Publications

Publications sélectionnées

Community and Hospital‐Based Laboratory Surveillance for Influenza, Respiratory Syncytial Virus, and SARS‐CoV‐2 During the 2023–2024 Season, Lyon, France

Chauvel C, Casalegno JS, Visseaux B, Vieillefond V, Haim-Boukozba S, Enouf V, Chanard E, Fabre M, Rameix-Welti MA, Oblette A, Giannoli JM, Paireau J, Josset L, Lina B, Gaymard A, Cauchemez S, Morfin F, Nunes MC, Bal A. Community and Hospital-Based Laboratory Surveillance for Influenza, Respiratory Syncytial Virus, and SARS-CoV-2 During the 2023-2024 Season, Lyon, France. J Med Virol. 2025 Sep;97(9):e70549. doi: 10.1002/jmv.70549. PMID: 40880188; PMCID: PMC12396161.

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Association of influenza viral genetic information with severity markers in patients hospitalised with influenza: multicentre retrospective cohort study

Myint AP, Shirreff G, Baillie V, Bal A, Boutros CF, Burtseva E, Coulibaly D, Danilenko D, Dbaibo G, Destras G, Dia N, Drăgănescu AC, Giamberardino HIG, Komissarov AB, Koul PA, Laguna-Torres VA, LeBlanc JJ, Mira-Iglesias A, Mironenko A, Orrico-Sánchez A, Otieno NA, Săndulescu O, Simon V, Sominina A, Sordillo E, Tanriover MD, Teteriuk N, Unal S, Van Bakel H, Andrew MK, Bresee J, Lina B, López-Labrador FX, Ortiz JR, Raboni SM, Zhang W, Chaves SS, Cacciapaglia G, Josset L, Chauvel C, Nunes MC. Association of influenza viral genetic information with severity markers in patients hospitalised with influenza: multicentre retrospective cohort study. BMJ Open. 2026 Jan 8;16(1):e111643. doi: 10.1136/bmjopen-2025-111643. PMID: 41506775.

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Toutes les publications par le CERP

Association of influenza viral genetic information with severity markers in patients hospitalised with influenza: multicentre retrospective cohort study

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Community and Hospital‐Based Laboratory Surveillance for Influenza, Respiratory Syncytial Virus, and SARS‐CoV‐2 During the 2023–2024 Season, Lyon, France

Chauvel C, Casalegno JS, Visseaux B, Vieillefond V, Haim-Boukozba S, Enouf V, Chanard E, Fabre M, Rameix-Welti MA, Oblette A, Giannoli JM, Paireau J, Josset L, Lina B, Gaymard A, Cauchemez S, Morfin F, Nunes MC, Bal A. Community and Hospital-Based Laboratory Surveillance for Influenza, Respiratory Syncytial Virus, and SARS-CoV-2 During the 2023-2024 Season, Lyon, France. J Med Virol. 2025 Sep;97(9):e70549. doi: 10.1002/jmv.70549. PMID: 40880188; PMCID: PMC12396161.

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Impact of Respiratory Syncytial Virus and Severe Acute Respiratory Syndrome Coronavirus 2 Coinfection on Clinical Severity and Outcomes Among Children Hospitalized With Lower Respiratory Tract Infections in Soweto, South Africa

Mrubata KL, Bailie V, Solomon F, Izu A, Ncube M, Nunes MC, Dangor Z, Madhi SA, Moore DP, Verwey C. Impact of Respiratory Syncytial Virus and Severe Acute Respiratory Syndrome Coronavirus 2 Coinfection on Clinical Severity and Outcomes Among Children Hospitalized With Lower Respiratory Tract Infections in Soweto, South Africa. Pediatr Infect Dis J. 2025 Feb 1;44(2):107-111

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Changes in Respiratory Syncytial Virus-Associated Hospitalisations Epidemiology After Nirsevimab Introduction in Lyon, France

Chauvel C, Horvat C, Javouhey E, Gillet Y, Hassenboehler J, Chakra CNA, Ragouilliaux C, Plaisant F, Ploin D, Butin M, Casalegno JS, Nunes MC. Changes in Respiratory Syncytial Virus-Associated Hospitalisations Epidemiology After Nirsevimab Introduction in Lyon, France. Influenza Other Respir Viruses. 2024 Dec;18(12):e70054.

