An RNA-Seq analysis of coronavirus in the skin of the Pangolin | Scientific Reports – Nature.com
January 11, 2024
Choo, S. W. et al. Pangolin genomes and the evolution of mammalian scales and immunity. Genome Res. 26, 13121322 (2016).
Article CAS PubMed PubMed Central Google Scholar
The IUCN Red List of Threatened Species. In: IUCN Red List Threat. Species. https://www.iucnredlist.org/en. Accessed 3 Mar 2021.
Hua, L. Gong, S. Wang, F. Li, W. Ge, Y. Li, X. & Hou, F. Captive breeding of pangolins: current status, problems and future prospects. Zookeys 99114 (2015).
Yan, D. et al. Successful captive breeding of a Malayan pangolin population to the third filial generation. Commun. Biol. 4, 1212 (2021).
Article PubMed PubMed Central Google Scholar
Fischer, H., Tschachler, E. & Eckhart, L. Pangolins lack IFIH1/MDA5, a cytoplasmic RNA sensor that initiates innate immune defense upon coronavirus infection. Front. Immunol. 11, 939 (2020).
Article CAS PubMed PubMed Central Google Scholar
Fischer, H., Tschachler, E. & Eckhart, L. Cytosolic DNA sensing through cGAS and STING is inactivated by gene mutations in pangolins. Apoptosis Int. J. Program Cell Death 25, 474480 (2020).
Article CAS Google Scholar
Sharma, V., Hecker, N., Walther, F., Stuckas, H. & Hiller, M. Convergent losses of TLR5 suggest altered extracellular flagellin detection in four mammalian lineages. Mol. Biol. Evol. 37, 18471854 (2020).
Article CAS PubMed Google Scholar
Choo, S. W. et al. Are pangolins scapegoats of the COVID-19 outbreak-CoV transmission and pathology evidence?. Conserv. Lett. 13, e12754 (2020).
Article Google Scholar
Xiao, K. et al. Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins. Nature 583, 286289 (2020).
Article ADS CAS PubMed Google Scholar
Lam, T.T.-Y. et al. Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature 583, 282285 (2020).
Article ADS CAS PubMed Google Scholar
Michel, C. J., Mayer, C., Poch, O. & Thompson, J. D. Characterization of accessory genes in coronavirus genomes. Virol. J. 17, 131 (2020).
Article CAS PubMed PubMed Central Google Scholar
Lopes, L. R., de Mattos, C. G. & Paiva, P. B. Molecular evolution and phylogenetic analysis of SARS-CoV-2 and hosts ACE2 protein suggest Malayan pangolin as intermediary host. Braz. J. Microbiol. Publ. Braz. Soc. Microbiol. 51, 15931599 (2020).
Article CAS Google Scholar
Zhao, J., Cui, W. & Tian, B.-P. The potential intermediate hosts for SARS-CoV-2. Front. Microbiol. 11, 580137 (2020).
Article PubMed PubMed Central Google Scholar
Greenig, M. HERVs, immunity, and autoimmunity: Understanding the connection. PeerJ 7, e6711 (2019).
Article PubMed PubMed Central Google Scholar
Russ, E. & Iordanskiy, S. Endogenous retroviruses as modulators of innate immunity. Pathog. Basel Switz. 12, 162 (2023).
Article CAS Google Scholar
Srinivasachar Badarinarayan, S. & Sauter, D. Switching sides: How endogenous retroviruses protect us from viral infections. J. Virol. 95, e02299-e2320 (2021).
Article PubMed PubMed Central Google Scholar
Andrews S (2010) FastQC: A quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. Accessed 13 Dec 2020.
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 1012 (2011).
Article Google Scholar
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357359 (2012).
Article CAS PubMed PubMed Central Google Scholar
Kim, D. & Salzberg, S. L. TopHat-Fusion: An algorithm for discovery of novel fusion transcripts. Genome Biol. 12, R72 (2011).
Article CAS PubMed PubMed Central Google Scholar
Kim, D. et al. TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).
Article PubMed PubMed Central Google Scholar
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
Article PubMed PubMed Central Google Scholar
Blanco-Melo, D. et al. Imbalanced host response to SARS-CoV-2 drives development of COVID-19. Cell 181, 1036-1045.e9 (2020).
Article CAS PubMed PubMed Central Google Scholar
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 17541760 (2009).
Article CAS PubMed PubMed Central Google Scholar
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 20782079 (2009).
Article PubMed PubMed Central Google Scholar
Li, H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27, 29872993 (2011).
Article CAS PubMed PubMed Central Google Scholar
Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 2426 (2011).
Article CAS PubMed PubMed Central Google Scholar
Robinson, J. T., Thorvaldsdttir, H., Wenger, A. M., Zehir, A. & Mesirov, J. P. Variant review with the integrative genomics viewer. Cancer Res. 77, e31e34 (2017).
