• Abdelwhab EM, Mettenleiter TC (2023) Zoonotic Animal Influenza Virus and Potential Mixing Vessel Hosts. Viruses 15:980.

  • Ali A, Kemter E, Wolf E (2024) Advances in Organ and Tissue Xenotransplantation. Annu Rev Anim Biosci 12:369-390.

  • Bray NL, Pimentel H, Melsted P, Pachter L (2016) Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol 34:525-527.

  • Charlier J, Barkema HW, Becher P, De Benedictis P, Hansson I, Hennig-Pauka I, La Ragione R, Larsen LE, Madoroba E, Maes D, Marin CM, Mutinelli F, Nisbet AJ, Podgorska K, Vercruysse J, Vitale F, Williams DJL, Zadoks RN (2022) Disease control tools to secure animal and public health in a densely populated world. Lancet Planet Health 6:e812-e824.

  • Chen S, Zhou Y, Chen Y, Gu J (2018) fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884-i890.

  • Debisarun PA, Gossling KL, Bulut O, Kilic G, Zoodsma M, Liu Z, Oldenburg M, Ruchel N, Zhang B, Xu CJ, Struycken P, Koeken V, Dominguez-Andres J, Moorlag S, Taks E, Ostermann PN, Muller L, Schaal H, Adams O, Borkhardt A, Ten Oever J, van Crevel R, Li Y, Netea MG (2021) Induction of trained immunity by influenza vaccination - impact on COVID-19. PLoS Pathog 17:e1009928.

  • Denner J (2017) The porcine virome and xenotransplantation. Virol J 14:171.

  • Griffith BP, Goerlich CE, Singh AK, Rothblatt M, Lau CL, Shah A, Lorber M, Grazioli A, Saharia KK, Hong SN, Joseph SM, Ayares D, Mohiuddin MM (2022) Genetically Modified Porcine-to-Human Cardiac Xenotransplantation. N Engl J Med 387:35-44.

  • Hasan MR, Rahman M, Khan T, Saeed A, Sundararaju S, Flores A, Hawken P, Rawat A, Elkum N, Hussain K, Tan R, Tang P, Marr N (2021) Virome-wide serological profiling reveals association of herpesviruses with obesity. Sci Rep 11:2562.

  • Hause BM, Padmanabhan A, Pedersen K, Gidlewski T (2016) Feral swine virome is dominated by single-stranded DNA viruses and contains a novel Orthopneumovirus which circulates both in feral and domestic swine. J Gen Virol 97:2090-2095.

  • Henritzi D, Petric PP, Lewis NS, Graaf A, Pessia A, Starick E, Breithaupt A, Strebelow G, Luttermann C, Parker LMK, Schroder C, Hammerschmidt B, Herrler G, Beilage EG, Stadlbauer D, Simon V, Krammer F, Wacheck S, Pesch S, Schwemmle M, Beer M, Harder TC (2020) Surveillance of European Domestic Pig Populations Identifies an Emerging Reservoir of Potentially Zoonotic Swine Influenza A Viruses. Cell Host Microbe 28:614-627.e616.

  • Hu ZM, Yang YL, Xu LD, Wang B, Qin P, Huang YW (2019) Porcine Torovirus (PToV)-A Brief Review of Etiology, Diagnostic Assays and Current Epidemiology. Front Vet Sci 6:120.

  • Isnard P, Kula T, Avettand Fenoel V, Anglicheau D, Terzi F, Legendre C, Elledge SJ, Canaud G (2019) Temporal virus serological profiling of kidney graft recipients using VirScan. Proc Natl Acad Sci U S A 116:10899-10904.

  • Jacobsen H, Klein SL (2021) Sex Differences in Immunity to Viral Infections. Front Immunol 12:720952.

  • Kamar N, Izopet J, Pavio N, Aggarwal R, Labrique A, Wedemeyer H, Dalton HR (2017) Hepatitis E virus infection. Nat Rev Dis Primers 3:17086.

  • Kechin A, Boyarskikh U, Kel A, Filipenko M (2017) cutPrimers: A New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing. J Comput Biol 24:1138-1143.

  • Kitikoon P, Vincent AL, Jones KR, Nilubol D, Yu S, Janke BH, Thacker BJ, Thacker EL (2009) Vaccine efficacy and immune response to swine influenza virus challenge in pigs infected with porcine reproductive and respiratory syndrome virus at the time of SIV vaccination. Vet Microbiol 139:235-244.

