{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T11:31:04Z","timestamp":1789731064250,"version":"4.0.1"},"reference-count":86,"publisher":"MDPI AG","issue":"16","license":[{"start":{"date-parts":[[2022,8,21]],"date-time":"2022-08-21T00:00:00Z","timestamp":1661040000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gate Foundation","doi-asserted-by":"publisher","award":["BMGF-OPP1180423_2017"],"award-info":[{"award-number":["BMGF-OPP1180423_2017"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gate Foundation","doi-asserted-by":"publisher","award":["120814"],"award-info":[{"award-number":["120814"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gate Foundation","doi-asserted-by":"publisher","award":["19\/16"],"award-info":[{"award-number":["19\/16"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001321","name":"National Research Foundation (NRF), South Africa","doi-asserted-by":"publisher","award":["BMGF-OPP1180423_2017"],"award-info":[{"award-number":["BMGF-OPP1180423_2017"]}],"id":[{"id":"10.13039\/501100001321","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001321","name":"National Research Foundation (NRF), South Africa","doi-asserted-by":"publisher","award":["120814"],"award-info":[{"award-number":["120814"]}],"id":[{"id":"10.13039\/501100001321","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001321","name":"National Research Foundation (NRF), South Africa","doi-asserted-by":"publisher","award":["19\/16"],"award-info":[{"award-number":["19\/16"]}],"id":[{"id":"10.13039\/501100001321","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001323","name":"Poliomyelitis Research Foundation (PRF), South Africa","doi-asserted-by":"publisher","award":["BMGF-OPP1180423_2017"],"award-info":[{"award-number":["BMGF-OPP1180423_2017"]}],"id":[{"id":"10.13039\/501100001323","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001323","name":"Poliomyelitis Research Foundation (PRF), South Africa","doi-asserted-by":"publisher","award":["120814"],"award-info":[{"award-number":["120814"]}],"id":[{"id":"10.13039\/501100001323","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001323","name":"Poliomyelitis Research Foundation (PRF), South Africa","doi-asserted-by":"publisher","award":["19\/16"],"award-info":[{"award-number":["19\/16"]}],"id":[{"id":"10.13039\/501100001323","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJERPH"],"abstract":"<jats:p>Severe acute respiratory infections (SARI) contribute to mortality in children \u22645 years. Their microbiological aetiologies are often unknown and may be exacerbated in light of coronavirus disease 19 (COVID-19). This study reports on respiratory pathogens in children \u22645 years (n = 84) admitted with SARI during and between the second and third waves of COVID-19 infection in South Africa. Nasopharyngeal\/oropharyngeal swabs collected were subjected to viral detection using QIAstat-Dx\u00ae Respiratory SARS-CoV-2 Panel. The results revealed viral positivity and negativity detection rates of 88% (74\/84) and 12% (10\/84), respectively. Of the 21 targeted pathogens, human rhinovirus\/enterovirus (30%), respiratory syncytial virus (RSV; 26%), and severe acute respiratory syndrome coronavirus 2 (24%) were mostly detected, with other viruses being 20% and a co-infection rate of 64.2% (54\/84). Generally, RSV-positive samples had lower Ct values, and fewer viruses were detected during the third wave. Changes in the circulation patterns of respiratory viruses with total absence of influenza virus could be attributed to measures against COVID-19 transmission, which may result in waned immunity, thereby increasing susceptibility to severe infections in the following season. High viral co-infection rate, as detected, may complicate diagnosis. Nonetheless, accurate identification of the pathogens may guide treatment decisions and infection control.<\/jats:p>","DOI":"10.3390\/ijerph191610418","type":"journal-article","created":{"date-parts":[[2022,8,21]],"date-time":"2022-08-21T22:23:13Z","timestamp":1661120593000},"page":"10418","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":23,"title":["Pathogen Profile of Children Hospitalised with Severe Acute Respiratory Infections during COVID-19 Pandemic in the Free State Province, South Africa"],"prefix":"10.3390","volume":"19","author":[{"given":"Ayodeji E.","family":"Ogunbayo","sequence":"first","affiliation":[{"name":"Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6755-1945","authenticated-orcid":false,"given":"Milton T.","family":"Mogotsi","sequence":"additional","affiliation":[{"name":"Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hlengiwe","family":"Sondlane","sequence":"additional","affiliation":[{"name":"Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kelebogile