Estimation of temporal covariances in pathogen dynamics using Bayesian multivariate autoregressive models

Mair, C., Nickbakhsh, S. , Reeve, R. , McMenamin, J., Reynolds, A., Gunson, R. N., Murcia, P. R. and Matthews, L. (2019) Estimation of temporal covariances in pathogen dynamics using Bayesian multivariate autoregressive models. PLoS Computational Biology, 15(12), e1007492. (doi:10.1371/journal.pcbi.1007492) (PMID:31834896)

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Abstract

It is well recognised that animal and plant pathogens form complex ecological communities of interacting organisms within their hosts, and there is growing interest in the health implications of such pathogen interactions. Although community ecology approaches have been used to identify pathogen interactions at the within-host scale, methodologies enabling robust identification of interactions from population-scale data such as that available from health authorities are lacking. To address this gap, we developed a statistical framework that jointly identifies interactions between multiple viruses from contemporaneous non-stationary infection time series. Our conceptual approach is derived from a Bayesian multivariate disease mapping framework. Importantly, our approach captures within- and between-year dependencies in infection risk while controlling for confounding factors such as seasonality, demographics and infection frequencies, allowing genuine pathogen interactions to be distinguished from simple correlations. We validated our framework using a broad range of synthetic data. We then applied it to diagnostic data available for five respiratory viruses co-circulating in a major urban population between 2005 and 2013: adenovirus, human coronavirus, human metapneumovirus, influenza B virus and respiratory syncytial virus. We found positive and negative covariances indicative of epidemiological interactions among specific virus pairs. This statistical framework enables a community ecology perspective to be applied to infectious disease epidemiology with important utility for public health planning and preparedness.

Item Type:Articles
Additional Information:This work was funded by the Medical Research Council of the United Kingdom MC_UU_12014/9, www.mrc.ukri.org/ (S.N, C.M, P.M, R.R and L.M). We are grateful for the support from the National Science Foundation DEB1216040/BB/K01126X/1, www.nsf.gov (L.M), MR/S004815/1 (L.M) MR/R00241X/1 (L.M. and R.R), www.mrc.ukri.org, BB/L018926/1 (L.M), BB/M003949/1 (L.M) BB/L004070/1 (L.M and R.R), BB/R012679/1 (R.R), www.bbsrc.ukri.org, the Foods Standards Agency FS101055, www.food.gov.uk (L.M) and the Scottish Government Rural and Environment Science and Analytical Services Division, as part of the Centre of Expertise on Animal Disease Outbreaks (EPIC), www.epicscotland.org (L.M).
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Mair, Dr Colette and Reynolds, Dr Arlene and McMenamin, Dr Jim and Nickbakhsh, Dr Sema and Reeve, Dr Richard and Gunson, Dr Rory and Matthews, Professor Louise and Murcia, Dr Pablo
Creator Roles:
Mair, C.Formal analysis, Funding acquisition, Methodology, Validation, Visualization, Writing – original draft, Writing – review and editing
Nickbakhsh, S.Conceptualization, Data curation, Funding acquisition, Investigation, Validation, Writing – review and editing
Reeve, R.Formal analysis, Funding acquisition, Investigation, Methodology, Supervision, Validation, Writing – review and editing
McMenamin, J.Data curation, Writing – review and editing
Reynolds, A.Data curation, Writing – review and editing
Gunson, R. N.Data curation, Writing – review and editing
Murcia, P. R.Conceptualization, Formal analysis, Funding acquisition, Investigation, Supervision, Validation, Writing – review and editing
Matthews, L.Formal analysis, Funding acquisition, Methodology, Supervision, Validation, Writing – review and editing
Authors: Mair, C., Nickbakhsh, S., Reeve, R., McMenamin, J., Reynolds, A., Gunson, R. N., Murcia, P. R., and Matthews, L.
College/School:College of Medical Veterinary and Life Sciences > Institute of Biodiversity Animal Health and Comparative Medicine
College of Medical Veterinary and Life Sciences > Institute of Health and Wellbeing > Public Health
College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
College of Science and Engineering > School of Mathematics and Statistics > Statistics
Journal Name:PLoS Computational Biology
Publisher:Public Library of Science
ISSN:1553-734X
ISSN (Online):1553-7358
Copyright Holders:Copyright © 2019 Mair et al.
First Published:First published in PLoS Computational Biology 15:e1007492
Publisher Policy:Reproduced under a creative commons licence

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
172630Quinquennial Core FundsMassimo PalmariniMedical Research Council (MRC)MC_UU_12014/9III-MRC-GU CVR Support Services
190643Ecological and socioeconomic factors impacting maintenance and dissemination of antibiotic resistance in the Greater Serengeti EcosystemLouise MatthewsBiotechnology and Biological Sciences Research Council (BBSRC)BB/K01126X/1Institute of Biodiversity, Animal Health and Comparative Medicine
303374Supporting the National Action Plan for Antimicrobial Resistance (SNAP-AMR) in TanzaniaShona HiltonMedical Research Council (MRC)MR/S004815/1Institute of Biodiversity, Animal Health and Comparative Medicine
190825Social, economic and environmental drivers of zoonoses in Tanzania (SEEDZ)Sarah CleavelandBiotechnology and Biological Sciences Research Council (BBSRC)BB/L018926/1Institute of Biodiversity, Animal Health and Comparative Medicine
190824The BUG consortium Building Upon the Genome: using H. contortus genomic resources to develop novel interventions to control endemic GI parasitesEileen DevaneyBiotechnology and Biological Sciences Research Council (BBSRC)BB/M003949/1Institute of Biodiversity, Animal Health and Comparative Medicine
169191The influence of selective breeding on MHC diversityLouise MatthewsBiotechnology and Biological Sciences Research Council (BBSRC)BB/L004070/1Institute of Biodiversity, Animal Health and Comparative Medicine