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Supplementary Information For Supplementary Information for Viral zoonotic risk is homogenous among taxonomic orders of mammalian and avian reservoir hosts Nardus Mollentze and Daniel G. Streicker E-mail: [email protected] / [email protected] This PDF file includes: Figs. S1 to S7 SI References Other supplementary materials for this manuscript include the following: Data and all code (available at https://doi.org/10.5281/zenodo.3516613) www.pnas.org/cgi/doi/10.1073/pnas.1919176117 Nardus Mollentze and Daniel G. Streicker 1 of9 Passeriformes Perissodactyla Carnivora Galliformes Anseriformes Tog Ort Ort Ort Coronaviridae Rha Fla Paramyxoviridae Reo Flaviviridae Hepe Phe Picornaviridae Nai Cor Tog Paramyxoviridae Diprotodontia Rhabdoviridae Togaviridae Flaviviridae Peribunyaviridae Hepe Caliciviridae Fla Tog Reoviridae Cetartiodactyla Are Caliciviridae Poxviridae Nai Reo Chiroptera Peribunyaviridae Rhabdoviridae Filoviridae Togaviridae Rhabdoviridae Coronaviridae Flaviviridae Cal Reo Paramyxoviridae Flaviviridae Picornaviridae Poxviridae Herpesviridae Flaviviridae Poxviridae Reoviridae Togaviridae Primates Rodentia Hepa Per Pol Arenaviridae Hantaviridae Retroviridae Adenoviridae Picornaviridae Proportion zoonotic 0.00 0.25 0.50 0.75 1.00 Fig. S1. Number of zoonotic viruses linked to key mammalian and avian reservoir orders. Each rectangle represents a reservoir – virus family combination, with its size corresponding to the number of zoonotic virus species definitively linked to that reservoir and its colour indicating the proportion of the total number of viruses in that reservoir–family combination that this represents. Ade = Adenoviridae, Are = Arenaviridae, Art = Arteriviridae, Asf = Asfarviridae, Ast = Astroviridae, Cal = Caliciviridae, Cor = Coronaviridae, Fla = Flaviviridae, Hepa = Hepadnaviridae, Hepe = Hepeviridae, Nai = Nairoviridae, Ort = Orthomyxoviridae, Pap = Papillomaviridae, Per = Peribunyaviridae, Phe = Phenuiviridae, Pic = Picornaviridae, Pne = Pneumoviridae, Pol = Polyomaviridae, Pox = Poxviridae, Reo = Reoviridae, Rha = Rhabdoviridae, Tob = Tobaniviridae, Tog = Togaviridae. 2 of9 Nardus Mollentze and Daniel G. Streicker Adenoviridae Arenaviridae Arteriviridae Rodentia Rodentia Primates Rodentia Perissodactyla Primates Diprotodontia Perissodactyla Cetartiodactyla Chiroptera Carnivora Cetartiodactyla Asfarviridae Astroviridae Caliciviridae Cetartiodactyla Rodentia Carnivora Lagomorpha Cetartiodactyla Galliformes Cetartiodactyla Anseriformes Carnivora Circoviridae Coronaviridae Filoviridae Rodentia Perissodactyla Chiroptera Cetartiodactyla Chiroptera Cetartiodactyla Carnivora Galliformes Flaviviridae Hantaviridae Hepadnaviridae Rodentia Primates Perissodactyla Rodentia Diprotodontia Chiroptera Rodentia Cetartiodactyla Primates Passeriformes Galliformes Hepeviridae Herpesviridae Nairoviridae Rodentia Rodentia Rodentia Chiroptera Primates Perissodactyla Cetartiodactyla Chiroptera Diprotodontia Carnivora Cetartiodactyla Cetartiodactyla Galliformes Carnivora Orthomyxoviridae Papillomaviridae Paramyxoviridae Rodentia Rodentia Cetartiodactyla Primates Chiroptera Perissodactyla Cetartiodactyla Carnivora Lagomorpha Carnivora Cetartiodactyla Galliformes Anseriformes Carnivora Anseriformes Parvoviridae Peribunyaviridae Phenuiviridae Rodentia Rodentia Primates Primates Lagomorpha Cetartiodactyla Cetartiodactyla Cetartiodactyla Carnivora Passeriformes Picornaviridae Pneumoviridae Polyomaviridae Rodentia Primates Rodentia Rodentia Perissodactyla Chiroptera Cetartiodactyla Cetartiodactyla Primates Carnivora Passeriformes Galliformes Galliformes Cetartiodactyla Anseriformes Poxviridae Reoviridae Retroviridae Rodentia Rodentia Rodentia Primates Primates Perissodactyla Primates Lagomorpha Diprotodontia Perissodactyla Cetartiodactyla Chiroptera Cetartiodactyla Cetartiodactyla Carnivora Galliformes Carnivora Rhabdoviridae Tobaniviridae Togaviridae Rodentia Rodentia Perissodactyla Primates Diprotodontia Perissodactyla Chiroptera Diprotodontia Cetartiodactyla Cetartiodactyla Cetartiodactyla Carnivora Carnivora Passeriformes −2.5 0.0 2.5 5.0 −2.5 0.0 2.5 5.0 −2.5 0.0 2.5 5.0 log(Odds zoonotic) Fig. S2. Partial effects plot for the family-specific reservoir effect in the top-ranked model in Fig. 2A. Points represent partial residuals, after accounting for the other effects in the model, while lines indicate the predicted effect. Shaded areas show the 95% confidence intervals of each predicted effect. Effects which are clearly separated from 0 (defined as having a confidence interval which does not cross 0) are highlighted in blue. Nardus Mollentze and Daniel G. Streicker 3 of9 A Hantaviridae B Nairoviridae Rodentia Peribunyaviridae Primates Arenaviridae Perissodactyla Phenuiviridae Lagomorpha Orthomyxoviridae Diprotodontia Filoviridae