Transmission of SARS-CoV-2 from humans to animals and potential host adaptation
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Abstract
SARS-CoV-2, the causative agent of the COVID-19 pandemic, can infect a wide range of mammals. Since its spread in humans, secondary host jumps of SARS-CoV-2 from humans to multiple domestic and wild populations of mammals have been documented. Understanding the extent of adaptation to these animal hosts is critical for assessing the threat that the spillback of animal-adapted SARS-CoV-2 into humans poses. We compare the genomic landscapes of SARS-CoV-2 isolated from animal species to that in humans, profiling the mutational biases indicative of potentially different selective pressures in animals. We focus on viral genomes isolated from mink ( Neovison vison ) and white-tailed deer ( Odocoileus virginianus ) for which multiple independent outbreaks driven by onward animal-to-animal transmission have been reported. We identify five candidate mutations for animal-specific adaptation in mink (NSP9_G37E, Spike_F486L, Spike_N501T, Spike_Y453F, ORF3a_L219V), and one in deer (NSP3a_L1035F), though they appear to confer a minimal advantage for human-to-human transmission. No considerable changes to the mutation rate or evolutionary trajectory of SARS-CoV-2 has resulted from circulation in mink and deer thus far. Our findings suggest that minimal adaptation was required for onward transmission in mink and deer following human-to-animal spillover, highlighting the ‘generalist’ nature of SARS-CoV-2 as a mammalian pathogen.
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SciScore for 10.1101/2020.11.16.384743: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources All genome assemblies were profile aligned to the SARS-CoV-2 reference genome Wuhan-Hu-1 (NC_045512.2) using MAFFT v7.20550. MAFFTsuggested: (MAFFT, RRID:SCR_011811)We constructured a maximum likelihood phylogenetic tree over the 55,030 included genomes using IQ-TREE v2.1.0 Covid release54 specifying the fast mode. IQ-TREEsuggested: (IQ-TREE, RRID:SCR_017254)Trees were queried and plotted using the R packages Ape v5.456 and ggtree v1.16.657 (see Figure 1). Apesuggested: (APE, RRID:SCR_009122)This was done by retrieving the amino acid changes corresponding to all SNPs at these positions using … SciScore for 10.1101/2020.11.16.384743: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources All genome assemblies were profile aligned to the SARS-CoV-2 reference genome Wuhan-Hu-1 (NC_045512.2) using MAFFT v7.20550. MAFFTsuggested: (MAFFT, RRID:SCR_011811)We constructured a maximum likelihood phylogenetic tree over the 55,030 included genomes using IQ-TREE v2.1.0 Covid release54 specifying the fast mode. IQ-TREEsuggested: (IQ-TREE, RRID:SCR_017254)Trees were queried and plotted using the R packages Ape v5.456 and ggtree v1.16.657 (see Figure 1). Apesuggested: (APE, RRID:SCR_009122)This was done by retrieving the amino acid changes corresponding to all SNPs at these positions using a custom Biopython (v1.76) script (https://github.com/cednotsed/mink_homoplasies/blob/main/dnds/snp_to_sav_parser.py) with annotations reported in Table S3. Biopythonsuggested: (Biopython, RRID:SCR_007173)Assemblies were also uploaded to CoVSurver (https://www.gisaid.org/epiflu-applications/covsurver-mutations-app/) to report the prevalence of mutations and indels relative to SARS-CoV-2 assemblies available on the GISAID database48,49. GISAIDsuggested: (GISAID, RRID:SCR_018279)CpG dinucleotide frequencies for both SARS-CoV-2 alignments of genomes isolated from human and mink were also calculated using a custom R script (https://github.com/cednotsed/mink_homoplasies/blob/main/CpG/plot_CpG.R) (Figure S6). SARS-CoV-2suggested: (Active Motif Cat# 91351, RRID:AB_2847848)Identification of recurrent mutations: We screened for the presence of recurrent mutations in the mink SARS-CoV-2 masked alignment using HomoplasyFinder v0.0.0.960, as described in our previous work61,62. HomoplasyFindersuggested: (HomoplasyFinder, RRID:SCR_017300)We visualised this structure using PyMOL v2.4.166. PyMOLsuggested: (PyMOL, RRID:SCR_000305)We generated query–template alignments using HH-suite67 and predicted 3D models using MODELLER v.9.2468. MODELLERsuggested: (MODELLER, RRID:SCR_008395)Results from OddPub: Thank you for sharing your code.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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SciScore for 10.1101/2020.11.16.384743: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources All genome assemblies were profile aligned to the SARSCoV-2 reference genome Wuhan-Hu-1 (NC_045512.2) using MAFFT v7.20550. MAFFTsuggested: (MAFFT, RRID:SCR_011811)We constructured a maximum likelihood phylogenetic tree over the 55,030 included genomes using IQ-TREE v2.1.0 Covid release54 specifying the fast mode. IQ-TREEsuggested: (IQ-TREE, RRID:SCR_017254)SciScore for 10.1101/2020.11.16.384743: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources All genome assemblies were profile aligned to the SARSCoV-2 reference genome Wuhan-Hu-1 (NC_045512.2) using MAFFT v7.20550. MAFFTsuggested: (MAFFT, RRID:SCR_011811)We constructured a maximum likelihood phylogenetic tree over the 55,030 included genomes using IQ-TREE v2.1.0 Covid release54 specifying the fast mode. IQ-TREEsuggested: (IQ-TREE, RRID:SCR_017254)Trees were queried and plotted using the R packages Ape v5.456 and ggtree v1.16.657 (see Figure 1). Apesuggested: (APE, RRID:SCR_009122)This was done by retrieving the amino acid changes corresponding to all SNPs at these positions using a custom Biopython (v1.76) script (https://github.com/cednotsed/mink_homoplasies/blob/main/dnds/snp_to_sav_parser.py) with annotations reported in Table S3. Biopythonsuggested: (Biopython, RRID:SCR_007173)CpG dinucleotide frequencies for both SARS-CoV-2 alignments of genomes isolated from human and mink were also calculated using a custom R script (https://github.com/cednotsed/mink_homoplasies/blob/main/CpG/plot_CpG.R) (Figure S6). SARS-CoV-2suggested: (SARS-CoV-2-Sequences, RRID:SCR_018319)Identification of recurrent mutations We screened for the presence of recurrent mutations in the mink SARS-CoV-2 masked alignment using HomoplasyFinder v0.0.0.960, as described in our previous work61,62. HomoplasyFindersuggested: (HomoplasyFinder, RRID:SCR_017300)We generated query–template alignments using HH-suite67 and predicted 3D models using MODELLER v.9.2468. MODELLERsuggested: (MODELLER, RRID:SCR_008395)This figure was rendered using PyMOL (v2.4.1). PyMOLsuggested: (PyMOL, RRID:SCR_000305)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
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