R.","family":"Nkwadipo","sequence":"additional","affiliation":[{"name":"Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7209-9220","authenticated-orcid":false,"given":"Saheed","family":"Sabiu","sequence":"additional","affiliation":[{"name":"Department of Biotechnology and Food Science, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5017-5584","authenticated-orcid":false,"given":"Martin M.","family":"Nyaga","sequence":"additional","affiliation":[{"name":"Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,8,21]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"122","DOI":"10.2471\/BLT.17.194514","article-title":"Revision of clinical case definitions: Influenza-like illness and severe acute respiratory infection","volume":"96","author":"Fitzner","year":"2018","journal-title":"Bull. World Health Organ."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Tomczyk, S., McCracken, J.P., Contreras, C.L., Lopez, M.R., Bernart, C., Moir, J.C., Escobar, K., Reyes, L., Arvelo, W., and Lindblade, K. (2019). Factors associated with fatal cases of acute respiratory infection (ARI) among hospitalized patients in Guatemala. BMC Public Health, 19.","DOI":"10.1186\/s12889-019-6824-z"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"5026","DOI":"10.1038\/s41467-021-25120-6","article-title":"Etiological and epidemiological features of acute respiratory infections in China","volume":"12","author":"Li","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Fathmawati, F., Rauf, S., and Indraswari, B.W. (2021). Factors related with the incidence of acute respiratory infections in toddlers in Sleman, Yogyakarta, Indonesia: Evidence from the Sleman Health and Demographic Surveillance System. PLoS ONE, 16.","DOI":"10.1371\/journal.pone.0257881"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1016\/S2352-4642(21)00311-4","article-title":"Global, regional, and national causes of under-5 mortality in 2000\u201319: An updated systematic analysis with implications for the Sustainable Development Goals","volume":"6","author":"Perin","year":"2022","journal-title":"Lancet Child Adolesc. Health"},{"key":"ref_6","first-page":"CD006452","article-title":"Rapid viral diagnosis for acute febrile respiratory illness in children in the Emergency Department","volume":"9","author":"Doan","year":"2014","journal-title":"Cochrane Database Syst. Rev."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Cebey-L\u00f3pez, M., Herberg, J., Pardo-Seco, J., G\u00f3mez-Carballa, A., Martin\u00f3n-Torres, N., Salas, A., Martin\u00f3n-S\u00e1nchez, J.M., Gormley, S., Sumner, E., and Fink, C. (2015). Viral Co-Infections in Pediatric Patients Hospitalized with Lower Tract Acute Respiratory Infections. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0136526"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Chen, J., Hu, P., Zhou, T., Zheng, T., Zhou, L., Jiang, C., and Pei, X. (2018). Epidemiology and clinical characteristics of acute respiratory tract infections among hospitalized infants and young children in Chengdu, West China, 2009\u20132014. BMC Pediatr., 18.","DOI":"10.1186\/s12887-018-1203-y"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"N\u00fa\u00f1ez-Samudio, V., and Landires, I. (2021). Epidemiology of viral respiratory infections in a pediatric reference hospital in Central Panama. BMC Infect. Dis., 21.","DOI":"10.1186\/s12879-020-05720-1"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Kurskaya, O., Ryabichenko, T., Leonova, N., Shi, W., Bi, H., Sharshov, K., Kazachkova, E., Sobolev, I., Prokopyeva, E., and Kartseva, T. (2018). Viral etiology of acute respiratory infections in hospitalized children in Novosibirsk City, Russia (2013\u20132017). PLoS ONE, 13.","DOI":"10.1101\/353037"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1007\/s40291-019-00433-x","article-title":"FebriDx\u00ae: A Rapid Diagnostic Test for Differentiating Bacterial and Viral Aetiologies in Acute Respiratory Infections","volume":"23","author":"Shirley","year":"2019","journal-title":"Mol. Diagn. Ther."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"e742","DOI":"10.1097\/MD.0000000000000742","article-title":"Detection of Viral and Bacterial Pathogens in Hospitalized Children With Acute Respiratory Illnesses, Chongqing, 2009\u20132013","volume":"94","author":"Wei","year":"2015","journal-title":"Medicine"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Juliana, A.E., Tang, M.