Article CAS PubMed PubMed Central Google Scholar
Thorvaldsdttir, H., Robinson, J. T. & Mesirov, J. P. Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration. Brief. Bioinform. 14, 178192 (2013).
Article PubMed Google Scholar
Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 15471549 (2018).
Article CAS PubMed PubMed Central Google Scholar
Edgar, R. C. MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinform. 5, 113 (2004).
Article Google Scholar
Trapnell, C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 7, 562578 (2012).
Article CAS PubMed PubMed Central Google Scholar
Yu, G., Wang, L.-G., Han, Y. & He, Q.-Y. clusterProfiler: An R package for comparing biological themes among gene clusters. Omics J. Integr. Biol. 16, 284287 (2012).
Article CAS Google Scholar
Sergushichev, AA. An algorithm for fast preranked gene set enrichment analysis using cumulative statistic calculation. bioRxiv 060012. (2016).
Ashburner, M. et al. Gene ontology: Tool for the unification of biology. Nat. Genet. 25, 2529 (2000).
Article CAS PubMed PubMed Central Google Scholar
Morgan M, Carlson M, Tenenbaum D, Arora S, Oberchain V, Morrell K, Shepherd L (2020) AnnotationHub: Client to access AnnotationHub resources. https://doi.org/10.18129/B9.bioc.AnnotationHub
Kanehisa, M. & Goto, S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 2730 (2000).
Article CAS PubMed PubMed Central Google Scholar
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403410 (1990).
Article CAS PubMed Google Scholar
Nomburg, J., Meyerson, M. & DeCaprio, J. A. Pervasive generation of non-canonical subgenomic RNAs by SARS-CoV-2. Genome Med. 12, 108 (2020).
Article CAS PubMed PubMed Central Google Scholar
Kim, D. et al. The architecture of SARS-CoV-2 transcriptome. Cell 181, 914-921.e10 (2020).
Article CAS PubMed PubMed Central Google Scholar
Liu, P. et al. Are pangolins the intermediate host of the 2019 novel coronavirus (SARS-CoV-2)?. PLoS Pathog. 16, e1008421 (2020).
Article CAS PubMed PubMed Central Google Scholar
Day, S. L., Ramshaw, I. A., Ramsay, A. J. & Ranasinghe, C. Differential effects of the type I interferons alpha4, beta, and epsilon on antiviral activity and vaccine efficacy. J. Immunol. Baltim. Md. 1950 180, 71587166 (2008).
CAS Google Scholar
Pontn, F., Jirstrm, K. & Uhlen, M. The Human Protein AtlasA tool for pathology. J. Pathol. 216, 387393 (2008).
Article PubMed Google Scholar
Xi, Y., Day, S. L., Jackson, R. J. & Ranasinghe, C. Role of novel type I interferon epsilon in viral infection and mucosal immunity. Mucosal Immunol. 5, 610622 (2012).
Article CAS PubMed PubMed Central Google Scholar
Fung, K. Y. et al. Interferon- protects the female reproductive tract from viral and bacterial infection. Science 339, 10881092 (2013).
Article ADS CAS PubMed PubMed Central Google Scholar
Demers, A. et al. The mucosal expression pattern of interferon- in rhesus macaques. J. Leukoc. Biol. 96, 11011107 (2014).
Article PubMed PubMed Central Google Scholar
Uhln, M. et al. Proteomics. Tissue-based map of the human proteome. Science 347, 1260419 (2015).
Article PubMed Google Scholar
Guo, Y. et al. Molecular and functional characterization of ovis aries IFN-epsilon. Mol. Immunol. 119, 17 (2020).
Article CAS PubMed Google Scholar
Jassal, B. et al. The reactome pathway knowledgebase. Nucleic Acids Res. 48, D498D503 (2020).
CAS PubMed Google Scholar
Subramanian, A. et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. U. S. A. 102, 1554515550 (2005).
Article ADS CAS PubMed PubMed Central Google Scholar
Barh, D. et al. Multi-omics-based identification of SARS-CoV-2 infection biology and candidate drugs against COVID-19. Comput. Biol. Med. 126, 104051 (2020).
Article CAS PubMed PubMed Central Google Scholar
Gendrot, M. et al. Antimalarial drugs inhibit the replication of SARS-CoV-2: An in vitro evaluation. Travel Med. Infect. Dis. 37, 101873 (2020).
Article PubMed PubMed Central Google Scholar
Yan, B. et al. Characterization of the lipidomic profile of human coronavirus-infected cells: Implications for lipid metabolism remodeling upon coronavirus replication. Viruses 11, 73 (2019).
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An RNA-Seq analysis of coronavirus in the skin of the Pangolin | Scientific Reports - Nature.com