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RSV Severe Infection Risk Stratification in a French 5-Year Birth Cohort Using Machine-learning

Horvat C, Chauvel C, Casalegno JS, Benchaib M, Ploin D, Nunes MC; VRS Study Group in Lyon. RSV Severe Infection Risk Stratification in a French 5-Year Birth Cohort Using Machine-learning. Pediatr Infect Dis J. 2024 Sep 1;43(9):819-824.

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The genomic evolutionary dynamics and global circulation patterns of respiratory syncytial virus

Langedijk AC, Vrancken B, Lebbink RJ, Wilkins D, Kelly EJ, Baraldi E, Mascareñas de Los Santos AH, Danilenko DM, Choi EH, Palomino MA, Chi H, Keller C, Cohen R, Papenburg J, Pernica J, Greenough A, Richmond P, Martinón-Torres F, Heikkinen T, Stein RT, Hosoya M, Nunes MC, Verwey C, Evers A, Kragten-Tabatabaie L, Suchard MA, Kosakovsky Pond SL, Poletto C, Colizza V, Lemey P, Bont LJ; INFORM-RSV Study Group. The genomic evolutionary dynamics and global circulation patterns of respiratory syncytial virus. Nat Commun. 2024 Apr 10;15(1):3083.

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Severe respiratory syncytial virus infection in children: burden, management, and emerging therapies

Mazur NI, Caballero MT, Nunes MC. Severe respiratory syncytial virus infection in children: burden, management, and emerging therapies. Lancet. 2024 Sep 21;404(10458):1143-1156.

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T-cell responses to ancestral SARS-CoV-2 and Omicron variant among unvaccinated pregnant and postpartum women living with and without HIV in South Africa

McMahon WC, Kwatra G, Izu A, Jones SA, Mbele NJ, Jafta N, Lala R, Shalekoff S, Tiemessen CT, Madhi SA, Nunes MC. T-cell responses to ancestral SARS-CoV-2 and Omicron variant among unvaccinated pregnant and postpartum women living with and without HIV in South Africa. Sci Rep. 2024 Sep 2;14(1):20348.

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T-cell responses to ancestral SARS-CoV-2 and Omicron variant among unvaccinated pregnant and postpartum women living with and without HIV in South Africa

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Hemagglutinin Stalk-Specific Fc-Mediated Functions Are Associated With Protection Against Influenza Illness After Seasonal Influenza Vaccination

Motsoeneng BM, Dhar N, Nunes MC, Krammer F, Madhi SA, Moore PL, Richardson SI. Hemagglutinin Stalk-Specific Fc-Mediated Functions Are Associated With Protection Against Influenza Illness After Seasonal Influenza Vaccination. J Infect Dis. 2024 Dec 16;230(6):1329-1336.

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Post-disappearance scenarios: policy implications following the potential disappearance of B/Yamagata lineage influenza viruses

Del Riccio M, Nunes MC, Cowling BJ, Lina B, McCauley JW, Meijer A, Nohynek H, Boudewijns B, Caini S. Post-disappearance scenarios: policy implications following the potential disappearance of B/Yamagata lineage influenza viruses. Euro Surveill. 2024 Nov;29(45):2400196.

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Assessing New York City’s COVID-19 Vaccine Rollout Strategy: A Case for Risk-Informed Distribution

Schwalbe N, Nunes MC, Cutland C, Wahl B, Reidpath D. Assessing New York City’s COVID-19 Vaccine Rollout Strategy: A Case for Risk-Informed Distribution. J Urban Health. 2024 Oct;101(5):923-933.

