Respiratory infections
Lead Research Organisation:
University of Glasgow
Department Name: UNLISTED
Abstract
Respiratory Infections: Epidemiology, evolution and ecology of respiratory viruses
Dr Pablo Murcia, Lead Investigator, in collaboration with Dr Louise Matthews (Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow); Dr Rory Gunson (West of Scotland Specialist Virology Centre); Dr Jim McMenamin (Health Protection Scotland); Dr Robert Gifford, (MRC-University of Glasgow Centre for Virus Research).
Respiratory infections are the most common disease of humans and a large proportion of them is caused by viral pathogens that include influenza A and B viruses, respiratory syncytial virus, human metapneumovirus, coronaviruses, rhinoviruses, adenoviruses and parainfluenzaviruses. From an ecological perspective, the respiratory tract could be considered the ecosystem that the aforementioned viruses cohabitate. Notably, respiratory viruses have been traditionally studied in isolation, an approach that does not capture the interactions among viruses that commonly exist and are likely to play a role in disease presentation and spread. Here we will study respiratory viruses as a group in order to understand how virus-virus interactions impact on their evolution and epidemiology. To this end we will first examine the epidemiology of viral respiratory infections in the Glasgow population. Further we will sequence
the genomes of a large number of respiratory viruses derived from patients in order to link changes in virus genetic composition with patterns of virus circulation. Results from this work will have profound public health implications, from improved forecasting of epidemics to the design of novel vaccination strategies against the most common pathogens of humans.
Dr Pablo Murcia, Lead Investigator, in collaboration with Dr Louise Matthews (Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow); Dr Rory Gunson (West of Scotland Specialist Virology Centre); Dr Jim McMenamin (Health Protection Scotland); Dr Robert Gifford, (MRC-University of Glasgow Centre for Virus Research).
Respiratory infections are the most common disease of humans and a large proportion of them is caused by viral pathogens that include influenza A and B viruses, respiratory syncytial virus, human metapneumovirus, coronaviruses, rhinoviruses, adenoviruses and parainfluenzaviruses. From an ecological perspective, the respiratory tract could be considered the ecosystem that the aforementioned viruses cohabitate. Notably, respiratory viruses have been traditionally studied in isolation, an approach that does not capture the interactions among viruses that commonly exist and are likely to play a role in disease presentation and spread. Here we will study respiratory viruses as a group in order to understand how virus-virus interactions impact on their evolution and epidemiology. To this end we will first examine the epidemiology of viral respiratory infections in the Glasgow population. Further we will sequence
the genomes of a large number of respiratory viruses derived from patients in order to link changes in virus genetic composition with patterns of virus circulation. Results from this work will have profound public health implications, from improved forecasting of epidemics to the design of novel vaccination strategies against the most common pathogens of humans.
Technical Summary
Multiple viruses are responsible for respiratory infections and co-infections causing a variety of disease outcomes that range from a mild cold to life-threatening viral pneumonia. Occasionally, respiratory viruses result in emerging infections such as the swine-origin influenza A virus (that caused the 2009 pandemic) or the severe acute respiratory syndrome coronavirus that caused an extended outbreak in several countries in early 2000s.
Molecular diagnostic assays are routinely used in the UK healthcare system and they can simultaneously test for the presence of multiple viruses. Databases with results from such diagnostic tests represent a rich source of information that can reveal insight into the epidemiology of viral respiratory infections in the patient population.
Respiratory viruses are generally studied as single entities and not as a community. Since they are obligate intracellular pathogens that infect a well-defined ecological niche (the human respiratory tract), studying them as a community is a logical approach to capture the impact of their complex interactions on their infection dynamics.
We propose to study the infection dynamics of a group of respiratory viruses in a large and well-defined population over an extended period of time. We will analyse the long-term trends in viral respiratory infections using information on diagnostic test results (and associated metadata) of the Greater Glasgow and Clyde Health Board (GGCHB, the largest Health Board in Scotland) patient population. We will sequence a large number of viruses from clinical specimens to determine their complete genomes, study their evolutionary dynamics and to identify mutations that might be associated with changes in their phenotype (virulence, seasonality, age group distribution, etc.). We will use mathematical and statistical models to infer interactions among viruses at the patient level and their impact at the epidemiological scale. Finally, we will develop bioinformatics tools to facilitate the future use of complex sequence data in diagnostic laboratories and public health bodies.
Molecular diagnostic assays are routinely used in the UK healthcare system and they can simultaneously test for the presence of multiple viruses. Databases with results from such diagnostic tests represent a rich source of information that can reveal insight into the epidemiology of viral respiratory infections in the patient population.
Respiratory viruses are generally studied as single entities and not as a community. Since they are obligate intracellular pathogens that infect a well-defined ecological niche (the human respiratory tract), studying them as a community is a logical approach to capture the impact of their complex interactions on their infection dynamics.