-J., Kemps, L., Noort, A.C., Hermelijn, S., Pl\u00f6tz, F.B., Zonneveld, R., and Wilschut, J.C. (2021). Viral causes of severe acute respiratory infection in hospitalized children and association with outcomes: A two-year prospective surveillance study in Suriname. PLoS ONE, 16.","DOI":"10.1371\/journal.pone.0247000"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Horton, K.C., Dueger, E.L., Kandeel, A., Abdallat, M., El Kholy, A., Al-Awaidy, S., Kohlani, A.H., Amer, H., El-Khal, A.L., and Said, M. (2017). Viral etiology, seasonality and severity of hospitalized patients with severe acute respiratory infections in the Eastern Mediterranean Region, 2007\u20132014. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0180954"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"163","DOI":"10.4103\/ijmm.IJMM_18_84","article-title":"Profile of Respiratory Pathogens Causing Acute Respiratory Infections in Hospitalised Children at Rajasthan a 4 Year\u2019s Study","volume":"36","author":"Swamy","year":"2018","journal-title":"Indian J. Med. Microbiol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"877","DOI":"10.4103\/ijmr.IJMR_22_15","article-title":"Viruses causing severe acute respiratory infections (SARI) in children \u22645 years of age at a tertiary care hospital in Rajasthan, India","volume":"144","author":"Malhotra","year":"2016","journal-title":"Indian J. Med. Res."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"316","DOI":"10.12980\/apjtd.7.2017D6-423","article-title":"Pathogenic viruses of the respiratory tract\u2014A review","volume":"7","author":"Kabir","year":"2017","journal-title":"Asian Pac. J. Trop. Dis."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1000","DOI":"10.1128\/JCM.03060-15","article-title":"Unbiased Detection of Respiratory Viruses by Use of RNA Sequencing-Based Metagenomics: A Systematic Comparison to a Commercial PCR Panel","volume":"54","author":"Graf","year":"2016","journal-title":"J. Clin. Microbiol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"921","DOI":"10.1016\/j.ijid.2022.07.060","article-title":"Metagenomic next-generation sequencing for accurate diagnosis and management of lower respiratory tract infections","volume":"122","author":"Liang","year":"2022","journal-title":"Int. J. Infect. Dis."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"S\u00e1nchez, X., Orrico, M., Morillo, T., Manzano, A., Jimbo, R., and Armijos, L. (2021). Reducing unnecessary antibiotic prescription through implementation of a clinical guideline on self-limiting respiratory tract infections. PLoS ONE, 16.","DOI":"10.1371\/journal.pone.0249475"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1007\/s10096-018-03454-2","article-title":"Antibiotic misuse in respiratory tract infections in children and adults\u2014A prospective, multicentre study (TAILORED Treatment)","volume":"38","author":"Cohen","year":"2019","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1093\/cid\/cix461","article-title":"Rapid Tests for Influenza, Respiratory Syncytial Virus, and Other Respiratory Viruses: A Systematic Review and Meta-analysis","volume":"65","author":"Bruning","year":"2017","journal-title":"Clin. Infect. Dis."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1001\/jamapediatrics.2020.3988","article-title":"Clinical Characteristics and Viral RNA Detection in Children With Coronavirus Disease 2019 in the Republic of Korea","volume":"175","author":"Han","year":"2021","journal-title":"JAMA Pediatr."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"586","DOI":"10.1001\/jamapediatrics.2021.0001","article-title":"Prevalence of SARS-CoV-2 Infection in Children and Their Parents in Southwest Germany","volume":"175","author":"Elling","year":"2021","journal-title":"JAMA Pediatr."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1007\/s40272-017-0257-x","article-title":"Advances in Vaccines to Prevent Viral Respiratory Illnesses in Children","volume":"19","author":"Anderson","year":"2017","journal-title":"Pediatr. Drugs"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Bianchini, S., Argentiero, A., Camilloni, B., Silvestri, E., Alunno, A., and Esposito, S. (2019). Vaccination against Paediatric Respiratory Pathogens. Vaccines, 7.","DOI":"10.3390\/vaccines7040168"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Zhu, Y., Li, W., Yang, B., Qian, R., Wu, F., He, X., Zhu, Q., Liu, J., Ni, Y., and Wang, J. (2021). Epidemiological and virological characteristics of respiratory tract infections in children during COVID-19 outbreak. BMC Pediatr., 21.","DOI":"10.1186\/s12887-021-02654-8"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1186\/s12985-021-01627-8","article-title":"Impact of COVID-19 pandemic on the prevalence of respiratory viruses in children with lower respiratory tract infections in China","volume":"18","author":"Liu","year":"2021","journal-title":"Virol. J."