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CERP - Center of Excellence in Respiratory Pathogens


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.

Our projects are divided in three work streams:

  1. Producing robust burden of disease estimates for influenza, Respiratory syncytial (RSV) and SARS-CoV-2 at a local, national, and global level using different data sources.
  2. Evaluating the real-life performance of vaccines against different outcomes.
  3. Assessing viral genetic evolution.


Team members


Director, Chargée de mission


Senior Biostatistician/Data scientist

ZOUNON Malaika


















(Publications by a team member in the last 2 years)

1.           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).

2.           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.

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

4.           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.

5.           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).

6.           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.

7.           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.

8.           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).

9.           Nunes MC, Madhi SA. COVID-19 vaccines in pregnancy. Trends Mol Med. 2022;28(8):662-80.

10.         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.

11.         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.

12.         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.

13.         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.

14.         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.

15.         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.

16.         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.

17.         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.

18.         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.

19.         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.

20.         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.

21.         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.

22.         Wang X, Li Y, Deloria-Knoll M, Madhi SA, Cohen C, Ali A, Basnet S, Bassat Q, Brooks WA, Chittaganpitch M, Echavarria M, Fasce RA, Goswami D, Hirve S, Homaira N, Howie SRC, Kotloff KL, Khuri-Bulos N, Krishnan A, Lucero MG, Lupisan S, Mira-Iglesias A, Moore DP, Moraleda C, Nunes M, et al. Global burden of acute lower respiratory infection associated with human metapneumovirus in children under 5 years in 2018: a systematic review and modelling study. Lancet Glob Health. 2021;9(1):e33-e43.

23.         Rees CA, Hooli S, King C, McCollum ED, Colbourn T, Lufesi N, Mwansambo C, Lazzerini M, Madhi SA, Cutland C, Nunes M, et al. External validation of the RISC, RISC-Malawi, and PERCH clinical prediction rules to identify risk of death in children hospitalized with pneumonia. J Glob Health. 2021;11:04062.

24.         Nunes MC, Johnson MJ, Kwatra G, Weinberg A, Madhi SA. T-cell responses to SARS-CoV-2 in unexposed South African women. Gates Open Res. 2021;5:150.

25.         Nunes MC, Cutland CL, Klugman KP, Madhi SA. Pneumococcal Conjugate Vaccine Protection against Coronavirus-Associated Pneumonia Hospitalization in Children Living with and without HIV. mBio. 2021;12(1).

26.         Nunes MC, Baillie VL, Kwatra G, Bhikha S, Verwey C, Menezes C, et al. Severe Acute Respiratory Syndrome Coronavirus 2 Infection Among Healthcare Workers in South Africa: A Longitudinal Cohort Study. Clin Infect Dis. 2021;73(10):1896-900.

27.         Navarro Alonso JA, Bont LJ, Bozzola E, Herting E, Lega F, Mader S, Nunes MC, et al. RSV: perspectives to strengthen the need for protection in all infants. Emerg Themes Epidemiol. 2021;18(1):15.

28.         Macias AE, McElhaney JE, Chaves SS, Nealon J, Nunes MC, Samson SI, et al. The disease burden of influenza beyond respiratory illness. Vaccine. 2021;39 Suppl 1:A6-A14.

29.         Mabena FC, Baillie VL, Hale MJ, Thwala BN, Mthembu N, Els T, Serafin N, du Plessis J, Swart P, Velaphi SC, Petersen KL, Wadula J, Govender NP, Verwey C, Moore DP, Moosa FY, Nakwa FL, Maroane BV, Okudo G, Mabaso TM, Dangor Z, Nunes MC, et al. Clinical Characteristics and Histopathology of Coronavirus Disease 2019-Related Deaths in African Children. The Pediatric infectious disease journal. 2021;40(9):e323-e32.

30.         Lowensteyn YN, Nair H, Nunes MC, van Roessel I, Vernooij FS, Willemsen J, et al. Estimated impact of maternal vaccination on global paediatric influenza-related in-hospital mortality: A retrospective case series. EClinicalMedicine. 2021;37:100945.

31.         Liu C, Ginn HM, Dejnirattisai W, Supasa P, Wang B, Tuekprakhon A, Nutalai R, Zhou D, Mentzer AJ, Zhao Y, Duyvesteyn HME, Lopez-Camacho C, Slon-Campos J, Walter TS, Skelly D, Johnson SA, Ritter TG, Mason C, Costa Clemens SA, Gomes Naveca F, Nascimento V, Nascimento F, Fernandes da Costa C, Resende PC, Pauvolid-Correa A, Siqueira MM, Dold C, Temperton N, Dong T, Pollard AJ, Knight JC, Crook D, Lambe T, Clutterbuck E, Bibi S, Flaxman A, Bittaye M, Belij-Rammerstorfer S, Gilbert SC, Malik T, Carroll MW, Klenerman P, Barnes E, Dunachie SJ, Baillie V, Serafin N, Ditse Z, Da Silva K, Paterson NG, Williams MA, Hall DR, Madhi S, Nunes MC, et al. Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum. Cell. 2021;184(16):4220-36 e13.