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Post-acute sequelae of SARS-CoV-2 infection in health care workers from South Africa Mbotwe-Sibanda

S, Kwatra G, Madhi SA, Nunes MC. Post-acute sequelae of SARS-CoV-2 infection in health care workers from South Africa. Oxf Open Immunol. 2024 Mar 9;5(1):iqae001.

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Changing epidemiology of COVID-19: potential future impact on vaccines and vaccination strategies

Ulrichs T, Rolland M, Wu J, Nunes MC, El Guerche-Séblain C, Chit A. Changing epidemiology of COVID-19: potential future impact on vaccines and vaccination strategies. Expert Rev Vaccines. 2024 Jan-Dec;23(1):510-522.

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Survival of bronchopulmonary cancers according to radon exposure.

Dessemon J, Perol O, Chauvel C, Noelle H, Coudon T, Grassot L, Foray N, Belladame E, Fayette J, Fournie F, Swalduz A, Neidhart EM, Saintigny P, Tabutin M, Boussageon M, Gomez F, Avrillon V, Perol M, Charbotel B, Fervers B. Survival of bronchopulmonary cancers according to radon exposure. Front Public Health. 2024 Jan 24;11:1306455.

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Epidemiology of community-acquired pneumonia caused by Streptococcus pneumoniae in older adults: a narrative review.

Elias C, Nunes MC, Saadatian-Elahi M. Epidemiology of community-acquired pneumonia caused by S treptococcus pneumoniae in older adults: a narrative review. Curr Opin Infect Dis. 2024 Apr 1;37(2):144-153.

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Redefining pandemic preparedness: Multidisciplinary insights from the CERP modelling workshop in infectious diseases, workshop report.

Nunes MC, Thommes E, Fröhlich H, Flahault A, Arino J, Baguelin M, Biggerstaff M, Bizel-Bizellot G, Borchering R, Cacciapaglia G, Cauchemez S, Barbier-Chebbah A, Claussen C, Choirat C, Cojocaru M, Commaille-Chapus C, Hon C, Kong J, Lambert N, Lauer KB, Lehr T, Mahe C, Marechal V, Mebarki A, Moghadas S, Niehus R, Opatowski L, Parino F, Pruvost G, Schuppert A, Thiébaut R, Thomas-Bachli A, Viboud C, Wu J, Crépey P, Coudeville L. Redefining pandemic preparedness: Multidisciplinary insights from the CERP modelling workshop in infectious diseases, workshop report. Infect Dis Model. 2024 Feb 23;9(2):501-518.

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SARS-CoV-2 Viral Replication Persists in the Human Lung for Several Weeks after Symptom Onset.

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., … Dheda, K. (2024). SARS-CoV-2 Viral Replication Persists in the Human Lung for Several Weeks after Symptom Onset. American journal of respiratory and critical care medicine, 10.1164/rccm.202308-1438OC. Advance online publication.

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Global disease burden of and risk factors for acute lower respiratory infections caused by respiratory syncytial virus in preterm infants and young children in 2019: a systematic review and meta-analysis of aggregated and individual participant data.

Wang X, Li Y, Shi T, Bont LJ, Chu HY, Zar HJ, Wahi-Singh B, Ma Y, Cong B, Sharland E, Riley RD, Deng J, Figueras-Aloy J, Heikkinen T, Jones MH, Liese JG, Markić J, Mejias A, Nunes MC, Resch B, Satav A, Yeo KT, Simões EAF, Nair H; Respiratory Virus Global Epidemiology Network; RESCEU investigators. Global disease burden of and risk factors for acute lower respiratory infections caused by respiratory syncytial virus in preterm infants and young children in 2019: a systematic review and meta-analysis of aggregated and individual participant data. Lancet. 2024 Feb 14:S0140-6736(24)00138-7.

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Effects of pneumococcal conjugate vaccines on reducing the risk of respiratory disease associated with coronavirus infection.

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 (Nathan). 2023 May 25;15(1):10.

