Co-existence and co-infection of influenza A viruses and coronaviruses: Public health challenges

Taubenberger, 1997, Initial genetic characterization of the 1918 "Spanish" influenza virus, Science, 275, 1793, 10.1126/science.275.5307.1793 Kilbourne, 2006, Influenza pandemics of the 20th century, Emerg. Infect. Dis., 12, 9, 10.3201/eid1201.051254 Gao, 2018, From "A"IV to "Z"IKV: attacks from emerging and re-emerging pathogens, Cell, 172, 1157, 10.1016/j.cell.2018.02.025 Yang, 2020, Uncovering two phases of early intercontinental COVID-19 transmission dynamics, J. Travel. Med., 27, taaa200, 10.1093/jtm/taaa200 Dai, 2020, A universal design of betacoronavirus vaccines against COVID-19, MERS, and SARS, Cell, 182, 722, 10.1016/j.cell.2020.06.035 Taylor, 2021, Neutralizing monoclonal antibodies for treatment of COVID-19, Nat. Rev. Immunol., 21, 382, 10.1038/s41577-021-00542-x Ma, 2022, Omicron XE emerges as SARS-CoV-2 keeps evolving, Innovation, 3, 100248 Su, 2016, Epidemiology, genetic recombination, and pathogenesis of coronaviruses, Trends Microbiol., 24, 490, 10.1016/j.tim.2016.03.003 Peiris, 2003, Coronavirus as a possible cause of severe acute respiratory syndrome, Lancet, 361, 1319, 10.1016/S0140-6736(03)13077-2 Raj, 2014, MERS: emergence of a novel human coronavirus, Curr. Opin. Virol., 5, 58, 10.1016/j.coviro.2014.01.010 Sabir, 2016, Co-circulation of three camel coronavirus species and recombination of MERS-CoVs in Saudi Arabia, Science, 351, 81, 10.1126/science.aac8608 Zhou, 2020, A pneumonia outbreak associated with a new coronavirus of probable bat origin, Nature, 579, 270, 10.1038/s41586-020-2012-7 Lam, 2020, Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins, Nature, 583, 282, 10.1038/s41586-020-2169-0 Shi, 2020, Susceptibility of ferrets, cats, dogs, and other domesticated animals to SARS-coronavirus 2, Science, 368, 1016, 10.1126/science.abb7015 Wille, 2020, The ecology and evolution of influenza viruses, Cold. Spring. Harb. Perspect. Med., 10, a038489, 10.1101/cshperspect.a038489 Ozaras, 2020, Influenza and COVID-19 coinfection: report of six cases and review of the literature, J. Med. Virol., 92, 2657, 10.1002/jmv.26125 Xiang, 2021, Co-infection of SARS-CoV-2 and influenza A virus: a case series and fast review, Curr. Med. Sci., 41, 51, 10.1007/s11596-021-2317-2 Dadashi, 2021, COVID-19 and influenza co-infection: a systematic review and meta-analysis, Front. Med., 8, 681469, 10.3389/fmed.2021.681469 Wang, 2020, Structural and functional basis of SARS-CoV-2 entry by using human ACE2, Cell, 181, 894, 10.1016/j.cell.2020.03.045 Matrosovich, 2015, Sialic acid receptors of viruses, Top. Curr. Chem., 367, 1 Liu, 2021, SARS-CoV-2 cell tropism and multiorgan infection, Cell Discov., 7, 17, 10.1038/s41421-021-00249-2 Krauss, 2010, Avian influenza virus surveillance and wild birds: past and present, Avian Dis., 54, 394, 10.1637/8703-031609-Review.1 Liu, 2022, Emerging HxNy influenza A viruses, Cold. Spring. Harb. Perspect. Med., 12, a038406, 10.1101/cshperspect.a038406 Tong, 2012, A distinct lineage of influenza A virus from bats, Proc. Natl. Acad. Sci. USA, 109, 4269, 10.1073/pnas.1116200109 Tong, 2013, New world bats harbor diverse influenza A viruses, PLoS Pathog., 9, e1003657, 10.1371/journal.ppat.1003657 Li, 2021, Re-emergence of H5N8 highly pathogenic avian influenza virus in wild birds, China. Emerg. Microbes. Infect., 10, 1819, 10.1080/22221751.2021.1968317 Kwon, 2018, Comparison of the pathogenic potential of highly pathogenic avian influenza (HPAI) H5N6, and H5N8 viruses isolated in South Korea during the 2016-2017 winter season, Emerg. Microbes Infect., 7, 29, 10.1038/s41426-018-0029-x Kim, 2015, Pathologic changes in