Meldau R, Oelofse S, Mandviwala C, Burns J, Londt R, Davids M, van der Merwe C, Roomaney A, Kühn L, Perumal T, Scott AJ, Hale MJ, Baillie V, Mahtab S, Williamson C, Joseph R, Sigal A, Joubert I, Piercy J, Thomson D, Fredericks DL, Miller MG, Nunes MC, Madhi SA, Dheda K. SARS-CoV-2 Viral Replication Persists in the Human Lung for Several Weeks after Symptom Onset. Am J Respir Crit Care Med. 2024.
Moosa F, du Plessis M, Weigand MR, Peng Y, Mogale D, de Gouveia L, Nunes MC, Madhi SA, Zar HJ, Reubenson G, Ismail A, Tondella ML, Cohen C, Walaza S, von Gottberg A, Wolter N. Genomic characterization of Bordetella pertussis in South Africa, 2015-2019. Microb Genom. 2023;9(12):001162.
Nunes MC, Tamblyn A, Jose L, Ntsimane M, Lerotholi N, Machimana C, Taylor A, Laher F, Madhi SA. Immunogenicity of tetanus, diphtheria and acellular pertussis vaccination among pregnant women living with and without HIV. AIDS. 2023; 37(15):2305–10.
Olwagen CP, Downs SL, Izu A, Tharasimbi L, Van Der Merwe L, Nunes MC, Madhi SA. Bacterial nasopharyngeal colonisation in children in South Africa before and during the COVID-19 pandemic: an observational study. Lancet Microbe. 2023 Dec;S2666524723002604.
Olwagen CP, Jeche TR, Van Der Merwe L, Nunes MC, Madhi SA, Baillie VL. Nanofluidic qPCR unable to detect and serotype Streptococcus pneumoniae in urine samples of hospitalized South African patients with community-acquired pneumonia. Sci Rep. 2023;13(1):21332.
Andrew MK, Pott H, Staadegaard L, Paget J, Chaves SS, Ortiz JR, McCauley J, Bresee J, Nunes MC, et al. Age Differences in Comorbidities, Presenting Symptoms, and Outcomes of Influenza Illness Requiring Hospitalization: A Worldwide Perspective From the Global Influenza Hospital Surveillance Network. Open Forum Infect Dis. 2023;10(6):ofad244.
Wilson L, Chang JW, Meier S, Ganief T, Ganief N, Oelofse S, Baillie V, Nunes MC, Madhi SA, Blackburn J, Dheda K. Proteomic Profiling of Urine From Hospitalized Patients With Severe Pneumonia due to SARS-CoV-2 vs Other Causes: A Preliminary Report. Open Forum Infect Dis. 2023 Aug 31;10(10):ofad451.
Kaplonek P, Cizmeci D, Kwatra G, Izu A, Lee JS, Bertera HL, Fischinger S, Mann C, Amanat F, Wang W, Koen AL, Fairlie L, Cutland CL, Ahmed K, Dheda K, Barnabas SL, Bhorat QE, Briner C, Krammer F, Saphire EO, Gilbert SC, Lambe T, Pollard AJ, Nunes M, Wuhrer M, Lauffenburger DA, Madhi SA, Alter G. ChAdOx1 nCoV-19 (AZD1222) vaccine-induced Fc receptor binding tracks with differential susceptibility to COVID-19. Nat Immunol. 2023;24(7):1161-1172.
Dunne EM, Nunes MC, Slack MPE, Theilacker C, Gessner BD. Effects of pneumococcal conjugate vaccines on reducing the risk of respiratory disease associated with coronavirus infection. Pneumonia. 2023;15(1):10.
Saadatian-Elahi M, Henaff L, Elias C, Nunes MC, Hot A, Martin-Gaujard G, Escuret V, Amour S, Vanhems P. Patient influenza vaccination reduces the risk of hospital-acquired influenza: An incident test negative-case control study in Lyon university hospital, France (2004-2020). Vaccine. 2023;41(30):4341-4346.