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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.

Izu A, Nunes MC, Solomon F, Baillie V, Serafin N, Verwey C, Moore DP, Laubscher M, Ncube M, Olwagen C, Dangor Z, Madhi SA. 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 Sep;23(9):1031-1041.

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Immunogenicity of tetanus, diphtheria and acellular pertussis vaccination among pregnant women living with and without HIV.

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 Dec 1;37(15):2305-2310.

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Bacterial nasopharyngeal colonisation in children in South Africa before and during the COVID-19 pandemic: an observational study.

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. 2024 Jan;5(1):e34-e42.

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Nanofluidic qPCR unable to detect and serotype Streptococcus pneumoniae in urine samples of hospitalized South African patients with community-acquired pneumonia.

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 Dec 4;13(1):21332.

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Patient influenza vaccination reduces the risk of hospital-acquired influenza: An incident test negative-case control study in Lyon university hospital, France (2004-2020).

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 Jul 5;41(30):4341-4346.

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Toutes les publications depuis 2022

Community and Hospital‐Based Laboratory Surveillance for Influenza, Respiratory Syncytial Virus, and SARS‐CoV‐2 During the 2023–2024 Season, Lyon, France

Chauvel C, Casalegno JS, Visseaux B, Vieillefond V, Haim-Boukozba S, Enouf V, Chanard E, Fabre M, Rameix-Welti MA, Oblette A, Giannoli JM, Paireau J, Josset L, Lina B, Gaymard A, Cauchemez S, Morfin F, Nunes MC, Bal A. Community and Hospital-Based Laboratory Surveillance for Influenza, Respiratory Syncytial Virus, and SARS-CoV-2 During the 2023-2024 Season, Lyon, France. J Med Virol. 2025 Sep;97(9):e70549. doi: 10.1002/jmv.70549. PMID: 40880188; PMCID: PMC12396161.

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Association of influenza viral genetic information with severity markers in patients hospitalised with influenza: multicentre retrospective cohort study

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Probable extinction of influenza B/Yamagata and its public health implications: a systematic literature review and assessment of global surveillance Databases

Caini S, Meijer A, Nunes MC, Henaff L, Zounon M, Boudewijns B, Del Riccio M, Paget J. Probable extinction of influenza B/Yamagata and its public health implications: a systematic literature review and assessment of global surveillance databases. Lancet Microbe2024

Publications

Publications sélectionnées

Community and Hospital‐Based Laboratory Surveillance for Influenza, Respiratory Syncytial Virus, and SARS‐CoV‐2 During the 2023–2024 Season, Lyon, France

Association of influenza viral genetic information with severity markers in patients hospitalised with influenza: multicentre retrospective cohort study

Toutes les publications par le CERP

Toutes les publications depuis 2022

Community and Hospital‐Based Laboratory Surveillance for Influenza, Respiratory Syncytial Virus, and SARS‐CoV‐2 During the 2023–2024 Season, Lyon, France

Association of influenza viral genetic information with severity markers in patients hospitalised with influenza: multicentre retrospective cohort study

Probable extinction of influenza B/Yamagata and its public health implications: a systematic literature review and assessment of global surveillance Databases

RSV Severe Infection Risk Stratification in a French 5-Year Birth Cohort Using Machine-learning

Survival of bronchopulmonary cancers according to radon exposure.

Epidemiology of community-acquired pneumonia caused by S treptococcus pneumoniae in older adults: a narrative review.

Redefining pandemic preparedness: Multidisciplinary insights from the CERP modelling workshop in infectious diseases, workshop report.

SARS-CoV-2 Viral Replication Persists in the Human Lung for Several Weeks after Symptom Onset.

Global disease burden of and risk factors for acute lower respiratory infections caused by respiratory syncytial virus in preterm infants and young children in 2019: a systematic review and meta-analysis of aggregated and individual participant data.