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"E170","DOI":"10.1017\/S0950268821001606","article-title":"Pathogen spectrum changes of respiratory tract infections in children in Chaoshan area under the influence of COVID-19","volume":"149","author":"Lin","year":"2021","journal-title":"Epidemiol. Infect."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.1038\/s41467-021-21157-9","article-title":"Impact of the COVID-19 nonpharmaceutical interventions on influenza and other respiratory viral infections in New Zealand","volume":"12","author":"Huang","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Vittucci, A.C., Piccioni, L., Coltella, L., Ciarlitto, C., Antilici, L., Bozzola, E., Midulla, F., Palma, P., Perno, C.F., and Villani, A. (2021). The Disappearance of Respiratory Viruses in Children during the COVID-19 Pandemic. Int. J. Environ. Res. Public Health, 18.","DOI":"10.3390\/ijerph18189550"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"e00155-20","DOI":"10.1128\/JCM.00155-20","article-title":"Multicenter Evaluation of the QIAstat-Dx Respiratory Panel for Detection of Viruses and Bacteria in Nasopharyngeal Swab Specimens","volume":"58","author":"Leber","year":"2020","journal-title":"J. Clin. Microbiol."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Par\u010dina, M., Vest Schneider, U., Visseaux, B., Jozi\u0107, R., Hannet, I., and Lisby, J.G. (2020). Multicenter evaluation of the QIAstat Respiratory Panel\u2014A new rapid highly multiplexed PCR based assay for diagnosis of acute respiratory tract infections. PLoS ONE, 15.","DOI":"10.1371\/journal.pone.0230183"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"e00630-20","DOI":"10.1128\/JCM.00630-20","article-title":"Evaluation of the QIAstat-Dx Respiratory SARS-CoV-2 Panel, the First Rapid Multiplex PCR Commercial Assay for SARS-CoV-2 Detection","volume":"58","author":"Visseaux","year":"2020","journal-title":"J. Clin. Microbiol."},{"key":"ref_35","unstructured":"National Institute for Communicable Diseases (2021). Proposed definition of COVID-19 wave in South Africa. Commun. Dis. Commun., 20, 11."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"e01793-19","DOI":"10.1128\/JCM.01793-19","article-title":"Multicenter Evaluation of QIAstat-Dx Respiratory Panel V2 for Detection of Viral and Bacterial Respiratory Pathogens","volume":"58","author":"Boers","year":"2020","journal-title":"J. Clin. Microbiol."},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Breiman, R.F., Cosmas, L., Njenga, M.K., Williamson, J., A Mott, J., A Katz, M., Erdman, D.D., Schneider, E., Oberste, M.S., and Neatherlin, J.C. (2015). Severe acute respiratory infection in children in a densely populated urban slum in Kenya, 2007\u20132011. BMC Infect. Dis., 15.","DOI":"10.1186\/s12879-015-0827-x"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1111\/irv.12360","article-title":"Surveillance for severe acute respiratory infections in S outhern A rizona, 2010\u20132014","volume":"10","author":"Wansaula","year":"2016","journal-title":"Influ. Other Respir. Viruses"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/s40248-019-0174-7","article-title":"Clinical characteristics and outcomes of patients with severe acute respiratory infections (SARI): Results from the Egyptian surveillance study 2010\u20132014","volume":"14","author":"Hatem","year":"2019","journal-title":"Multidiscip. Respir. Med."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Wishaupt, J.O., Van Der Ploeg, T., De Groot, R., Versteegh, F.G.A., and Hartwig, N.G. (2017). Single- and multiple viral respiratory infections in children: Disease and management cannot be related to a specific pathogen. BMC Infect. Dis., 17.","DOI":"10.1186\/s12879-016-2118-6"},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Lei, C., Yang, L., Lou, C.T., Yang, F., SiTou, K.I., Hu, H., Io, K., Cheok, K.T., Pan, B., and Ung, C.O.L. (2021). Viral etiology and epidemiology of pediatric patients hospitalized for acute respiratory tract infections in Macao: A retrospective study from 2014 to 2017. BMC Infect. Dis., 21.","DOI":"10.1186\/s12879-021-05996-x"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"e000887","DOI":"10.1136\/bmjresp-2021-000887","article-title":"Aetiology of acute respiratory infection in preschool children requiring hospitalisation in Europe\u2014results from the PED-MERMAIDS multicentre case\u2013control study","volume":"8","author":"Vasconcelos","year":"2021","journal-title":"BMJ Open Respir. Res."