Publications

The Global Influenza Hospital Surveillance Network: A Multicountry Public Health Collaboration.

Nunes MC, Chauvel C, Raboni SM, López-Labrador FX, Andrew MK, Badar N, Baillie V, Bal A, Baral K, Baumeister E, Boutros C, Burtseva E, Coulibaly D, Cowling B, Danilenko D, Dbaibo G, Destras G, Dia N, Drăgănescu AC, Giamberardino HIG, Gomez-Camargo D, Josset L, Koul PA, Kyncl J, Laguna-Torres VA, Launay O, Nugyen LBL, McNeil S, Medić S, Mira-Iglesias A, Mironenko A, Nitsch-Osuch A, Orrico-Sánchez A, Otieno NA, Regue H, Ruiz-Palacios GM, Salah AB, Salman M, Săndulescu O, Simon V, Sominina A, Sordillo E, Tanriover MD, Unal S, van Bakel H, Vanhems P, Zhang T, Commaille-Chapus C, Hunsinger C, Bresee J, Lina B, McCauley JW, Ortiz JR, Viboud C, Zhang W, Torcel-Pagnon L, Mahe C, Chaves SS. The Global Influenza Hospital Surveillance Network: A Multicountry Public Health Collaboration. Influenza Other Respir Viruses. 2025 Mar;19(3):e70091.

Cross-sectional Study About Respiratory Viruses and the SARS-CoV-2 Pandemic in Southern Brazil: Results of a Prospective Epidemiologic Active Surveillance Study

Miyasaki CYP, Gonçalves RL, Krys P, Pereira LA, Petterle R, Giamberardino HIG, Nunes MC, Diaz-Quijano FA, Raboni SM. Cross-sectional Study About Respiratory Viruses and the SARS-CoV-2 Pandemic in Southern Brazil: Results of a Prospective Epidemiologic Active Surveillance Study. Pediatr Infect Dis J. 2025 Apr 8.

Gut microbiota and other factors associated with increased T cell regulation in HIV-exposed uninfected infants

Johnson MJ, Lazarus SK, Bennett AE, Tovar-Salazar A, Robertson CE, Kofonow JM, Li S, McCollister B, Nunes MC, Madhi SA, Frank DN, Weinberg A. Gut microbiota and other factors associated with increased T cell regulation in HIV-exposed uninfected infants. Front Immunol. 2025 Mar 3;16:1533003.

Severity Scale of Influenza and Acute Respiratory Illness Hospitalizations to Support Viral Genomic Surveillance: A Global Influenza Hospital Surveillance Network Pilot Study

Boudewijns B, Caini S, Del Riccio M, Nunes MC, Chaves SS, Andrew MK, Ortiz JR, Săndulescu O, Bresee JS, Burtseva E, Coulibaly D, Danilenko DM, Stolyarov K, Drăgănescu AC, Tanriover MD, Giamberardino HIG, Koul PA, Lopez-Labrador FX, McNeil SA, Mira-Iglesias A, Orrico-Sanchez A, Otieno NA, Ayugi J, Raboni SM, Spreeuwenberg P. Severity Scale of Influenza and Acute Respiratory Illness Hospitalizations to Support Viral Genomic Surveillance: A Global Influenza Hospital Surveillance Network Pilot Study. Influenza Other Respir Viruses. 2025 Mar;19(3):e70085.

Vaccine Effectiveness Dynamics against Influenza and SARS-CoV-2 in Community-tested Patients in France 2023-2024

Abou Chakra CN, Blanquart F, Vieillefond V, Enouf V, Visseaux B, Haim-Boukobza S, … Nunes MC; RELAB study group; Bal, A. (2025). Vaccine Effectiveness Dynamics against Influenza and SARS-CoV-2 in Community-tested Patients in France 2023-2024. Emerging Microbes & Infections.

Severity Scale of Influenza and Acute Respiratory Illness Hospitalizations to Support Viral Genomic Surveillance: A Global Influenza Hospital Surveillance Network Pilot Study

Boudewijns B, Caini S, Del Riccio M, Nunes MC, Chaves SS, Andrew MK, Ortiz JR, Săndulescu O, Bresee JS, Burtseva E, Coulibaly D, Danilenko DM, Stolyarov K, Drăgănescu AC, Tanriover MD, Giamberardino HIG, Koul PA, Lopez-Labrador FX, McNeil SA, Mira-Iglesias A, Orrico-Sanchez A, Otieno NA, Ayugi J, Raboni SM, Spreeuwenberg P. Severity Scale of Influenza and Acute Respiratory Illness Hospitalizations to Support Viral Genomic Surveillance: A Global Influenza Hospital Surveillance Network Pilot Study. Influenza Other Respir Viruses. 2025 Mar;19(3):e70085.

Influenza vaccine effectiveness against detected infection in the community

Blanquart F, Vieillefond V, Visseaux B, Abou Chakra CN, Nunes MC, Jacques A, Haim-Boukobza S, Josset L, Wehrle V, Deleglise G, Duret T, Rameix-Welti MA, Lina B, Enouf V; RELAB study group; Bal A. Influenza vaccine effectiveness against detected infection in the community, France, October 2024 to February 2025. Euro Surveill. 2025 Feb;30(7):2500074.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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. 

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. 

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.

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. 

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.

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.

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.

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.

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

Vanhems P, Nunes MC. Further Cautions When Modeling the Public Health Impact of Infectious Diseases. Am J Public Health. 2022 Nov;112(11):e1-e2.