1
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Klimov PB, He Q. Predicting host range expansion in parasitic mites using a global mammalian-acarine dataset. Nat Commun 2024; 15:5431. [PMID: 38926409 PMCID: PMC11208579 DOI: 10.1038/s41467-024-49515-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
Multi-host parasites pose greater health risks to wildlife, livestock, and humans than single-host parasites, yet our understanding of how ecological and biological factors influence a parasite's host range remains limited. Here, we assemble the largest and most complete dataset on permanently parasitic mammalian mites and build a predictive model assessing the probability of single-host parasites to become multi-hosts, while accounting for potentially unobserved host-parasite links and class imbalance. This model identifies statistically significant predictors related to parasites, hosts, climate, and habitat disturbance. The most important predictors include the parasite's contact level with the host immune system and two variables characterizing host phylogenetic similarity and spatial co-distribution. Our model reveals an overrepresentation of mites associated with Rodentia (rodents), Chiroptera (bats), and Carnivora in the multi-host risk group. This highlights both the potential vulnerability of these hosts to parasitic infestations and the risk of serving as reservoirs of parasites for new hosts. In addition, we find independent macroevolutionary evidence that supports our prediction of several single-host species of Notoedres, the bat skin parasites, to be in the multi-host risk group, demonstrating the forecasting potential of our model.
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Affiliation(s)
- Pavel B Klimov
- Lilly Hall of Life Sciences, Purdue University, 915 Mitch Daniels Blvd, West Lafayette, Indiana, 47907, USA.
| | - Qixin He
- Lilly Hall of Life Sciences, Purdue University, 915 Mitch Daniels Blvd, West Lafayette, Indiana, 47907, USA.
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2
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Sjodin AR, Willig MR, Rodríguez‐Durán A, Anthony SJ. Rapid taxonomic categorization of short, abundant virus sequences for ecological analyses. Ecol Evol 2024; 14:e11501. [PMID: 38895563 PMCID: PMC11183940 DOI: 10.1002/ece3.11501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 05/10/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
Public health concerns about recent viral epidemics have motivated researchers to seek novel ways to understand pathogen infection in native, wildlife hosts. With its deep history of tools and perspectives for understanding the abundance and distribution of organisms, ecology can shed new light on viral infection dynamics. However, datasets allowing deep explorations of viral communities from an ecological perspective are lacking. We sampled 1086 bats from two, adjacent Puerto Rican caves and tested them for infection by herpesviruses, resulting in 3131 short, viral sequences. Using percent identity of nucleotides and a machine learning algorithm (affinity propagation), we categorized herpesviruses into 43 operational taxonomic units (OTUs) to be used in place of species in subsequent ecological analyses. Herpesvirus metacommunities demonstrated long-tailed rank frequency distributions at all analyzed levels of host organization (i.e., individual, population, and community). Although 13 herpesvirus OTUs were detected in more than one host species, OTUs generally exhibited host specificity by infecting a single core host species at a significantly higher prevalence than in all satellite species combined. We describe the natural history of herpesvirus metacommunities in Puerto Rican bats and suggest that viruses follow the general law that communities comprise few common and many rare species. To guide future efforts in the field of viral ecology, hypotheses are presented regarding mechanisms that contribute to these patterns.
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Affiliation(s)
- Anna R. Sjodin
- Department of Ecology & Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | - Michael R. Willig
- Department of Ecology & Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
- Center for Environmental Sciences & Engineering and Institute of the EnvironmentUniversity of ConnecticutStorrsConnecticutUSA
| | | | - Simon J. Anthony
- Center for Infection and ImmunityColumbia UniversityNew YorkNew YorkUSA
- Department of Pathology, Microbiology, and ImmunologyUC Davis School of Veterinary MedicineDavisCaliforniaUSA
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3
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Aljabali AAA, Obeid MA, El-Tanani M, Mishra V, Mishra Y, Tambuwala MM. Precision epidemiology at the nexus of mathematics and nanotechnology: Unraveling the dance of viral dynamics. Gene 2024; 905:148174. [PMID: 38242374 DOI: 10.1016/j.gene.2024.148174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
The intersection of mathematical modeling, nanotechnology, and epidemiology marks a paradigm shift in our battle against infectious diseases, aligning with the focus of the journal on the regulation, expression, function, and evolution of genes in diverse biological contexts. This exploration navigates the intricate dance of viral transmission dynamics, highlighting mathematical models as dual tools of insight and precision instruments, a theme relevant to the diverse sections of Gene. In the context of virology, ethical considerations loom large, necessitating robust frameworks to protect individual rights, an aspect essential in infectious disease research. Global collaboration emerges as a critical pillar in our response to emerging infectious diseases, fortified by the predictive prowess of mathematical models enriched by nanotechnology. The synergy of interdisciplinary collaboration, training the next generation to bridge mathematical rigor, biology, and epidemiology, promises accelerated discoveries and robust models that account for real-world complexities, fostering innovation and exploration in the field. In this intricate review, mathematical modeling in viral transmission dynamics and epidemiology serves as a guiding beacon, illuminating the path toward precision interventions, global preparedness, and the collective endeavor to safeguard human health, resonating with the aim of advancing knowledge in gene regulation and expression.