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1016\/j.ijid.2021.04.066","article-title":"Performance evaluation of the QIAstat-Dx\u00ae Respiratory SARS-CoV-2 Panel","volume":"107","author":"Lebourgeois","year":"2021","journal-title":"Int. J. Infect. Dis."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"902","DOI":"10.1016\/j.jmii.2019.08.013","article-title":"Viral etiologies of acute respiratory tract infections among hospitalized children\u2013A comparison between single and multiple viral infections","volume":"52","author":"Yen","year":"2019","journal-title":"J. Microbiol. Immunol. Infect."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"106054","DOI":"10.1016\/j.ijantimicag.2020.106054","article-title":"Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2): A global pandemic and treatment strategies","volume":"56","author":"Sharma","year":"2020","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_46","first-page":"5807056","article-title":"Comparison of Different Waves during the COVID-19 Pandemic: Retrospective Descriptive Study in Thailand","volume":"8","author":"Kunno","year":"2021","journal-title":"Adv. Prev. Med."},{"key":"ref_47","first-page":"e2021082","article-title":"The profiles of first and second SARS-CoV-2 waves in the top ten COVID-19 affected countries","volume":"5","author":"Malhotra","year":"2021","journal-title":"J. Glob. Health Rep."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"742","DOI":"10.1016\/j.ijid.2021.02.004","article-title":"Comparison of the second and third waves of the COVID-19 pandemic in South Korea: Importance of early public health intervention","volume":"104","author":"Seong","year":"2021","journal-title":"Int. J. Infect. Dis."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"o7","DOI":"10.1136\/bmj.o7","article-title":"Omicron: South Africa says fourth wave peak has passed as it lifts curfew","volume":"376","author":"Mahase","year":"2022","journal-title":"BMJ"},{"key":"ref_50","first-page":"1","article-title":"Acute respiratory infections in children during Coronavirus Disease 2019: Without reverse transcriptase-polymerase chain reaction test and with risk of over-prescription of antibiotics, the perfect storm","volume":"5","author":"Turabian","year":"2020","journal-title":"Pediatr. Infect. Dis."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"2001600","DOI":"10.2807\/1560-7917.ES.2021.26.29.2001600","article-title":"Decline of influenza and respiratory syncytial virus detection in facility-based surveillance during the COVID-19 pandemic, South Africa, January to October 2020","volume":"26","author":"Tempia","year":"2021","journal-title":"Eurosurveillance"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1111\/irv.12854","article-title":"Increased risk of rhinovirus infection in children during the coronavirus disease-19 pandemic","volume":"15","author":"Takashita","year":"2021","journal-title":"Influenza Other Respir. Viruses"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1111\/irv.12894","article-title":"Impact of coronavirus disease 2019 on respiratory surveillance and explanation of high detection rate of human rhinovirus during the pandemic in the Republic of Korea","volume":"15","author":"Kim","year":"2021","journal-title":"Influ. Other Respir. Viruses"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"6063","DOI":"10.1002\/jmv.27180","article-title":"Rhinovirus spread in children during the COVID-19 pandemic despite social restrictions\u2014A nationwide register study in Finland","volume":"93","author":"Kuitunen","year":"2021","journal-title":"J. Med. Virol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1002\/jmv.23222","article-title":"Single treatment with ethanol hand rub is ineffective against human rhinovirus-hand washing with soap and water removes the virus efficiently","volume":"84","author":"Korpela","year":"2012","journal-title":"J. Med. Virol."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"1606","DOI":"10.1002\/jmv.20956","article-title":"Environmental contamination with rhinovirus and transfer to fingers of healthy individuals by daily life activity","volume":"79","author":"Winther","year":"2007","journal-title":"J. Med. Virol."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"2199","DOI":"10.1093\/cid\/ciaa1475","article-title":"Impact of Coronavirus Disease 2019 Public Health Measures on Detections of Influenza and Respiratory Syncytial Virus in Children During the 2020 Australian Winter","volume":"72","author":"Yeoh","year":"2021","journal-title":"Clin. Infect. Dis."