Abstract
Low-pathogenic human coronaviruses (HCoVs) infect the upper respiratory tract and cause mild, cold-like respiratory illness. Although several studies have shown evidence of the global distribution of HCoVs, information about their distribution in Italy are often focused only on hospitalized children and elderly with respiratory symptoms. In this study, a total of 916 swab samples collected during the first two SARS-CoV-2 pandemic waves in Abruzzo region (central Italy) was selected for molecular screening of low pathogenic HCoVs by real-time RT-PCR. We identified low-pathogenic HCoV in nine samples. Positive samples underwent whole genome sequencing for genome characterization; indeed, we also report the whole genome sequence of a HCoV-229E strain.
References
Brian, D. A., & Baric, R. S. (2005). Coronavirus genome structure and replication. Current topics in microbiology and immunology, 287, 1–30. https://doi.org/10.1007/3-540-26765-4_1.
Chen, Y., Liu, Q., & Guo, D. (2020). Emerging coronaviruses: Genome structure, replication, and pathogenesis. Journal of medical virology, 92(10), 2249. https://doi.org/10.1002/jmv.26234.
Ciotti, M., Maurici, M., Santoro, V., Coppola, L., Sarmati, L., De Carolis, G., De Filippis, P., & Pica, F. (2020). Viruses of Respiratory Tract: an Observational Retrospective Study on Hospitalized Patients in Rome, Italy. Microorganisms, 8(4), 501. https://doi.org/10.3390/microorganisms8040501.
Corman, V. M., Muth, D., Niemeyer, D., & Drosten, C. (2018). Hosts and Sources of Endemic Human Coronaviruses. Advances in virus research, 100, 163–188. https://doi.org/10.1016/bs.aivir.2018.01.001.
Curini, V., Ancora, M., Jurisic, L., Di Lollo, V., Secondini, B., Mincarelli, L. F., Caporale, M., Puglia, I., Di Gialleonardo, L., Mangone, I., Di Domenico, M., Di Pasquale, A., Lorusso, A., Marcacci, M., & Cammà, C. (2023). Evaluation of next generation sequencing approaches for SARS-CoV-2. Heliyon, 9(11), e21101. https://doi.org/10.1016/j.heliyon.2023.e21101.
Decaro, N., & Lorusso, A. (2020). Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses. Veterinary microbiology, 244, 108693. https://doi.org/10.1016/j.vetmic.2020.108693.
De Conto, F., Conversano, F., Medici, M. C., Ferraglia, F., Pinardi, F., Arcangeletti, M. C., Chezzi, C., & Calderaro, A. (2019). Epidemiology of human respiratory viruses in children with acute respiratory tract infection in a 3-year hospital-based survey in Northern Italy. Diagnostic microbiology and infectious disease, 94(3), 260–267. https://doi.org/10.1016/j.diagmicrobio.2019.01.008.
Farsani, S. M., Dijkman, R., Jebbink, M. F., Goossens, H., Ieven, M., Deijs, M., Molenkamp, R., & van der Hoek, L. (2012). The first complete genome sequences of clinical isolates of human coronavirus 229E. Virus genes, 45(3), 433–439. https://doi.org/10.1007/s11262-012-0807-9.
Gagneur, A., Vallet, S., Talbot, P. J., Legrand-Quillien, M. C., Picard, B., Payan, C., & Sizun, J. (2008). Outbreaks of human coronavirus in a pediatric and neonatal intensive care unit. European journal of pediatrics, 167(12), 1427–1434. https://doi.org/10.1007/s00431-008-0687-0.
Gaunt, E. R., Hardie, A., Claas, E. C., Simmonds, P., & Templeton, K. E. (2010). Epidemiology and clinical presentations of the four human coronaviruses 229E, HKU1, NL63, and OC43 detected over 3 years using a novel multiplex real-time PCR method. Journal of clinical microbiology, 48(8), 2940–2947. https://doi.org/10.1128/JCM.00636-10.
Hamre, D., & Procknow, J. J. (1966). A new virus isolated from the human respiratory tract. Proceedings of the Society for Experimental Biology and Medicine. Society for Experimental Biology and Medicine (New York, N.Y.), 121(1), 190–193. https://doi.org/10.3181/00379727-121-30734.
Hand, J., Rose, E. B., Salinas, A., Lu, X., Sakthivel, S. K., Schneider, E., & Watson, J. T. (2018). Severe Respiratory Illness Outbreak Associated with Human Coronavirus NL63 in a Long-Term Care Facility. Emerging infectious diseases, 24(10), 1964–1966. https://doi.org/10.3201/eid2410.180862.
Lorusso, A., Calistri, P., Mercante, M. T., Monaco, F., Portanti, O., Marcacci, M., Cammà, C., Rinaldi, A., Mangone, I., Di Pasquale, A., Iommarini, M., Mattucci, M., Fazii, P., Tarquini, P., Mariani, R., Grimaldi, A., Morelli, D., Migliorati, G., Savini, G., Borrello, S., … D'Alterio, N. (2020). A "One-Health" approach for diagnosis and molecular characterization of SARS-CoV-2 in Italy. One health (Amsterdam, Netherlands), 10, 100135. https://doi.org/10.1016/j.onehlt.2020.100135.