wild birds infected with highly pathogenic avian influenza A(H5N8) viruses, South Korea, 2014, Emerg. Infect. Dis., 21, 775, 10.3201/eid2105.141967 Kwon, 2020, Domestic ducks play a major role in the maintenance and spread of H5N8 highly pathogenic avian influenza viruses in South Korea, Transboundary Emerg. Dis., 67, 844, 10.1111/tbed.13406 Mine, 2019, Genetics and pathogenicity of H5N6 highly pathogenic avian influenza viruses isolated from wild birds and a chicken in Japan during winter 2017-2018, Virology, 533, 1, 10.1016/j.virol.2019.04.011 Bi, 2016, Highly pathogenic avian influenza H5N1 clade 2.3.2.1c virus in migratory birds, Virol. Sin., 31, 300, 10.1007/s12250-016-3750-4 Bi, 2016, Novel avian influenza A (H5N6) viruses isolated in migratory waterfowl before the first human case reported in China, 2014, Sci. Rep., 6, 29888, 10.1038/srep29888 Shi, 2021, Emerging H5N8 avian influenza viruses, Science, 372, 784, 10.1126/science.abg6302 Liu, 2005, Highly pathogenic H5N1 influenza virus infection in migratory birds, Science, 309, 1206, 10.1126/science.1115273 Chen, 2005, Avian flu: H5N1 virus outbreak in migratory waterfowl, Nature, 436, 191, 10.1038/nature03974 Petrova, 2018, The evolution of seasonal influenza viruses, Nat. Rev. Microbiol., 16, 47, 10.1038/nrmicro.2017.118 Bi, 2016, Genesis, evolution and prevalence of H5N6 avian influenza viruses in China, Cell Host Microbe, 20, 810, 10.1016/j.chom.2016.10.022 Bi, 2020, Dominant subtype switch in avian influenza viruses during 2016-2019 in China, Nat. Commun., 11, 5909, 10.1038/s41467-020-19671-3 Chen, 2016, First documented case of avian influenza (H5N1) virus infection in a lion, Emerg. Microbes. Infect., 5, e125, 10.1038/emi.2016.127 Liu, 2009, Panorama phylogenetic diversity and distribution of type A influenza virus, PLoS One, 4, e5022, 10.1371/journal.pone.0005022 L'vov, 1979, Isolation of strains of the Hong Kong complex (H3N2) influenza virus from Nyctalus noctula bats in Kazakhstan, Vopr. Virusol., 4, 338 Liu, 2009, Emergence of European avian influenza virus-like H1N1 swine influenza A viruses in China, J. Clin. Microbiol., 47, 2643, 10.1128/JCM.00262-09 Sun, 2020, Prevalent Eurasian avian-like H1N1 swine influenza virus with 2009 pandemic viral genes facilitating human infection, Proc. Natl. Acad. Sci. USA, 117, 17204, 10.1073/pnas.1921186117 Cui, 2019, Origin and evolution of pathogenic coronaviruses, Nat. Rev. Microbiol., 17, 181, 10.1038/s41579-018-0118-9 Woo, 2012, J. Virol., 86, 3995, 10.1128/JVI.06540-11 Zhou, 2020, A novel bat coronavirus closely related to SARS-CoV-2 contains natural insertions at the S1/S2 cleavage site of the spike protein, Curr. Biol., 30, 2196, 10.1016/j.cub.2020.05.023 Zhou, 2021, Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses, Cell, 184, 4380, 10.1016/j.cell.2021.06.008 Xiao, 2020, Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins, Nature, 583, 286, 10.1038/s41586-020-2313-x Mallapaty, 2021, Closest known relatives of virus behind COVID-19 found in Laos, Nature, 597, 603, 10.1038/d41586-021-02596-2 Oude Munnink, 2021, Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans, Science, 371, 172, 10.1126/science.abe5901 Wang, 2021, Assessing the extent of community spread caused by mink-derived SARS-CoV-2 variants, Innovation, 2, 100128 Kim, 2020, Infection and rapid transmission of SARS-CoV-2 in ferrets, Cell Host Microbe, 27, 704, 10.1016/j.chom.2020.03.023 Munster, 2020, Respiratory disease in rhesus macaques inoculated with SARS-CoV-2, Nature, 585, 268, 10.1038/s41586-020-2324-7 Rockx, 2020, Comparative pathogenesis of COVID-19, MERS, and SARS in a nonhuman primate model, Science, 368, 1012, 10.1126/science.abb7314 Cross, 