Age Differences in Comorbidities, Presenting Symptoms, and Outcomes of Influenza Illness Requiring Hospitalization: A Worldwide Perspective From the Global Influenza Hospital Surveillance Network.

Predictors of severity of influenza-related hospitalizations: Results from the Global Influenza Hospital Surveillance Network (GIHSN).

Optimization of a high-throughput nanofluidic real-time PCR to detect and quantify of 15 bacterial species and 92 Streptococcus pneumoniae serotypes.

Streptococcus pneumoniae and other bacterial nasopharyngeal colonization seven years post-introduction of 13-valent pneumococcal conjugate vaccine in South African children.

Effects of pneumococcal conjugate vaccines on reducing the risk of respiratory disease associated with coronavirus infection.

In-hospital mortality risk stratification in children aged under 5 years with pneumonia with or without pulse oximetry: A secondary analysis of the Pneumonia REsearch Partnership to Assess WHO REcommendations (PREPARE) dataset.

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.

ChAdOx1 nCoV-19 (AZD1222) vaccine-induced Fc receptor binding tracks with differential susceptibility to COVID-19.

Respiratory syncytial virus prevention within reach: the vaccine and monoclonal antibody landscape.

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.

Genomic characterization of Bordetella pertussis in South Africa, 2015-2019.

Immunogenicity of tetanus, diphtheria and acellular pertussis vaccination among pregnant women living with and without HIV.

Bacterial nasopharyngeal colonisation in children in South Africa before and during the COVID-19 pandemic: an observational study.

Nanofluidic qPCR unable to detect and serotype Streptococcus pneumoniae in urine samples of hospitalized South African patients with community-acquired pneumonia.

Human Metapneumovirus-Associated Hospitalization in HIV-1 Exposed Uninfected and HIV-1 Uninfected Children Less Than 5 Years in South Africa.

Patient influenza vaccination reduces the risk of hospital-acquired influenza: An incident test negative-case control study in Lyon university hospital, France (2004-2020).

Adverse maternal, fetal, and newborn outcomes among pregnant women with SARS-CoV-2 infection: an individual participant data meta-analysis.

Clinical risk factors of adverse outcomes among women with COVID-19 in the pregnancy and postpartum period: a sequential, prospective meta-analysis.

Pulmonary sequelae in 2-year-old children after hospitalisation for respiratory syncytial virus lower respiratory tract infection during infancy: an observational study.

Nirsevimab binding-site conservation in respiratory syncytial virus fusion glycoprotein worldwide between 1956 and 2021: an analysis of observational study sequencing data.

Proteomic Profiling of Urine From Hospitalized Patients With Severe Pneumonia due to SARS-CoV-2 vs Other Causes: A Preliminary Report.

Identifying the research, advocacy, policy and implementation needs for the prevention and management of respiratory syncytial virus lower respiratory tract infection in low- and middle-income countries.

SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses.

Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life.

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.

Assembling a global database of child pneumonia studies to inform WHO pneumonia management algorithm: Methodology and applications.

Coronavirus Host Genomics Study: South Africa (COVIGen-SA).

Influenza Vaccination Results in Differential Hemagglutinin Stalk-Specific Fc-Mediated Functions in Individuals Living With or Without HIV.

Clinical characteristics and histopathology of COVID-19 related deaths in South African adults.

T-cell responses to SARS-CoV-2 in unexposed South African women.

Maternal-foetal transfer of SARS-CoV-2 antibodies among women with and those without HIV infection.

Antepartum SARS-CoV-2 infection and adverse birth outcomes in South African women.

Active Intrapartum SARS-CoV-2 Infection and Pregnancy Outcomes.

COVID-19 vaccines in pregnancy.

SARS-CoV-2 Omicron Symptomatic Infections in Previously Infected or Vaccinated South African Healthcare Workers.

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.

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.

Use of financial incentives to increase adult vaccination coverage: A narrative review of lessons learned from COVID-19 and other adult vaccination efforts.

Further Cautions When Modeling the Public Health Impact of Infectious Diseases.