32.         Downs SL, Madhi SA, Van der Merwe L, Nunes MC, Olwagen CP. High-throughput nanofluidic real-time PCR to discriminate Pneumococcal Conjugate Vaccine (PCV)-associated serogroups 6, 18, and 22 to serotypes using modified oligonucleotides. Sci Rep. 2021;11(1):23728.

33.         Verwey C, Nunes MC, Dangor Z, Madhi SA. Pulmonary function sequelae after respiratory syncytial virus lower respiratory tract infection in children: A systematic review. Pediatr Pulmonol. 2020;55(7):1567-83.

34.         Verwey C, Nunes MC. RSV lower respiratory tract infection and lung health in the first 2 years of life. Lancet Glob Health. 2020;8(10):e1247-e8.

35.         Omer SB, Clark DR, Madhi SA, Tapia MD, Nunes MC, Cutland CL, et al. Efficacy, duration of protection, birth outcomes, and infant growth associated with influenza vaccination in pregnancy: a pooled analysis of three randomised controlled trials. Lancet Respir Med. 2020;8(6):597-608.

36.         Nunes MC, Moreira M, Koen A, van Niekerk N, Jose L, Cutland CL, et al. Bacterial nasopharyngeal carriage following infant immunization with pneumococcal conjugate vaccines according to a 2+1 schedule in children in South Africa: an exploratory analysis of two clinical trials. Expert Rev Vaccines. 2020;19(12):1177-89.

37.         Nunes MC, Kim S, Zeldow B, Violari A, Dittmer S, Cassim H, et al. Streptococcus pneumoniae colonization in pneumococcal vaccine-naive human immunodeficiency virus-exposed infected and -uninfected South African children. Medicine (Baltimore). 2020;99(9):e19353.

38.         Nunes MC, Cutland CL, Moultrie A, Jones S, Ortiz JR, Neuzil KM, et al. Immunogenicity and safety of different dosing schedules of trivalent inactivated influenza vaccine in pregnant women with HIV: a randomised controlled trial. Lancet HIV. 2020;7(2):e91-e103.

39.         Mutsaerts E, Nunes MC, Bhikha S, Ikulinda BT, Jose L, Koen A, et al. Short-term immunogenicity and safety of hepatitis-A and varicella vaccines in HIV-exposed uninfected and HIV-unexposed South African children. Vaccine. 2020;38(22):3862-8.

40.         Madhi SA, Nzenze SA, Nunes MC, Chinyanganya L, Van Niekerk N, Kahn K, et al. Residual colonization by vaccine serotypes in rural South Africa four years following initiation of pneumococcal conjugate vaccine immunization. Expert Rev Vaccines. 2020;19(4):383-93.

41.         Liu H, Lu B, Tabor DE, Tovchigrechko A, Wilkins D, Jin H, Madhi SA, Soofie N, Esser MT, Nunes MC. Characterization of human respiratory syncytial virus (RSV) isolated from HIV-exposed-uninfected and HIV-unexposed infants in South Africa during 2015-2017. Influenza Other Respir Viruses. 2020;14(4):403-11.

42.         Lina B, Georges A, Burtseva E, Nunes MC, Andrew MK, McNeil SA, et al. Complicated hospitalization due to influenza: results from the Global Hospital Influenza Network for the 2017-2018 season. BMC infectious diseases. 2020;20(1):465.

43.         Langedijk AC, Lebbink RJ, Naaktgeboren C, Evers A, Viveen MC, Greenough A, Heikkinen T, Stein RT, Richmond P, Martinón-Torres F, Nunes M, et al. Global molecular diversity of RSV - the "INFORM RSV" study. BMC infectious diseases. 2020;20(1):450.

44.         Gieles NC, Mutsaerts E, Kwatra G, Bont L, Cutland CL, Jones S, Moultrie A, Madhi SA, Nunes MC. Measles seroprevalence in pregnant women in Soweto, South Africa: a nested cohort study. Clin Microbiol Infect. 2020;26(4):515 e1- e4.

45.         Gieles NC, Mutsaerts E, Kwatra G, Bont L, Cutland CL, Jones S, Moultrie A, Madhi SA, Nunes MC. Rubella seroprevalence in pregnant women living with and without HIV in Soweto, South Africa. Int J Infect Dis. 2020;91:255-60.

46.         Dhar N, Kwatra G, Nunes MC, Cutland C, Izu A, Nachbagauer R, et al. Hemagglutinin Stalk Antibody Responses Following Trivalent Inactivated Influenza Vaccine Immunization of Pregnant Women and Association With Protection From Influenza Virus Illness. Clin Infect Dis. 2020;71(4):1072-9.

47.         Cohen C, Nunes MC. Vaccinating Mothers to Protect Their Babies Against Influenza. The Journal of infectious diseases. 2020;221(1):5-7.

48.         Clark DR, Omer SB, Tapia MD, Nunes MC, Cutland CL, Tielsch JM, et al. Influenza or Meningococcal Immunization During Pregnancy and Mortality in Women and Infants: A Pooled Analysis of Randomized Controlled Trials. The Pediatric infectious disease journal. 2020;39(7):641-4.

49.         Amin AB, Nunes MC, Tapia MD, Madhi SA, Cutland CL, Wairagkar N, et al. Immunogenicity of influenza vaccines administered to pregnant women in randomized clinical trials in Mali and South Africa. Vaccine. 2020;38(41):6478-83.