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Affiliation(s)
- Alaa A A Aljabali
- Faculty of Pharmacy, Department of Pharmaceutics & Pharmaceutical Technology, Yarmouk University, Irbid 21163, Jordan.
| | - Mohammad A Obeid
- Faculty of Pharmacy, Department of Pharmaceutics & Pharmaceutical Technology, Yarmouk University, Irbid 21163, Jordan
| | - Mohamed El-Tanani
- College of Pharmacy, Ras Al Khaimah Medical and Health Sciences University, Ras Al Khaimah, United Arab Emirates.
| | - Vijay Mishra
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab 144411, India
| | - Yachana Mishra
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab 144411, India
| | - Murtaza M Tambuwala
- Lincoln Medical School, University of Lincoln, Brayford Pool Campus, Lincoln LN6 7TS, United Kingdom.
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4
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Silva PV, Nobre CN. Computational methods in the analysis of SARS-CoV-2 in mammals: A systematic review of the literature. Comput Biol Med 2024; 173:108264. [PMID: 38564853 DOI: 10.1016/j.compbiomed.2024.108264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 02/15/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024]
Abstract
SARS-CoV-2 is an enveloped RNA virus that causes severe respiratory illness in humans and animals. It infects cells by binding the Spike protein to the host's angiotensin-converting enzyme 2 (ACE2). The bat is considered the natural host of the virus, and zoonotic transmission is a significant risk and can happen when humans come into close contact with infected animals. Therefore, understanding the interconnection between human, animal, and environmental health is important to prevent and control future coronavirus outbreaks. This work aimed to systematically review the literature to identify characteristics that make mammals suitable virus transmitters and raise the main computational methods used to evaluate SARS-CoV-2 in mammals. Based on this review, it was possible to identify the main factors related to transmissions mentioned in the literature, such as the expression of ACE2 and proximity to humans, in addition to identifying the computational methods used for its study, such as Machine Learning, Molecular Modeling, Computational Simulation, between others. The findings of the work contribute to the prevention and control of future outbreaks, provide information on transmission factors, and highlight the importance of advanced computational methods in the study of infectious diseases that allow a deeper understanding of transmission patterns and can help in the development of more effective control and intervention strategies.
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Affiliation(s)
- Paula Vitória Silva
- Pontifical Catholic University of Minas Gerais - PUC Minas, 500 Dom José Gaspar Street, Building 41, Coração Eucarístico, Belo Horizonte, MG 30535-901, Brazil.
| | - Cristiane N Nobre
- Pontifical Catholic University of Minas Gerais - PUC Minas, 500 Dom José Gaspar Street, Building 41, Coração Eucarístico, Belo Horizonte, MG 30535-901, Brazil.
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5
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Lu L, Zhang F, Brierley L, Robertson G, Chase-Topping M, Lycett S, Woolhouse M. Temporal Dynamics, Discovery, and Emergence of Human-Transmissible RNA Viruses. Mol Biol Evol 2024; 41:msad272. [PMID: 38241079 PMCID: PMC10797954 DOI: 10.1093/molbev/msad272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/03/2023] [Accepted: 11/28/2023] [Indexed: 01/21/2024] Open
Abstract
Transmissibility, the ability to spread within host populations, is a prerequisite for a pathogen to have epidemic or pandemic potential. Here, we estimate the phylogenies of human infectivity and transmissibility using 1,408 genome sequences from 743 distinct RNA virus species/types in 59 genera. By repeating this analysis using data sets censored by virus discovery date, we explore how temporal changes in the known diversity of RNA viruses-especially recent increases in recognized nonhuman viruses-have altered these phylogenies. Over time, we find significant increases in the proportion of RNA virus genera estimated to have a nonhuman-infective ancestral state, in the fraction of distinct human virus lineages that are purely human-transmissible or strictly zoonotic (compared to mixed lineages), and in the number of human viruses with nearest relatives known not to infect humans. Our results are consistent with viruses that are capable of spreading in human populations commonly emerging from a nonhuman reservoir. This is more likely in lineages that already contain human-transmissible viruses but is rare in lineages that contain only strictly zoonotic viruses.