Cohen LE, Hansen CL, Andrew MK, McNeil SA, Vanhems P, Kyncl J, Díez Domingo J, Zhang T, Dbaibo G, Laguna-Torres VA, Draganescu A, Baumeister E, Gomez D, Raboni SM, Giamberardino HIG, Nunes MC, et al. Predictors of severity of influenza-related hospitalizations: Results from the Global Influenza Hospital Surveillance Network (GIHSN). J Infect Dis. 2023.
Downs SL, Olwagen CP, Van der Merwe L, Nzenze S, Nunes MC, Madhi SA. Streptococcus pneumoniae and other bacterial nasopharyngeal colonisation eight years post-introduction of 13-valent pneumococcal conjugate vaccine in South African children. Int J Infect Dis. 2023;134:45-52.
Verwey C, Ramocha L, Laubscher M, Baillie V, Nunes M, Gray D, et al. Pulmonary sequelae in 2-year-old children after hospitalisation for respiratory syncytial virus lower respiratory tract infection during infancy: an observational study. BMJ Open Respir Res;10(1).
Izu A, Nunes MC, Solomon F, Baillie V, Serafin N, Verwey C, et al. All-cause and pathogen-specific lower respiratory tract infection hospital admissions in children younger than 5 years during the COVID-19 pandemic (2020–22) compared with the pre-pandemic period (2015–19) in South Africa: an observational study. Lancet Infect Dis. 2023;23(9):1031-1041.
Hooli S, King C, McCollum ED, Colbourn T, Lufesi N, Mwansambo C, Gregory CJ, Thamthitiwat S, Cutland C, Madhi SA, Nunes MC, Gessner BD, et al. In-Hospital Mortality Risk Stratification in Children Under 5 Years Old with Pneumonia with or without Pulse Oximetry: A Secondary Analysis of the Pneumonia REsearch Partnership to Assess WHO REcommendations (PREPARE) Dataset. Int J Infect Dis. 2023.
Downs SL, Madhi SA, Van der Merwe L, Nunes MC, Olwagen CP. Optimization of a high-throughput nanofluidic real-time PCR to detect and quantify of 15 bacterial species and 92 Streptococcus pneumoniae serotypes. Sci Rep. 2023;13(1):4588.
Wilkins D, Langedijk AC, Lebbink RJ, Morehouse C, Abram ME, Ahani B, Aksyuk AA, Baraldi E, Brady T, Chen AT, Chi H, Choi EH, Cohen R, Danilenko DM, Gopalakrishnan V, Greenough A, Heikkinen T, Hosoya M, Keller C, Kelly EJ, Kragten-Tabatabaie L, Martinón-Torres F, de Los Santos AHM, Nunes MC, et al. Nirsevimab binding-site conservation in respiratory syncytial virus fusion glycoprotein worldwide between 1956 and 2021: an analysis of observational study sequencing data. Lancet Infect Dis. 2023;17:S1473-3099(23)00062-2.
Smith ER, Oakley E, Grandner GW, Rukundo G, Farooq F, Ferguson K, Baumann S, Waldorf KA, Afshar Y, Ahlberg M, Ahmadzia H, Akelo V, Aldrovandi G, Bevilacqua E, Bracero N, Brandt JS, Broutet N, Carrillo J, Conry J, Cosmi E, Crispi F, Crovetto F, Gil MDM, Delgado-Lopez C, Divakar H, Driscoll AJ, Favre G, Buhigas IF, Flaherman V, Gale C, Godwin CL, Gottlieb S, Gratacos E, He S, Hernandez O, Jones S, Joshi S, Kalafat E, Khagayi S, Knight M, Kotloff K, Lanzone A, Longo VL, Le Doare K, Lees C, Litman E, Lokken EM, Madhi SA, Magee LA, Martinez-Portilla RJ, Metz TD, Miller ES, Money D, Moungmaithong S, Mullins E, Nachega JB, Nunes MC, et al. Adverse maternal, fetal, and newborn outcomes among pregnant women with SARS-CoV-2 infection: an individual participant data meta-analysis. BMJ Glob Health. 2023;8(1).
McMahon WC, Kwatra G, Izu A, Koen AL, Greffrath J, Fairlie L, Patel F, Mukendi CK, Mbele NJ, Lala R, Burgers W A., Nunes MC, et al. T-cell responses induced by ChAdOx1 nCoV-19 (AZD1222) vaccine to wild-type severe acute respiratory syndrome coronavirus 2 among people with and without HIV in South Africa. AIDS. 2023;37(1):105-12.