Chiroptera Paramyxoviridae Cetartiodactyla Pneumoviridae Reservoir Carnivora Rhabdoviridae Passeriformes Arteriviridae Galliformes Coronaviridae Anseriformes Tobaniviridae Reoviridae −2 −1 0 1 2 Astroviridae Caliciviridae log(Odds zoonotic) Flaviviridae C Hepeviridae Perissodactyla Virus taxonomy Picornaviridae Carnivora Togaviridae Cetartiodactyla Adenoviridae Chiroptera Asfarviridae Rodentia Herpesviridae Lagomorpha Papillomaviridae Primates Polyomaviridae Poxviridae Diprotodontia Hepadnaviridae Anseriformes Circoviridae Galliformes Parvoviridae Reservoir phylogeny Passeriformes Retroviridae 0 200 400 600 −2 −1 0 1 2 Distance (My) log(Odds zoonotic)log(Odds zoonotic) 0.00 0.25 0.50 0.75 1.00 1.25−4 −2 0 2 4 log(Odds zoonotic)log(Odds zoonotic) Fig. S3. Effect of virus taxonomy and reservoir phylogeny on the probability of being zoonotic, after accounting for all other effects in the model. (A) Partial effects for the individual families making up the taxonomic random effect, in the best model containing a virus taxonomy effect in the absence of any reservoir-related random effects (ranked 34th in Fig. 2; ∆AIC = 14.1). (B-C) Partial effects for the reservoir and reservoir phylogeny random effects from the top-ranked model in which each occurred without a virus taxonomy random effect (ranked 127th and 128th, respectively; ∆AIC = 30.8 in both cases). Bars indicate partial effects, after accounting for all other variables in the model, with shaded regions showing the extent of their 95% confidence intervals, while points indicate partial residuals for individual virus species. Families with effects clearly separated from 0 are highlighted in blue. 4 of9 Nardus Mollentze and Daniel G. Streicker A B E Deviance Rank ∆AIC explained Virus-related publications 1 0.00 56.4 2 1.81 57.1 140 3 1.92 56.7 Reservoir sp. richness 130 4 1.97 38.2 120 5 2.64 44.9 Phylogenetic distance 110 6 3.81 57.1 100 7 3.87 38.7 Mammalian reservoir 8 4.36 46.3 90 9 5.63 15.8 -1 0 1 2 80 10 5.71 0.0 Coefficient estimate 70 11 6.31 24.6 C D 60 12 6.50 9.4 6 13 7.15 4.5 5 50 14 7.61 28.9 40 Predicted number of virus species 15 7.62 15.8 4 30 16 8.46 9.8 4 20 10 of virus species Effect on number of virus3 species 2 Effect on number 0 2 3 4 5 6 7 8 9 0 10 20 30 40 50 60 70 80 90 100 110 Mammalian reservoir log(Reservoir spp. richness) Mammal Observed number of virus species Phylogenetic distance Phylogenetic Reservoir sp. richness Reservoir sp. Virus−related publications Fig. S4. Factors predicting the total number virus species maintained by different animal orders (viral richness). (A) Models for all possible variable combinations ranked by AIC. Each row represents a model, while columns represent variables. Filled cells and white cells indicate variable inclusion and absence, respectively. The top four model are colour coded, with colours re-used in all other panels to identify the respective models. (B) Coefficient estimates for the top 4 models: points indicate the maximum likelihood estimate; lines show 95% confidence intervals. All variables were scaled by dividing them by 2 times their standard deviation. (C–D) Partial effect plots for variables in the top model. Lines and shading indicate the partial effects and 95% confidence intervals, with points showing partial residuals. (E) Predicted viral richness for each reservoir group when using the top model (blue in panel A). Nardus Mollentze and Daniel G. Streicker 5 of9 A 60 Model rank 1 40 2 3 4 20 Predicted number of zoonotic species 0 0 10 20 30 40 0 10 20 30 40 0 10 20 30 40 0 10 20 30 40 Observed number of zoonotic species B 140 120 100 Model rank 1 80 2 60 3 4 40 Predicted number of virus species 20 0 20 40 60 80 100 20 40 60 80 100 20 40 60 80 100 20 40 60 80 100 Observed number of virus species Fig. S5. Predictions from the top four models predicting the number of zoonotic species and the total viral richness. (A) Observed and predicted number of zoonotic species for each reservoir group when using each of the top four models in Fig. 4A. (B) Observed and predicted total viral richness per reservoir group, for the top four models illustrated in Fig. S4A. 6 of9 Nardus Mollentze and Daniel G. Streicker A B 7.5 D Deviance explained (%) 0 4 8 12 16 2 Deviance 5.0 Rank ∆AIC explained 1 0.00 49.2% 2.5 0 2 1.13 49.4% 3 1.24 49.4% 0.0 −2 4 1.37 49.3% log(Odds zoonotic) log(Odds zoonotic) −2.5 5 2.19 49.7% 0 3 6 9 0 100 200 300 6 2.28 49.6% log(Virus publication count) Phylogenetic distance (My) 7 2.41 49.5% 8 2.59 50.3% C E 3 9 2.97 50.6% Retroviridae 2 2 10 3.29 49.9% 1 11 4.21 49.1% 1 0 12 5.11 49.4% −1 13 7.50 50.3% 0 −2 log(Odds zoonotic) 14 7.56 48.2% log(Odds zoonotic) −1 15 7.77 40.1% Primates 16 7.78 40.1% Rodentia Vector− Carnivora 17 7.83 40.1% borne Perissodactyla Cetartiodactyla 18
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