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"1305","DOI":"10.15585\/mmwr.mm6937a6","article-title":"Decreased Influenza Activity During the COVID-19 Pandemic\u2013United States, Australia, Chile, and South Africa, 2020","volume":"69","author":"Olsen","year":"2020","journal-title":"MMWR Morb. Mortal. Wkly. Rep."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"1969","DOI":"10.1001\/jama.2020.6173","article-title":"Seasonal Influenza Activity During the SARS-CoV-2 Outbreak in Japan","volume":"323","author":"Sakamoto","year":"2020","journal-title":"JAMA-J. Am. Med. Assoc."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"810","DOI":"10.3389\/fped.2021.721005","article-title":"Disappearance of Seasonal Respiratory Viruses in Children Under Two Years Old During COVID-19 Pandemic: A Monocentric Retrospective Study in Milan, Italy","volume":"9","author":"Ippolito","year":"2021","journal-title":"Front. Pediatr."},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Biggerstaff, M., Cauchemez, S., Reed, C., Gambhir, M., and Finelli, L. (2014). Estimates of the reproduction number for seasonal, pandemic, and zoonotic influenza: A systematic review of the literature. BMC Infect. Dis., 14.","DOI":"10.1186\/1471-2334-14-480"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/S0025-5564(01)00066-9","article-title":"Modeling epidemics caused by respiratory syncytial virus (RSV)","volume":"172","author":"Weber","year":"2001","journal-title":"Math. Biosci."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"27142","DOI":"10.1073\/pnas.1911083116","article-title":"Virus\u2013virus interactions impact the population dynamics of influenza and the common cold","volume":"116","author":"Nickbakhsh","year":"2019","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"e254","DOI":"10.1016\/S2666-5247(20)30114-2","article-title":"Interference between rhinovirus and influenza A virus: A clinical data analysis and experimental infection study","volume":"1","author":"Wu","year":"2020","journal-title":"Lancet Microbe"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1093\/jpids\/piaa097","article-title":"Burden of illness in households with SARS-CoV-2 infected children","volume":"9","author":"Teherani","year":"2020","journal-title":"J. Pediatr. Infect. Dis. Soc."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"011101","DOI":"10.7189\/jogh.10.011101","article-title":"The role of children in transmission of SARS-CoV-2: A rapid review","volume":"10","author":"Li","year":"2020","journal-title":"J. Glob. Health"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"1607","DOI":"10.1007\/s10096-016-2698-5","article-title":"The use of multiplex PCR for the diagnosis of viral severe acute respiratory infection in children: A high rate of co-detection during the winter season","volume":"35","author":"Mostafa","year":"2016","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref_68","doi-asserted-by":"crossref","unstructured":"Visseaux, B., Collin, G., Ichou, H., Charpentier, C., Bendhafer, S., Dumitrescu, M., Allal, L., Cojocaru, B., Desfr\u00e8re, L., and Descamps, D. (2017). Usefulness of multiplex PCR methods and respiratory viruses\u2019 distribution in children below 15 years old according to age, seasons and clinical units in France: A 3 years retrospective study. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0172809"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1016\/j.arbr.2014.11.020","article-title":"Viral Coinfection in Childhood Respiratory Tract Infections","volume":"51","year":"2015","journal-title":"Arch. Bronconeumol."},{"key":"ref_70","doi-asserted-by":"crossref","unstructured":"Asner, S.A., Science, M.E., Tran, D., Smieja, M., Merglen, A., and Mertz, D. (2014). Clinical Disease Severity of Respiratory Viral Co-Infection versus Single Viral Infection: A Systematic Review and Meta-Analysis. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0099392"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1016\/j.jcv.2010.05.007","article-title":"Correlation of viral load of respiratory pathogens and co-infections with disease severity in children hospitalized for lower respiratory tract infection","volume":"48","author":"Franz","year":"2010","journal-title":"J. Clin. Virol."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1111\/j.1750-2659.2011.00265.x","article-title":"Multiple versus single virus respiratory infections: Viral load and clinical disease severity in hospitalized children","volume":"6","author":"Martin","year":"2012","journal-title":"Influ. Other Respir. Viruses"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1017\/S0950268814000302","article-title":"Single, dual and multiple respiratory virus infections and risk of hospitalization and mortality","volume":"143","author":"Goka","year":"2015","journal-title":"Epidemiol. Infect."