  • Kumar N, Sharma S, Barua S, Tripathi BN, Rouse BT (2018) Virological and Immunological Outcomes of Coinfections. Clin Microbiol Rev 31: e00111-e00117.

  • Kwok KTT, Nieuwenhuijse DF, Phan MVT, Koopmans MPG (2020) Virus Metagenomics in Farm Animals: A Systematic Review. Viruses 12:107.

  • Li P, Ji Y, Li Y, Ma Z, Pan Q (2022) Estimating the global prevalence of hepatitis E virus in swine and pork products. One Health 14:100362.

  • Liu J, Tang W, Budhu A, Forgues M, Hernandez MO, Candia J, Kim Y, Bowman ED, Ambs S, Zhao Y, Tran B, Wu X, Koh C, Surana P, Liang TJ, Guarnera M, Mann D, Rajaure M, Greten TF, Wang Z, Yu H, Wang XW (2020) A Viral Exposure Signature Defines Early Onset of Hepatocellular Carcinoma. Cell 182:317-328 e310.

  • Liu P, Li L, Wang L, Bu Q, Fu H, Han J, Zhu Y, Lu F, Zhuang H (2012) Phylogenetic analysis of 626 hepatitis E virus (HEV) isolates from humans and animals in China (1986-2011) showing genotype diversity and zoonotic transmission. Infect Genet Evol 12:428-434.

  • Long JS, Mistry B, Haslam SM, Barclay WS (2019) Host and viral determinants of influenza A virus species specificity. Nat Rev Microbiol 17:67-81.

  • McLean RK, Graham SP (2022) The pig as an amplifying host for new and emerging zoonotic viruses. One Health 14:100384.

  • Meng XJ (2013) Zoonotic and foodborne transmission of hepatitis E virus. Semin Liver Dis 33:41-49.

  • Mina MJ, Kula T, Leng Y, Li M, de Vries RD, Knip M, Siljander H, Rewers M, Choy DF, Wilson MS, Larman HB, Nelson AN, Griffin DE, de Swart RL, Elledge SJ (2019) Measles virus infection diminishes preexisting antibodies that offer protection from other pathogens. Science 366:599-606.

  • Moazami N, Stern JM, Khalil K, Kim JI, Narula N, Mangiola M, Weldon EP, Kagermazova L, James L, Lawson N, Piper GL, Sommer PM, Reyentovich A, Bamira D, Saraon T, Kadosh BS, DiVita M, Goldberg RI, Hussain ST, Chan J, Ngai J, Jan T, Ali NM, Tatapudi VS, Segev DL, Bisen S, Jaffe IS, Piegari B, Kowalski H, Kokkinaki M, Monahan J, Sorrells L, Burdorf L, Boeke JD, Pass H, Goparaju C, Keating B, Ayares D, Lorber M, Griesemer A, Mehta SA, Smith DE, Montgomery RA (2023) Pig-to-human heart xenotransplantation in two recently deceased human recipients. Nat Med 29:1989-1997.

  • Mohan D, Wansley DL, Sie BM, Noon MS, Baer AN, Laserson U, Larman HB (2018) PhIP-Seq characterization of serum antibodies using oligonucleotide-encoded peptidomes. Nat Protoc 13:1958-1978.

  • Mueller NJ, Denner J (2022) Porcine cytomegalovirus/porcine roseolovirus (PCMV/PRV): A threat for xenotransplantation? Xenotransplantation 29:e12775.

  • Nelson MI, Viboud C, Vincent AL, Culhane MR, Detmer SE, Wentworth DE, Rambaut A, Suchard MA, Holmes EC, Lemey P (2015) Global migration of influenza A viruses in swine. Nat Commun 6:6696.

  • Olin A, Pou C, Jaquaniello A, Crook J, Tan Z, Roux M, Dubois F, Charbit B, Liu D, Donnadieu F, Garcia L, Lambert C, Bloch E, Clave E, Araujo IL, Toubert A, Rotival M, Simon-Loriere E, White M, Brodin P, Duffy D, Quintana-Murci L, Patin E, Milieu Interieur C (2026) Demographic and genetic factors shape the epitope specificity of the human antibody repertoire against viruses. Nat Immunol 27:600-612.

  • Opriessnig T, Halbur PG (2012) Concurrent infections are important for expression of porcine circovirus associated disease. Virus Res 164:20-32.