Dananché C, Elias C, Guibert N, Gardes S, Barreto C, Denis MA, Fascia P, Gerbier S, Grisi B, Khanafer N, Massardier-Pilonchéry A, Munier-Marion É, Pasquet C, Fassier JB, Vanhems P. COVID-19 clusters in a teaching hospital during the second wave of the SARS-CoV-2 pandemic in France: A descriptive study and lessons learned for waves to come. Am J Infect Control. 2022;50(9):1060-1063.
Dananché C, Paranhos-Baccalà G, Messaoudi M, Sylla M, Awasthi S, Bavdekar A, Pape JW, Rouzier V, Wang J, Sanghavi S, Diallo S, Chou M, Eap T, Rakoto-Andrianarivelo M, Endtz H, Ren L, Dash-Yandag B, Guillen R, Nymadawa P, Russomando G, Komurian-Pradel F, Vanhems P, Picot VS; Global Approach to Biological Research, Infectious Diseases and Epidemics in Low-Income Countries (GABRIEL) Network. Nasopharyngeal Viral and Bacterial Co-Detection among Children from Low- and Middle-Income Countries with and without Pneumonia. Am J Trop Med Hyg. 2022;106(4):1086-1093.
Dananché C, Elias C, Hénaff L, Amour S, Kuczewski E, Gustin MP, Escuret V, Saadatian-Elahi M, Vanhems P. Baseline clinical features of COVID-19 patients, delay of hospital admission and clinical outcome: A complex relationship. PLoS One. 2022 Jan 7;17(1):e0261428.
Vanhems P, Nunes MC. Further Cautions When Modeling the Public Health Impact of Infectious Diseases. Am J Public Health. 2022;112(11):e1-e2.
Schwalbe N, Hanbali L, Nunes MC, Lehtimaki S. Use of financial incentives to increase adult vaccination coverage: A narrative review of lessons learned from COVID-19 and other adult vaccination efforts. Vaccine X. 2022;12:100225.
Rees CA, Colbourn T, Hooli S, King C, Lufesi N, McCollum ED, Mwansambo C, Cutland C, Madhi SA, Nunes M, et al. Derivation and validation of a novel risk assessment tool to identify children aged 2-59 months at risk of hospitalised pneumonia-related mortality in 20 countries. BMJ Glob Health. 2022;7(4).
Ramocha LM, Dorfman JR, Groome M, Baillie V, Verwey C, Laubscher M, Nunes MC, et al. Human metapneumovirus-associated hospitalization in HIV-1 exposed uninfected and HIV-1 uninfected children less than 5 years in South Africa. J Pediatric Infect Dis Soc. 2022.
Nunes MC, Walaza S, Meiring S, Zar HJ, Reubenson G, McMorrow M, et al. Effectiveness of Influenza Vaccination of Pregnant Women for Prevention of Maternal and Early Infant Influenza-Associated Hospitalizations in South Africa: A Prospective Test-Negative Study. Open Forum Infect Dis. 2022;9(11):ofac552.
Nunes MC, Mbotwe-Sibanda S, Baillie VL, Kwatra G, Aguas R, Madhi SA, et al. SARS-CoV-2 Omicron Symptomatic Infections in Previously Infected or Vaccinated South African Healthcare Workers. Vaccines (Basel). 2022;10(3).
Nunes MC, Madhi SA. COVID-19 vaccines in pregnancy. Trends Mol Med. 2022;28(8):662-80.
Nunes MC, Jones S, Strehlau R, Baba V, Ditse Z, da Silva K, et al. Active Intrapartum SARS-CoV-2 Infection and Pregnancy Outcomes. Am J Perinatol. 2022;39(S 01):S42-S8.
Nunes MC, Jones S, Strehlau R, Baba V, Ditse Z, da Silva K, et al. Antepartum SARS-CoV-2 infection and adverse birth outcomes in South African women. J Glob Health. 2022;12:05050.