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Affiliation(s)
- Lu Lu
- Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Feifei Zhang
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
- National Institute of Health Data Science at Peking University, Beijing, China
| | - Liam Brierley
- Institute of Population Health, University of Liverpool, Liverpool, Unitied Kingdom
| | - Gail Robertson
- Biomathematics and Statistics Scotland, Edinburgh, United Kingdom
| | | | - Samantha Lycett
- Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Mark Woolhouse
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
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6
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Khot V, Strous M, Dong X, Kiesser AK. Viral diversity and dynamics and CRISPR-Cas-mediated immunity in a robust alkaliphilic cyanobacterial consortium. Microbiol Spectr 2023; 11:e0221723. [PMID: 37819096 PMCID: PMC10715143 DOI: 10.1128/spectrum.02217-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 08/25/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE Biotechnology applications utilizing the function of microbial communities have become increasingly important solutions as we strive for sustainable applications. Although viral infections are known to have a significant impact on microbial turnover and nutrient cycling, viral dynamics have remained largely overlooked in these engineered communities. Predatory perturbations to the functional stability of these microbial biotechnology applications must be investigated in order to design more robust applications. In this study, we closely examine virus-microbe dynamics in a model microbial community used in a biotechnology application. Our findings suggest that viral dynamics change significantly with environmental conditions and that microbial immunity may play an important role in maintaining functional stability. We present this study as a comprehensive template for other researchers interested in exploring predatory dynamics in engineered microbial communities.
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Affiliation(s)
- Varada Khot
- Department of Geoscience, University of Calgary, Calgary, Alberta, Canada
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, Alberta, Canada
| | - Xiaoli Dong
- Department of Geoscience, University of Calgary, Calgary, Alberta, Canada
- Public Health Laboratory, Alberta Precision Laboratories, Foothills Medical Centre, Calgary, Alberta, Canada
| | - Alyse K. Kiesser
- School of Engineering, University of British Columbia Okanagan, Kelowna, British Columbia, Canada
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Ming Z, Chen X, Wang S, Liu H, Yuan Z, Wu M, Xia H. HostNet: improved sequence representation in deep neural networks for virus-host prediction. BMC Bioinformatics 2023; 24:455. [PMID: 38041071 PMCID: PMC10691023 DOI: 10.1186/s12859-023-05582-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 11/24/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND The escalation of viruses over the past decade has highlighted the need to determine their respective hosts, particularly for emerging ones that pose a potential menace to the welfare of both human and animal life. Yet, the traditional means of ascertaining the host range of viruses, which involves field surveillance and laboratory experiments, is a laborious and demanding undertaking. A computational tool with the capability to reliably predict host ranges for novel viruses can provide timely responses in the prevention and control of emerging infectious diseases. The intricate nature of viral-host prediction involves issues such as data imbalance and deficiency. Therefore, developing highly accurate computational tools capable of predicting virus-host associations is a challenging and pressing demand. RESULTS To overcome the challenges of virus-host prediction, we present HostNet, a deep learning framework that utilizes a Transformer-CNN-BiGRU architecture and two enhanced sequence representation modules. The first module, k-mer to vector, pre-trains a background vector representation of k-mers from a broad range of virus sequences to address the issue of data deficiency. The second module, an adaptive sliding window, truncates virus sequences of various lengths to create a uniform number of informative and distinct samples for each sequence to address the issue of data imbalance. We assess HostNet's performance on a benchmark dataset of "Rabies lyssavirus" and an in-house dataset of "Flavivirus". Our results show that HostNet surpasses the state-of-the-art deep learning-based method in host-prediction accuracies and F1 score. The enhanced sequence representation modules, significantly improve HostNet's training generalization, performance in challenging classes, and stability. CONCLUSION HostNet is a promising framework for predicting virus hosts from genomic sequences, addressing challenges posed by sparse and varying-length virus sequence data. Our results demonstrate its potential as a valuable tool for virus-host prediction in various biological contexts. Virus-host prediction based on genomic sequences using deep neural networks is a promising approach to identifying their potential hosts accurately and efficiently, with significant impacts on public health, disease prevention, and vaccine development.