},{"key":"ref_74","first-page":"363","article-title":"Single and multiple respiratory virus infections and severity of respiratory disease: A systematic review","volume":"15","author":"Goka","year":"2014","journal-title":"Paediatr. Respir. Rev."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/j.jcv.2016.04.019","article-title":"Respiratory viral coinfection and disease severity in children: A systematic review and meta-analysis","volume":"80","author":"Scotta","year":"2016","journal-title":"J. Clin. Virol."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"648","DOI":"10.1111\/resp.12741","article-title":"Systematic review and meta-analysis of respiratory viral coinfections in children","volume":"21","author":"Lim","year":"2016","journal-title":"Respirology"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"e0255941","DOI":"10.1371\/journal.pone.0255941","article-title":"Mortality in children aged <5 years with severe acute respiratory illness in a high HIV-prevalence urban and rural areas of South Africa, 2009\u20132013","volume":"16","author":"Ayeni","year":"2021","journal-title":"PLoS ONE"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1067\/mpd.2000.105350","article-title":"Increased burden of respiratory viral associated severe lower respiratory tract infections in children infected with human immunodeficiency virus type-1","volume":"137","author":"Madhi","year":"2000","journal-title":"J. Pediatr."},{"key":"ref_79","doi-asserted-by":"crossref","unstructured":"Tazinya, A.A., Halle-Ekane, G.E., Mbuagbaw, L.T., Abanda, M., Atashili, J., and Obama, M.T. (2018). Risk factors for acute respiratory infections in children under five years attending the Bamenda Regional Hospital in Cameroon. BMC Pulm. Med., 18.","DOI":"10.1186\/s12890-018-0579-7"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1186\/s41479-016-0021-y","article-title":"Tuberculosis and pneumonia in HIV-infected children: An overview","volume":"8","author":"Rabie","year":"2016","journal-title":"Pneumonia"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"S217","DOI":"10.1093\/infdis\/jit479","article-title":"Epidemiology of Respiratory Syncytial Virus-Associated Acute Lower Respiratory Tract Infection Hospitalizations Among HIV-Infected and HIV-Uninfected South African Children, 2010\u20132011","volume":"208","author":"Moyes","year":"2013","journal-title":"J. Infect. Dis."},{"key":"ref_82","doi-asserted-by":"crossref","unstructured":"Famoroti, T., Sibanda, W., and Ndung, T. (2018). Prevalence and seasonality of common viral respiratory pathogens, including Cytomegalovirus in children, between 0\u20135 years of age in KwaZulu-Natal, an HIV endemic province in South Africa. BMC Pediatr., 18.","DOI":"10.1186\/s12887-018-1222-8"},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1097\/INF.0000000000000478","article-title":"Epidemiology of Viral-associated Acute Lower Respiratory Tract Infection among Children <5 Years of Age in a High HIV Prevalence Setting, South Africa, 2009\u20132012","volume":"34","author":"Cohen","year":"2015","journal-title":"Pediatr. Infect. Dis. J."},{"key":"ref_84","first-page":"154","article-title":"Association between HIV and proven viral lower respiratory tract infection in paediatric intensive care unit patients at Inkosi Albert Luthuli Central Hospital, Durban, South Africa","volume":"11","author":"Majozi","year":"2017","journal-title":"S. Afr. J. Child Health"},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"181","DOI":"10.3389\/fcimb.2020.00181","article-title":"Current and future point-of-care tests for emerging and new respiratory viruses and future perspectives","volume":"10","author":"Nelson","year":"2020","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1038\/s41579-020-00461-z","article-title":"Considerations for diagnostic COVID-19 tests","volume":"19","author":"Vandenberg","year":"2021","journal-title":"Nat. Rev. Microbiol."}],"container-title":["International Journal of Environmental Research and Public Health"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1660-4601\/19\/16\/10418\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T00:13:12Z","timestamp":1760141592000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1660-4601\/19\/16\/10418"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,8,21]]},"references-count":86,"journal-issue":{"issue":"16","published-online":{"date-parts":[[2022,8]]}},"alternative-id":["ijerph191610418"],"URL":"https:\/\/doi.org\/10.3390\/ijerph191610418","relation":{},"ISSN":["1660-4601"],"issn-type":[{"value":"1660-4601","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,8,21]]}}}