  • Palinski R, Pineyro P, Shang P, Yuan F, Guo R, Fang Y, Byers E, Hause BM (2017) A Novel Porcine Circovirus Distantly Related to Known Circoviruses Is Associated with Porcine Dermatitis and Nephropathy Syndrome and Reproductive Failure. J Virol 91: e01879-16.

  • Ruhs EC, Chia WN, Foo R, Peel AJ, Li Y, Larman HB, Irving AT, Wang L, Brook CE (2023) Applications of VirScan to broad serological profiling of bat reservoirs for emerging zoonoses. Front Public Health 11:1212018.

  • Safamanesh S, Azimian A, Shakeri A, Ghazvini K, Jamehdar SA, Khosrojerdi M, Youssefi M (2018) Detection of Porcine Bocavirus From a Child With Acute Respiratory Tract Infection. Pediatr Infect Dis J 37:e338-e339.

  • Scully EP, Haverfield J, Ursin RL, Tannenbaum C, Klein SL (2020) Considering how biological sex impacts immune responses and COVID-19 outcomes. Nat Rev Immunol 20:442-447.

  • Shan T, Li L, Simmonds P, Wang C, Moeser A, Delwart E (2011) The fecal virome of pigs on a high-density farm. J Virol 85:11697-11708.

  • Sharma KB, Vrati S, Kalia M (2021) Pathobiology of Japanese encephalitis virus infection. Mol Aspects Med 81:100994.

  • Shen W, Sipos B, Zhao L (2024) SeqKit2: A Swiss army knife for sequence and alignment processing. Imeta 3:e191.

  • Shrock E, Fujimura E, Kula T, Timms RT, Lee IH, Leng Y, Robinson ML, Sie BM, Li MZ, Chen Y, Logue J, Zuiani A, McCulloch D, Lelis FJN, Henson S, Monaco DR, Travers M, Habibi S, Clarke WA, Caturegli P, Laeyendecker O, Piechocka-Trocha A, Li JZ, Khatri A, Chu HY, Collection MC-, Processing T, Villani AC, Kays K, Goldberg MB, Hacohen N, Filbin MR, Yu XG, Walker BD, Wesemann DR, Larman HB, Lederer JA, Elledge SJ (2020) Viral epitope profiling of COVID-19 patients reveals cross-reactivity and correlates of severity. Science 370: eabd4250.

  • Suradhat S, Kesdangsakonwut S, Sada W, Buranapraditkun S, Wongsawang S, Thanawongnuwech R (2006) Negative impact of porcine reproductive and respiratory syndrome virus infection on the efficacy of classical swine fever vaccine. Vaccine 24:2634-2642.

  • Swine Health Information Center (2018) Swine Viral Disease Matrix. https://www.swinehealth.org/swine-disease-matrix/. Accessed 8 September 2025.

  • Sykes M, Sachs DH (2022) Progress in xenotransplantation: overcoming immune barriers. Nat Rev Nephrol 18:745-761.

  • VanderWaal K, Deen J (2018) Global trends in infectious diseases of swine. Proc Natl Acad Sci U S A 115:11495-11500.

  • Venkataraman T, Valencia C, Mangino M, Morgenlander W, Clipman SJ, Liechti T, Valencia A, Christofidou P, Spector T, Roederer M, Duggal P, Larman HB (2022) Analysis of antibody binding specificities in twin and SNP-genotyped cohorts reveals that antiviral antibody epitope selection is a heritable trait. Immunity 55:174-184 e175.

  • Wu A, Mihaylova VT, Landry ML, Foxman EF (2020) Interference between rhinovirus and influenza A virus: a clinical data analysis and experimental infection study. Lancet Microbe 1:e254-e262.

  • Wu FT, Liu LT, Jiang B, Kuo TY, Wu CY, Liao MH (2022) Prevalence and diversity of rotavirus A in pigs: Evidence for a possible reservoir in human infection. Infect Genet Evol 98:105198.

  • Xu GJ, Kula T, Xu Q, Li MZ, Vernon SD, Ndung'u T, Ruxrungtham K, Sanchez J, Brander C, Chung RT, O'Connor KC, Walker B, Larman HB, Elledge SJ (2015) Viral immunology. Comprehensive serological profiling of human populations using a synthetic human virome. Science 348:aaa0698.