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Affiliation(s)
- Zhaoyan Ming
- School of Computer and Computing Science, Hangzhou City University, Hangzhou, 310015, China
| | - Xiangjun Chen
- Polytechnic Institute, Zhejiang University, Hangzhou, 310058, China
| | - Shunlong Wang
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Hong Liu
- Institute of Biomedicine, Shandong University of Technology, Zibo, 255000, China
| | - Zhiming Yuan
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Minghui Wu
- School of Computer and Computing Science, Hangzhou City University, Hangzhou, 310015, China.
| | - Han Xia
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Wuhan, 430071, China.
- University of Chinese Academy of Sciences, Beijing, 100190, China.
- Hubei Jiangxia Laboratory, Wuhan, 430200, China.
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8
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Yi B, Deng Q, Guo C, Li X, Wu Q, Zha R, Wang X, Lu J. Evaluating the zoonotic potential of RNA viromes of rodents provides new insight into rodent-borne zoonotic pathogens in Guangdong, China. One Health 2023; 17:100631. [PMID: 38024253 PMCID: PMC10665145 DOI: 10.1016/j.onehlt.2023.100631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 12/01/2023] Open
Abstract
Emerging and re-emerging infectious diseases have been on the rise, with a significant proportion being zoonotic. Rodents, as the natural reservoirs of numerous diverse zoonotic viruses, pose a substantial threat to human health. To investigate the diversity of known and unknown viruses harbored by rodents in Guangdong (southern province of China), we conducted a comprehensive analysis of viral genomes through metagenomic sequencing of organs from 194 rodents. Our analysis yielded 2163 viral contigs that were assigned to 25 families known to infect a wide range of hosts, including vertebrates, invertebrates, amoebas, and plants. The viral compositions vary considerably among different organs, but not in rodent species. We also assessed and prioritized zoonotic potential of those detected viruses. Ninety-two viral species that are either known to infect vertebrates and invertebrates or only vertebrates were identified, among which 21 are considered high-risk to humans. The high-risk viruses included members of the Hantavirus, Picobirnaviruses, Astroviruses and Pestivirus. The phylogenetic trees of four zoonotic viruses revealed features of novel viral genomes that seem to fit evolutionarily into a zone of viruses that potentially pose a risk of transmission to humans. Recognizing that zoonotic diseases are a One Health issue, we approached the problem of identifying the zoonotic risk from rodent-transmitted disease in the Guangdong province by performing next-generation sequencing to look for potentially zoonotic viruses in these animals.
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Affiliation(s)
- Boyang Yi
- School of Public Health, Sun Yat-Sen University, Guangzhou 510080, China
- One Health Center of Excellence for Research & Training, Sun Yat-Sen University, Guangzhou 510080, China
| | - Qiang Deng
- School of Public Health, Sun Yat-Sen University, Guangzhou 510080, China
- One Health Center of Excellence for Research & Training, Sun Yat-Sen University, Guangzhou 510080, China
| | - Cheng Guo
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York 10032, USA
| | - Xiaokang Li
- School of Public Health, Sun Yat-Sen University, Guangzhou 510080, China
- One Health Center of Excellence for Research & Training, Sun Yat-Sen University, Guangzhou 510080, China
| | - Qin Wu
- School of Public Health, Sun Yat-Sen University, Guangzhou 510080, China
- One Health Center of Excellence for Research & Training, Sun Yat-Sen University, Guangzhou 510080, China
| | - Renyun Zha
- School of Public Health, Sun Yat-Sen University, Guangzhou 510080, China
- One Health Center of Excellence for Research & Training, Sun Yat-Sen University, Guangzhou 510080, China
| | - Xianhua Wang
- School of Health Sciences, Guangzhou Xinhua University, Guangzhou 510520, China
| | - Jiahai Lu
- School of Public Health, Sun Yat-Sen University, Guangzhou 510080, China
- One Health Center of Excellence for Research & Training, Sun Yat-Sen University, Guangzhou 510080, China
- National Medical Products Administration Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, Guangzhou 510080, China
- Hainan Key Novel Thinktank “Hainan Medical University ‘One Health’ Research Center”, Haikou 571199, China
- Key Laboratory of Tropical Diseases Control, Sun Yat-Sen University, Ministry of Education, Guangzhou 510080, China
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Bojko J, Duermit-Moreau E, Gandy R, Behringer DC. A new member of the Nudiviridae from the Florida stone crab (Menippe mercenaria). Virology 2023; 588:109910. [PMID: 37844408 DOI: 10.1016/j.virol.2023.109910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/04/2023] [Accepted: 10/09/2023] [Indexed: 10/18/2023]
Abstract
Menippe mercenaria, the Florida stone crab, supports an unconventional fishery across the southern USA and Caribbean that involves claw-removal and the return of de-clawed animals to the sea. We provide pathological, ultrastructural, and genomic detail for a novel hepatopancreatic, nucleus-specific virus - Menippe mercenaria nudivirus (MmNV) - isolated from M. mercenaria, captured during fisheries-independent monitoring. The virus has a genome of 99,336 bp and encodes 84 predicted protein coding genes and shows greatest similarity to Aratus pisonii nudivirus (ApNV) (<60% protein similarity and 31 shared genes of greatest similarity), collected from the Florida Keys, USA. MmNV is a member of the Gammanudivirus genus (Naldaviricetes: Lefavirales: Nudiviridae). Comparisons of virus genome size, preferred host environment, and gene number revealed no clear associations between the viral traits and phylogenetic position. Evolution of the virus alongside the diversification of host taxa, with the potential for host-switching, remain more likely evolutionary pathways.