We propose to study the infection dynamics of a group of respiratory viruses in a large and well-defined population over an extended period of time. We will analyse the long-term trends in viral respiratory infections using information on diagnostic test results (and associated metadata) of the Greater Glasgow and Clyde Health Board (GGCHB, the largest Health Board in Scotland) patient population. We will sequence a large number of viruses from clinical specimens to determine their complete genomes, study their evolutionary dynamics and to identify mutations that might be associated with changes in their phenotype (virulence, seasonality, age group distribution, etc.). We will use mathematical and statistical models to infer interactions among viruses at the patient level and their impact at the epidemiological scale. Finally, we will develop bioinformatics tools to facilitate the future use of complex sequence data in diagnostic laboratories and public health bodies.
Organisations
Publications
Zhu H
(2018)
Distribution, Diversity, and Evolution of Endogenous Retroviruses in Perissodactyl Genomes.
in Journal of virology
Related Projects
Project Reference | Relationship | Related To | Start | End | Award Value |
---|---|---|---|---|---|
MC_UU_12014/7 | 30/04/2013 | 30/03/2023 | £2,823,000 | ||
MC_UU_12014/8 | Transfer | MC_UU_12014/7 | 30/04/2013 | 30/03/2023 | £4,034,000 |
MC_UU_12014/9 | Transfer | MC_UU_12014/8 | 31/03/2016 | 30/03/2023 | £1,436,000 |
MC_UU_12014/10 | Transfer | MC_UU_12014/9 | 31/03/2016 | 30/03/2023 | £2,955,000 |
MC_UU_12014/11 | Transfer | MC_UU_12014/10 | 31/03/2016 | 30/03/2023 | £570,000 |
Description | Academy of Medical Sciences-Preparing for a challenging winter 2020/21 |
Geographic Reach | National |
Policy Influence Type | Participation in a guidance/advisory committee |
Impact | At the request of the Government Office for Science, the Academy of Medical Sciences established in June 2020 an Expert Advisory Group chaired by Professor Stephen Holgate CBE FMedSci to inform: ? A clear understanding of what a challenging winter 2020/21 may look like - a likely mix of COVID-19, bad seasonal influenza and cold weather. ? An understanding of what this would mean for deaths, NHS capacity and social care. ? An understanding of what challenges this would present for surveillance; test, trace and isolate (TTI); and non-pharmaceutical interventions. ? Plans being developed by policy/operational colleagues to manage this. This document informed the allocation of funds to the NHS for the winter of 2020/21. |
Description | Discussions on avian influenza preparedness and research gaps |
Geographic Reach | Multiple continents/international |
Policy Influence Type | Influenced training of practitioners or researchers |
Description | Invited to a gap analysis meeting on future research priorities of animal influenza |
Geographic Reach | National |
Policy Influence Type | Participation in a guidance/advisory committee |
Description | YY-EEID US-UK The evolutionary ecology of pathogen emergence via cross-species transmission in the avian-equine influenza system |
Amount | £852,342 (GBP) |
Funding ID | BB/V004697/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 03/2021 |
End | 01/2025 |
Title | M segment-based minigenomes and virus-like particle assays as an approach to assess the potential of tick-borne Phlebovirus genome reassortment |
Description | Data underpinning work to assess tick-borne phlebovirus reassortment potential in vitro. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
Title | Serology dataset |
Description | This dataset includes virus neutralisation data against different SARS-CoV-2 variants, as well as metadata from the patients from which serum samples were derived. |
Type Of Material | Database/Collection of data |
Year Produced | 2022 |
Provided To Others? | Yes |
Impact | This dataset shows that the nature and efficiency of the antibody mediated responses vary depending on the immunological history of the patient and the infecting strain involved. This is important to devise vaccination strategies against COVID-19 |
URL | https://academic.oup.com/jid/article/227/1/40/6653591#389801965 |
Title | Single-particle measurements of filamentous influenza virions reveal damage induced by freezing |
Description | The dataset contains all the micrographs of influenza virions used in analyses featured in the paper so that readers can download the images and examine them themselves should they wish. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
Title | Sugar feeding protects against arboviral infection by enhancing gut immunity in the mosquito vector Aedes aegypti |
Description | |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | Yes |
URL | http://researchdata.gla.ac.uk/id/eprint/1094 |
Title | Virulence mismatches in index hosts shape the outcomes of cross-species transmission |
Description | Supplemental data and code for the paper Virulence mismatches in index hosts shape the outcomes of cross-species transmission. Dataset 1 is an R Shiny app allowing the estimation of rabies disease progression parameters for all observed combinations of virus source (reservoir) and recipient species, including within-species inoculations. Dataset 2 contains the original data and the analysis code used in this study. See the README files in each dataset folder for further information and usage instructions. |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | Yes |
URL | https://zenodo.org/record/4081726 |
Title | Virulence mismatches in index hosts shape the outcomes of cross-species transmission |