Nunes MC, Jones S, Ditse Z, da Silva K, Serafin N, Strehlau R, et al. Maternal-foetal transfer of severe acute respiratory syndrome coronavirus 2 antibodies among women with and those without HIV infection. AIDS. 2022;36(13):1777-82.
Nunes MC, Hale MJ, Mahtab S, Mabena FC, Dludlu N, Baillie VL, et al. Clinical characteristics and histopathology of COVID-19 related deaths in South African adults. PLoS One. 2022;17(1):e0262179.
Motsoeneng BM, Dhar N, Nunes MC, Krammer F, Madhi SA, Moore PL, et al. Influenza Vaccination Results in Differential Hemagglutinin Stalk-Specific Fc-Mediated Functions in Individuals Living With or Without HIV. Front Immunol. 2022;13:873191.
Mazur NI, Terstappen J, Baral R, Bardaji A, Beutels P, Buchholz UJ, Cohen C, Crowe JE Jr, Cutland CL, Eckert L, Feikin D, Fitzpatrick T, Fong Y, Graham BS, Heikkinen T, Higgins D, Hirve S, Klugman KP, Kragten-Tabatabaie L, Lemey P, Libster R, Lowensteyn Y, Mejias A, Munoz FM, Munywoki PK, Mwananyanda L, Nair H, Nunes MC, et al. Respiratory syncytial virus prevention within reach: the vaccine and monoclonal antibody landscape. Lancet Infect Dis. 2022.
May AK, Seymour H, Etheredge H, Maher H, Nunes MC, Madhi SA, et al. Coronavirus Host Genomics Study: South Africa (COVIGen-SA). Global health, epidemiology and genomics. 2022;2022:7405349.
Martin H, Falconer J, Addo-Yobo E, Aneja S, Arroyo LM, Asghar R, Awasthi S, Banajeh S, Bari A, Basnet S, Bavdekar A, Bhandari N, Bhatnagar S, Bhutta ZA, Brooks A, Chadha M, Chisaka N, Chou M, Clara AW, Colbourn T, Cutland C, D'Acremont V, Echavarria M, Gentile A, Gessner B, Gregory CJ, Hazir T, Hibberd PL, Hirve S, Hooli S, Iqbal I, Jeena P, Kartasasmita CB, King C, Libster R, Lodha R, Lozano JM, Lucero M, Lufesi N, MacLeod WB, Madhi SA, Mathew JL, Maulen-Radovan I, McCollum ED, Mino G, Mwansambo C, Neuman MI, Nguyen NT V, Nunes MC, et al. Assembling a global database of child pneumonia studies to inform WHO pneumonia management algorithm: Methodology and applications. J Glob Health. 2022;12:04075.
Kwatra G, Nunes M, Dhar N, Baillie V, Serafin N, Jones S, et al. Correlation of dried blood spots and plasma for quantification of Immunoglobulin (IgG) against Receptor binding domain and full length spike protein of SARS-CoV-2. J Virol Methods. 2022;300:114394.
Jones S, Coelho Nunes M. Beyond COVID-19: Equitable epidemiology for studying the impact of maternal infections on neonatal mortality and morbidity. Paediatr Perinat Epidemiol. 2022;36(4):553-5.
Jackson CL, Frank DN, Robertson CE, Ir D, Kofonow JM, Montlha MP, Mutsaerts, E, Nunes MC, et al. Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life. mBio. 2022;13(5):e0122922.
Dejnirattisai W, Huo J, Zhou D, Zahradnik J, Supasa P, Liu C, Duyvesteyn HME, Ginn HM, Mentzer AJ, Tuekprakhon A, Nutalai R, Wang B, Dijokaite A, Khan S, Avinoam O, Bahar M, Skelly D, Adele S, Johnson SA, Amin A, Ritter TG, Mason C, Dold C, Pan D, Assadi S, Bellass A, Omo-Dare N, Koeckerling D, Flaxman A, Jenkin D, Aley PK, Voysey M, Costa Clemens SA, Naveca FG, Nascimento V, Nascimento F, Fernandes da Costa C, Resende PC, Pauvolid-Correa A, Siqueira MM, Baillie V, Serafin N, Kwatra G, Da Silva K, Madhi SA, Nunes MC, et al. SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses. Cell. 2022;185(3):467-84 e15.