2020, Intranasal exposure of African green monkeys to SARS-CoV-2 results in acute phase pneumonia with shedding and lung injury still present in the early convalescence phase, Virol. J., 17, 125, 10.1186/s12985-020-01396-w Wu, 2020, Broad host range of SARS-CoV-2 and the molecular basis for SARS-CoV-2 binding to cat ACE2, Cell Discov., 6, 68, 10.1038/s41421-020-00210-9 Lemey, 2014, Unifying viral genetics and human transportation data to predict the global transmission dynamics of human influenza H3N2, PLoS Pathog., 10, e1003932, 10.1371/journal.ppat.1003932 Chan, 2018, Frequent genetic mismatch between vaccine strains and circulating seasonal influenza viruses, Hong Kong, China, 1996-2012, Emerg. Infect. Dis., 24, 1825, 10.3201/eid2410.180652 Ferguson, 2003, Ecological and immunological determinants of influenza evolution, Nature, 422, 428, 10.1038/nature01509 Nelson, 2009, The early diversification of influenza A/H1N1pdm, PLoS Curr., 1, RRN1126, 10.1371/currents.RRN1126 Potter, 2019, Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017-2018 influenza season, Virus. Evol., 5, vez046, 10.1093/ve/vez046 Al-Qahtani, 2017, Phylogenetic and nucleotide sequence analysis of influenza A (H1N1) HA and NA genes of strains isolated from Saudi Arabia, J. Infect. Dev. Ctries., 11, 81, 10.3855/jidc.9259 Smith, 2015, World health organization/world organisation for animal health/food and agriculture organization (WHO/OIE/FAO) H5 evolution working group, Influenza. Other. Respir. Viruses., 9, 271, 10.1111/irv.12324 Yang, 2017, Genesis and spread of newly emerged highly pathogenic H7N9 avian viruses in mainland China, J. Virol., 91 Quan, 2018, New threats from H7N9 influenza virus: spread and evolution of high- and low-pathogenicity variants with high genomic diversity in wave five, J. Virol., 92, e00301, 10.1128/JVI.00301-18 Rambaut, 2020, A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology, Nat. Microbiol., 5, 1403, 10.1038/s41564-020-0770-5 Lythgoe, 2021, SARS-CoV-2 within-host diversity and transmission, Science, 372, eabg0821, 10.1126/science.abg0821 Grenfell, 2004, Unifying the epidemiological and evolutionary dynamics of pathogens, Science, 303, 327, 10.1126/science.1090727 Emary, 2021, Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 variant of concern 202012/01 (B.1.1.7): an exploratory analysis of a randomised controlled trial, Lancet, 397, 1351, 10.1016/S0140-6736(21)00628-0 Garcia-Beltran, 2021, Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity, Cell, 184, 2372, 10.1016/j.cell.2021.03.013 2020 Vasin, 2014, Molecular mechanisms enhancing the proteome of influenza A viruses: an overview of recently discovered proteins, Virus Res., 185, 53, 10.1016/j.virusres.2014.03.015 McDonald, 2016, Reassortment in segmented RNA viruses: mechanisms and outcomes, Nat. Rev. Microbiol., 14, 448, 10.1038/nrmicro.2016.46 Liu, 2013, Origin and diversity of novel avian influenza A H7N9 viruses causing human infection: phylogenetic, structural, and coalescent analyses, Lancet, 381, 1926, 10.1016/S0140-6736(13)60938-1 Lam, 2015, Dissemination, divergence and establishment of H7N9 influenza viruses in China, Nature, 522, 102, 10.1038/nature14348 Fehr, 2015, Coronaviruses: an overview of their replication and pathogenesis, Methods Mol. Biol., 1282, 1, 10.1007/978-1-4939-2438-7_1 Woo, 2009, Coronavirus diversity, phylogeny and interspecies jumping, Exp Biol Med (Maywood)., 234, 1117, 10.3181/0903-MR-94 Bentley, 2018, Mechanisms and consequences of positive-strand RNA virus recombination, J. Gen. Virol., 99, 1345, 10.1099/jgv.0.001142 Lau, 2006, Coronavirus HKU1 and other coronavirus infections in Hong Kong, J. Clin. Microbiol., 44, 2063, 10.1128/JCM.02614-05 Stanhope, 2004, Evidence from the evolutionary analysis of nucleotide sequences for a recombinant history of SARS-CoV, Infect. Genet. Evo., 4, 15, 10.1016/j.meegid.2003.10.001 Zhang, 2005, Testing the hypothesis of a recombinant origin of the SARS-associated coronavirus, Arch. Virol., 150, 1, 10.1007/s00705-004-0413-9 Hoffmann, 2020, A multibasic cleavage site in the spike protein of SARS-CoV-2 is essential for infection of human lung cells, Mol. Cell., 78, 779, 10.1016/j.molcel.2020.04.022 Johnson, 2021, Loss of furin cleavage site attenuates SARS-CoV-2 pathogenesis, Nature, 591, 293, 10.1038/s41586-021-03237-4 Kawaoka, 1988, Sequence requirements for cleavage activation of influenza virus hemagglutinin expressed in mammalian cells, Proc. Natl. Acad. Sci. U. S. A., 85, 324, 10.1073/pnas.85.2.324 Alexander, 2009, History of highly pathogenic avian influenza, Rev. Sci. Tech., 28, 19, 10.20506/rst.28.1.1856 Luczo, 2015, Molecular pathogenesis of H5 highly pathogenic avian influenza: the role of the haemagglutinin cleavage site motif, Rev. Med. Virol., 25, 406, 10.1002/rmv.1846 Zhang, 2012, A single amino acid at the hemagglutinin cleavage site contributes to the pathogenicity and neurovirulence of H5N1 influenza virus in mice, J. Virol., 86, 6924, 10.1128/JVI.07142-11 Andersen, 2020, The proximal origin of SARS-CoV-2, Nat. Med., 26, 450, 10.1038/s41591-020-0820-9 Wang, 2021, Characterization of an attenuated SARS-CoV-2 variant with a deletion at the S1/S2 junction of the spike protein, Nat. Commun., 12, 2790, 10.1038/s41467-021-23166-0 Lau, 2020, Attenuated SARS-CoV-2 variants with deletions at the S1/S2 junction, Emerg. Microbes Infect., 9, 837, 10.1080/22221751.2020.1756700 Peacock, 2021, The furin cleavage site in the SARS-CoV-2 spike protein is required for transmission in ferrets, Nat. Microbiol., 6, 899, 10.1038/s41564-021-00908-w Sorrell, 2011, Predicting 'airborne' influenza viruses: (trans-) mission impossible?, Curr. Opin. Virol., 1, 635, 10.1016/j.coviro.2011.07.003 Shinya, 2006, Avian flu: influenza virus receptors in the human airway, Nature, 440, 435, 10.1038/440435a Rajao, 2019, Adaptation of human influenza viruses to swine, Front. Vet. Sci., 5, 347, 10.3389/fvets.2018.00347 Shinya, 2006, Influenza virus receptors in the human airway, Nature, 440, 435, 10.1038/440435a Sriwilaijaroen, 2018, N-glycan structures of human alveoli provide insight into influenza A virus infection and pathogenesis, FEBS J., 285, 1611, 10.1111/febs.14431 van Riel, 2007, Human and avian influenza viruses target different cells in the lower respiratory tract of humans and other mammals, Am. J. Pathol., 171, 1215, 10.2353/ajpath.2007.070248 Li, 2007, The S proteins of human coronavirus NL63 and severe acute respiratory syndrome coronavirus bind overlapping regions of ACE2, Virology, 367, 367, 10.1016/j.virol.2007.04.035 Wrapp, 2020, Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation, Science, 367, 1260, 10.1126/science.abb2507 Tipnis, 2000, A human homolog of angiotensin-converting enzyme. Cloning and functional expression as a captopril-insensitive carboxypeptidase, J. Biol. Chem., 275, 33238, 10.1074/jbc.M002615200 Zhao, 2020, Single-cell RNA expression profiling of ACE2, the receptor of SARS-CoV-2, Am. J. Respir. Crit. Care Med., 202, 756, 10.1164/rccm.202001-0179LE Lukassen, 2020, SARS-CoV-2 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cells, EMBO J., 39, e105114, 10.15252/embj.2020105114 Barker, 2020, Bioinformatic characterization of angiotensin-converting enzyme 2, the entry receptor for SARS-CoV-2, PLoS One, 15, e0240647, 10.1371/journal.pone.0240647 Puelles, 2020, Multiorgan and renal tropism of SARS-CoV-2, N. Engl. J. Med., 383, 590, 10.1056/NEJMc2011400 Hou, 2020, SARS-CoV-2 reverse genetics reveals a variable infection gradient in the respiratory tract, Cell, 182, 429, 10.1016/j.cell.2020.05.042 Wang, 2021, Establishment of human distal lung organoids for SARS-CoV-2 infection, Cell Discov., 7, 108, 10.1038/s41421-021-00346-2 Hui, 2020, Tropism, replication competence, and innate immune responses of the coronavirus SARS-CoV-2 in human respiratory tract and conjunctiva: an analysis in ex-vivo and in-vitro cultures, Lancet Respir. Med., 8, 687, 10.1016/S2213-2600(20)30193-4 Bai, 2021, Coinfection with influenza A virus enhances SARS-CoV-2 infectivity, Cell Res., 31, 395, 10.1038/s41422-021-00473-1 Traylor, 2013, Influenza A H1N1 induces declines in alveolar gas exchange in mice consistent with rapid post-infection progression from acute lung injury to ARDS, Influenza. Other. Respir. Viruses., 7, 472, 10.1111/j.1750-2659.2012.00414.x Zhang, 2021, Coinfection by severe acute respiratory syndrome coronavirus 2 and influenza A(H1N1)pdm09 virus enhances the severity of pneumonia in golden syrian hamsters, Clin. Infect. Dis., 72, e978, 10.1093/cid/ciaa1747 Wang, 2020, Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China, JAMA, 323, 1061, 10.1001/jama.2020.1585 Huang, 2020, Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China, Lancet, 395, 497, 10.1016/S0140-6736(20)30183-5 Bi, 2019, Clinical and immunological characteristics of human infections with H5N6 avian influenza virus, Clin. Infect. Dis., 68, 1100, 10.1093/cid/ciy681 Guan, 2021, Impact of coinfection with SARS-CoV-2 and Influenza on disease severity: a systematic review and meta-analysis, Front. Public Health, 9, 773130, 10.3389/fpubh.2021.773130 Akhtar, 2021, SARS-CoV-2 and influenza virus coinfection among patients with severe acute respiratory infection during the first wave of COVID-19 pandemic in Bangladesh: a hospital-based descriptive study, BMJ Open, 11, e053768, 10.1136/bmjopen-2021-053768 Yue, 2020, The epidemiology and clinical characteristics of co-infection of SARS-CoV-2 and influenza viruses in patients during COVID-19 outbreak, J. Med. Virol., 92, 2870, 10.1002/jmv.26163 Swets, 2022, SARS-CoV-2 co-infection with influenza viruses, respiratory syncytial virus, or adenoviruses, Lancet, 399, 1463, 10.1016/S0140-6736(22)00383-X Olsen, 2021, Changes in influenza and other respiratory virus activity during the COVID-19 pandemic - United States, 2020-2021, MMWR Morb. Mortal. Wkly. Rep., 70, 1013, 10.15585/mmwr.mm7029a1 Zipfel, 2021, The missing season: the impacts of the COVID-19 pandemic on influenza, Vaccine, 39, 3645, 10.1016/j.vaccine.2021.05.049 Gomez, 2021, Uncertain effects of the pandemic on respiratory viruses, Science, 372, 1043, 10.1126/science.abh3986 Casalegno, 2010, Rhinoviruses delayed the circulation of the pandemic influenza A (H1N1) 2009 virus in France, Clin. Microbiol. Infect., 16, 326, 10.1111/j.1469-0691.2010.03167.x Nickbakhsh, 2019, Virus-virus interactions impact the population dynamics of influenza and the common cold, Proc. Natl. Acad. Sci. USA, 116, 27142, 10.1073/pnas.1911083116 Baker, 2020, The impact of COVID-19 nonpharmaceutical interventions on the future dynamics of endemic infections, Proc. Natl. Acad. Sci. USA, 117, 30547, 10.1073/pnas.2013182117 Rohani, 2003, Ecological interference between fatal diseases, Nature, 422, 885, 10.1038/nature01542 Rossman, 2021, COVID-19 dynamics after a national immunization program in Israel, Nat. Med., 27, 1055, 10.1038/s41591-021-01337-2 Chen, 2022, A live attenuated virus-based intranasal COVID-19 vaccine provides rapid, prolonged, and broad protection against SARS-CoV-2, Sci. Bull., 67, 1372, 10.1016/j.scib.2022.05.018