Description | Supplemental data and code for the paper Virulence mismatches in index hosts shape the outcomes of cross-species transmission. Dataset 1 is an R Shiny app allowing the estimation of rabies disease progression parameters for all observed combinations of virus source (reservoir) and recipient species, including within-species inoculations. Dataset 2 contains the original data and the analysis code used in this study. See the README files in each dataset folder for further information and usage instructions. |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | Yes |
URL | https://zenodo.org/record/3746609 |
Title | Virulence mismatches in index hosts shape the outcomes of cross-species transmission |
Description | Supplemental data and code for the paper "Virulence mismatches in index hosts shape the outcomes of cross-species transmission". Dataset 1 is an R Shiny app allowing the estimation of rabies disease progression parameters for all observed combinations of source and recipient species (including within-species inoculations). Dataset 2 contains the raw data and all code used in this study. See the readme files in each dataset folder for further information and usage instructions. |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | Yes |
URL | https://zenodo.org/record/3746610 |
Description | 07/01/2021: Pablo Murcia: CNN Radio Argentina |
Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Covid in the UK: restrictions and more than 50 thousand cases per day. |
Year(s) Of Engagement Activity | 2021 |
URL | https://cnnespanol.cnn.com/radio/2021/01/07/covid-en-el-reino-unido-restricciones-y-mas-de-50-mil-ca... |
Description | 17/03/2020: Pablo Murcia: Citrica Radio (Argentina) |
Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Pablo Murcia: "We do not yet know if a person who recovered can re-infect" |
Year(s) Of Engagement Activity | 2020 |
URL | https://radiocut.fm/audiocut/pablo-murcia-no-sabemos-todavia-si-una-persona-se-recupero-puede-volver... |
Description | Antonia Ho contributed to The Guardia article |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Public/other audiences |
Results and Impact | Toni talked about the implications of a new genome surveillance project at the Sanger Institute. |
Year(s) Of Engagement Activity | 2023 |
URL | https://www.theguardian.com/science/2023/jan/10/uk-genome-project-respiratory-viruses-sanger-institu... |
Description | Ed Hutchinson wins MRF/MRC Competition |
Form Of Engagement Activity | Engagement focused website, blog or social media channel |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Ed's design 'Cold Comforts' won this competiton and was featured on the MRC/MRF christmas cards. |
Year(s) Of Engagement Activity | 2022 |
URL | https://twitter.com/MedResFdn/status/1602307143499137028 |
Description | Ed Hutchinson's Virus Snowflakes Activity Book |
Form Of Engagement Activity | A magazine, newsletter or online publication |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Public/other audiences |
Results and Impact | Ed developed the existing Virus Snowflakes booklet further by adding 8 new designs. |
Year(s) Of Engagement Activity | 2022 |
URL | https://cvr-engagement.co.uk/virus-snowflakes |
Description | Educational Material about Influenza Viruses |
Form Of Engagement Activity | A magazine, newsletter or online publication |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Schools |
Results and Impact | influenza virus researchers have worked together to generate simple educational material to communicate their science to school students. Educational materials suitable for a range of ages are included, from coloring exercises for younger students through to explanations of cutting-edge science in straightforward language for older students. This article contains a handout with influenza facts, a coloring page, a glossary and word find and a connect-the-dots exercise explaining the ideas behind recently published scientific papers. Together, these materials are intended to make research on influenza viruses more accessible to students and teachers. |
Year(s) Of Engagement Activity | 2019 |
URL | https://www.mdpi.com/1999-4915/11/3/231 |
Description | Emma Davies at Festive Family Day at the ARC |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | Emma hosted a tabletop activity, Ed Hutchinsons' virus snowflakes, during this festive family day at the ARC. |
Year(s) Of Engagement Activity | 2022 |
Description | Interview for National News |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Public/other audiences |
Results and Impact | This was a TV interview to cover the first case of swine influenza in a human in the UK. This was covered by ITV. |
Year(s) Of Engagement Activity | 2023 |
Description | Jan 2020 - BBC "The Nine" Interview with Dr Antonia Ho |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Public/other audiences |
Results and Impact | Following the outbreak of the Coronavirus, BBC Scotland "The Nine" requested an interview with Dr Antonia Ho. |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.facebook.com/centreforvirusresearch/ |
Description | Jo Haney Research Goes Viral video for Nature paper |
Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Public/other audiences |
Results and Impact | Jo discusses her research which involved coinfection of human lunch tissue with Influenza A virus and respiratory syncytial virus, and revealed the existance of hybrid virus particles which have functional consequences. |
Year(s) Of Engagement Activity | 2023 |
URL | https://twitter.com/CVRinfo/status/1610984465177657345 |
Description | MRC Podcast with Dr Sema Nickbakhsh & Dr Pablo Murcia following their publication in PNAS |
Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | Interview with the Medical Research Council following the release of a paper in PNAS explaining why cold infections may be less frequent in people with the flu |
Year(s) Of Engagement Activity | 2019 |
URL | https://twitter.com/The_MRC/status/1207602826823766016 |