Lednicky, J. A., Tagliamonte, M. S., White, S. K., Elbadry, M. A., Alam, M. M., Stephenson, C. J., Bonny, T. S., Loeb, J. C., Telisma, T., Chavannes, S., Ostrov, D. A., Mavian, C., Beau De Rochars, V. M., Salemi, M., & Morris, J. G., Jr (2021). Independent infections of porcine deltacoronavirus among Haitian children. Nature, 600(7887), 133–137. https://doi.org/10.1038/s41586-021-04111-z.
Minosse, C., Selleri, M., Zaniratti, M. S., Cappiello, G., Longo, R., Schifano, E., Spanò, A., Petrosillo, N., Lauria, F. N., Puro, V., & Capobianchi, M. R. (2008). Frequency of detection of respiratory viruses in the lower respiratory tract of hospitalized adults. Journal of clinical virology: the official publication of the Pan American Society for Clinical Virology, 42(2), 215–220. https://doi.org/10.1016/j.jcv.2008.01.012.
Niu, P., Shen, J., Zhu, N., Lu, R., & Tan, W. (2016). Two-tube multiplex real-time reverse transcription PCR to detect six human coronaviruses. Virologica Sinica, 31(1), 85–88. https://doi.org/10.1007/s12250-015-3653-9.
Paules, C. I., Marston, H. D., & Fauci, A. S. (2020). Coronavirus Infections-More Than Just the Common Cold. JAMA, 323(8), 707–708. https://doi.org/10.1001/jama.2020.0757.
Raoult, D., Zumla, A., Locatelli, F., Ippolito, G., & Kroemer, G. (2020). Coronavirus infections: Epidemiological, clinical and immunological features and hypotheses. Cell stress, 4(4), 66–75. https://doi.org/10.15698/cst2020.04.216.
Su, S., Wong, G., Shi, W., Liu, J., Lai, A. C. K., Zhou, J., Liu, W., Bi, Y., & Gao, G. F. (2016). Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses. Trends in microbiology, 24(6), 490–502. https://doi.org/10.1016/j.tim.2016.03.003.
Theamboonlers, A., Samransamruajkit, R., Thongme, C., Amonsin, A., Chongsrisawat, V., & Poovorawan, Y. (2007). Human coronavirus infection among children with acute lower respiratory tract infection in Thailand. Intervirology, 50(2), 71–77. https://doi.org/10.1159/000097392.
van der Hoek, L., Pyrc, K., Jebbink, M. F., Vermeulen-Oost, W., Berkhout, R. J., Wolthers, K. C., Wertheim-van Dillen, P. M., Kaandorp, J., Spaargaren, J., & Berkhout, B. (2004). Identification of a new human coronavirus. Nature medicine, 10(4), 368–373. https://doi.org/10.1038/nm1024.
Vlasova, A. N., Diaz, A., Damtie, D., Xiu, L., Toh, T. H., Lee, J. S., Saif, L. J., & Gray, G. C. (2022). Novel Canine Coronavirus Isolated from a Hospitalized Patient With Pneumonia in East Malaysia. Clinical infectious diseases: an official publication of the Infectious Diseases Society of America, 74(3), 446–454. https://doi.org/10.1093/cid/ciab456.
Wells, H. L., Bonavita, C. M., Navarrete-Macias, I., Vilchez, B., Rasmussen, A. L., & Anthony, S. J. (2023). The coronavirus recombination pathway. Cell host & microbe, 31(6), 874–889. https://doi.org/10.1016/j.chom.2023.05.003.
Woo, P. C., Lau, S. K., Chu, C. M., Chan, K. H., Tsoi, H. W., Huang, Y., Wong, B. H., Poon, R. W., Cai, J. J., Luk, W. K., Poon, L. L., Wong, S. S., Guan, Y., Peiris, J. S., & Yuen, K. Y. (2005). Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia. Journal of virology, 79(2), 884–895. https://doi.org/10.1128/JVI.79.2.884-895.2005.
Woo, P. C. Y., de Groot, R. J., Haagmans, B., Lau, S. K. P., Neuman, B. W., Perlman, S., Sola, I., van der Hoek, L., Wong, A. C. P., & Yeh, S. H. (2023). ICTV Virus Taxonomy Profile: Coronaviridae 2023. The Journal of general virology, 104(4), 10.1099/jgv.0.001843. https://doi.org/10.1099/jgv.0.001843.
Zhou, W., Wang, W., Wang, H., Lu, R., & Tan, W. (2013). First infection by all four non-severe acute respiratory syndrome human coronaviruses takes place during childhood. BMC infectious diseases, 13, 433. https://doi.org/10.1186/1471-2334-13-433.