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Affiliation(s)
- Jamie Bojko
- National Horizons Centre, Teesside University, Darlington, DL1 1HG, United Kingdom; Teesside University, Middlesbrough, TS1 3BX, United Kingdom.
| | | | - Ryan Gandy
- Florida Fish and Wildlife Research Institute, St. Petersburg, FL, 33701, USA
| | - Donald C Behringer
- Fisheries and Aquatic Sciences, University of Florida, Gainesville, FL, 32653, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, USA
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10
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Weber N, Nagy M, Markotter W, Schaer J, Puechmaille SJ, Sutton J, Dávalos LM, Dusabe MC, Ejotre I, Fenton MB, Knörnschild M, López-Baucells A, Medellin RA, Metz M, Mubareka S, Nsengimana O, O'Mara MT, Racey PA, Tuttle M, Twizeyimana I, Vicente-Santos A, Tschapka M, Voigt CC, Wikelski M, Dechmann DK, Reeder DM. Robust evidence for bats as reservoir hosts is lacking in most African virus studies: a review and call to optimize sampling and conserve bats. Biol Lett 2023; 19:20230358. [PMID: 37964576 PMCID: PMC10646460 DOI: 10.1098/rsbl.2023.0358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/25/2023] [Indexed: 11/16/2023] Open
Abstract
Africa experiences frequent emerging disease outbreaks among humans, with bats often proposed as zoonotic pathogen hosts. We comprehensively reviewed virus-bat findings from papers published between 1978 and 2020 to evaluate the evidence that African bats are reservoir and/or bridging hosts for viruses that cause human disease. We present data from 162 papers (of 1322) with original findings on (1) numbers and species of bats sampled across bat families and the continent, (2) how bats were selected for study inclusion, (3) if bats were terminally sampled, (4) what types of ecological data, if any, were recorded and (5) which viruses were detected and with what methodology. We propose a scheme for evaluating presumed virus-host relationships by evidence type and quality, using the contrasting available evidence for Orthoebolavirus versus Orthomarburgvirus as an example. We review the wording in abstracts and discussions of all 162 papers, identifying key framing terms, how these refer to findings, and how they might contribute to people's beliefs about bats. We discuss the impact of scientific research communication on public perception and emphasize the need for strategies that minimize human-bat conflict and support bat conservation. Finally, we make recommendations for best practices that will improve virological study metadata.
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Affiliation(s)
- Natalie Weber
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
- University of Ulm, Institute of Evolutionary Ecology and Conservation Genomics, Ulm, Germany
| | - Martina Nagy
- Museum für Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Wanda Markotter
- Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Juliane Schaer
- Museum für Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science, Berlin, Germany
- Institute of Biology, Humboldt University, Berlin, Germany
| | - Sébastien J. Puechmaille
- ISEM, University of Montpellier, Montpellier, France
- Institut Universitaire de France, Paris, France
- Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
| | | | - Liliana M. Dávalos
- Department of Ecology and Evolution and Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, USA
| | | | - Imran Ejotre
- Institute of Biology, Humboldt University, Berlin, Germany
- Muni University, Arua, Uganda
| | - M. Brock Fenton
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Mirjam Knörnschild
- Museum für Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science, Berlin, Germany
- Evolutionary Ethology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
| | | | - Rodrigo A. