From North to South: transmission dynamics of H1N1pdm09 swine influenza A viruses in Italy

References

1. Tosta S, Moreno K, Schuab G, Fonseca V, Segovia FMC et al. Global SARS-CoV-2 genomic surveillance: What we have learned (so far). Infect Genet Evol 2023; 108:105405 [View Article] [PubMed]
   [Google Scholar]
2. Neumann G, Noda T, Kawaoka Y. Emergence and pandemic potential of swine-origin H1N1 influenza virus. Nature 2009; 459:931–939 [View Article] [PubMed]
   [Google Scholar]
3. Mena I, Nelson MI, Quezada-Monroy F, Dutta J, Cortes-Fernández R et al. Origins of the 2009 H1N1 influenza pandemic in swine in Mexico. Elife 2016; 5:e16777 [View Article] [PubMed]
   [Google Scholar]
4. Meng F, Yang H, Qu Z, Chen Y, Zhang Y et al. A Eurasian avian-like H1N1 swine influenza reassortant virus became pathogenic and highly transmissible due to mutations in its PA gene. Proc Natl Acad Sci USA 2022; 119:e2203919119 [View Article] [PubMed]
   [Google Scholar]
5. Chiapponi C, Prosperi A, Moreno A, Baioni L, Faccini S et al. Genetic variability among swine influenza viruses in Italy: data analysis of the period 2017–2020. Viruses 2021; 14:47 [View Article] [PubMed]
   [Google Scholar]
6. Samanlioglu F, Bilge AH. An overview of the 2009 A(H1N1) pandemic in Europe: efficiency of the vaccination and healthcare strategies. J Healthc Eng 2016; 2016:5965836 [View Article] [PubMed]
   [Google Scholar]
7. Smith GJD, Vijaykrishna D, Bahl J, Lycett SJ, Worobey M et al. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature 2009; 459:1122–1125 [View Article] [PubMed]
   [Google Scholar]
8. Moreno A, Di Trani L, Alborali L, Vaccari G, Barbieri I et al. First pandemic H1N1 outbreak from a pig farm in Italy. Open Virol J 2010; 4:52–56 [View Article] [PubMed]
   [Google Scholar]
9. Rovida F, Piralla A, Marzani FC, Moreno A, Campanini G et al. Swine influenza A (H1N1) virus (SIV) infection requiring extracorporeal life support in an immunocompetent adult patient with indirect exposure to pigs, Italy, October 2016. Euro Surveill 2017; 22:30456 [View Article] [PubMed]
   [Google Scholar]
10. Chiapponi C, Prosperi A, Moreno A, Baioni L, Faccini S et al. Genetic variability among swine influenza viruses in Italy: data analysis of the period 2017-2020. Viruses 2021; 14:47 [View Article] [PubMed]
    [Google Scholar]
11. Lycett SJ, Baillie G, Coulter E, Bhatt S, Kellam P et al. For the combating swine influenza initiative Cosi consortium. estimating reassortment rates in co-circulating Eurasian swine influenza viruses. J Gen Virol 2012; 93:2326–2336 2012 Sep 12 [View Article] [PubMed]
    [Google Scholar]
12. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
    [Google Scholar]
13. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp Ser 1999; 41:95–98
    [Google Scholar]
14. Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002; 30:3059–3066 [View Article] [PubMed]
    [Google Scholar]
15. Larsson A. AliView: a fast and lightweight alignment viewer and editor for large datasets. Bioinformatics 2014; 30:3276–3278 [View Article] [PubMed]
    [Google Scholar]
16. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 2020; 37:1530–1534 [View Article] [PubMed]
    [Google Scholar]
17. Suchard MA, Lemey P, Baele G, Ayres DL, Drummond AJ et al. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol 2018; 4:vey016 [View Article] [PubMed]
    [Google Scholar]
18. Hill V, Baele G. Bayesian estimation of past population dynamics in BEAST 1.10 using the skygrid coalescent model. Mol Biol Evol 2019; 36:2620–2628 [View Article] [PubMed]
    [Google Scholar]
19. Lemey P, Rambaut A, Bedford T, Faria N, Bielejec F et al. Unifying viral genetics and human transportation data to predict the global transmission dynamics of human influenza H3N2. PLOS Pathogens 2014 [View Article]
    [Google Scholar]
20. Yu G, Smith D, Zhu H, Guan Y, Lam TT. Ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol 2017; 8:28–36 [View Article]
    [Google Scholar]
21. Wickham H. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York; 2016 https://ggplot2.tidyverse.org
22. Ragonnet-Cronin M, Hodcroft E, Hué S, Fearnhill E, Delpech V et al. Automated analysis of phylogenetic clusters. BMC Bioinformatics 2013; 14:317 [View Article] [PubMed]
    [Google Scholar]
23. Kosakovsky Pond SL, Frost SDW. Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol 2005; 22:1208–1222 [View Article] [PubMed]
    [Google Scholar]
24. Pond SLK, Frost SDW, Muse SV. HyPhy: hypothesis testing using phylogenies. Bioinformatics 2005; 21:676–679 [View Article] [PubMed]
    [Google Scholar]
25. Murrell B, Wertheim JO, Moola S, Weighill T, Scheffler K et al. Detecting individual sites subject to episodic diversifying selection. PLoS Genet 2012; 8:e1002764 [View Article] [PubMed]
    [Google Scholar]
26. Weaver S, Shank SD, Spielman SJ, Li M, Muse SV et al. Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes. Mol Biol Evol 2018; 35:773–777 [View Article] [PubMed]
    [Google Scholar]
27. Henritzi D, Petric PP, Lewis NS, Graaf A, Pessia A et al. Surveillance of European domestic pig populations identifies an emerging reservoir of potentially zoonotic swine influenza A viruses. Cell Host Microbe 2020; 28:614–627 [View Article] [PubMed]
    [Google Scholar]
28. Sistema Informativo Veterinario Consistenza allevamenti suini; 2024 https://www.vetinfo.it/j6_statistiche/#/report-pbi/31
29. Anderson TK, Chang J, Arendsee ZW, Venkatesh D, Souza CK et al. Swine influenza A viruses and the tangled relationship with humans. Cold Spring Harb Perspect Med 2021; 11:a038737 [View Article] [PubMed]
    [Google Scholar]
30. Bonazzi G, Camanzi P, Ferri G, Manghi E, Iotti M. Economic sustainability of pig slaughtering firms in the production chain of denomination of origin hams in Italy. Sustainability 2021; 13:7639 [View Article]
    [Google Scholar]
31. Markin A, Ciacci Zanella G, Arendsee ZW, Zhang J, Krueger KM et al. Reverse-zoonoses of 2009 H1N1 pandemic influenza A viruses and evolution in United States swine results in viruses with zoonotic potential. PLoS Pathog 2023; 19:e1011476 [View Article] [PubMed]
    [Google Scholar]
32. Jones BA, Grace D, Kock R, Alonso S, Rushton J et al. Zoonosis emergence linked to agricultural intensification and environmental change. Proc Natl Acad Sci USA 2013; 110:8399–8404 [View Article] [PubMed]
    [Google Scholar]
33. European Union Veterinary Medicine. n.d https://medicines.health.europa.eu/veterinary/en/600000000229 accessed 13 October 2024
34. Ghai RR, Wallace RM, Kile JC, Shoemaker TR, Vieira AR et al. A generalizable one health framework for the control of zoonotic diseases. Sci Rep 2022; 12:8588 [View Article] [PubMed]
    [Google Scholar]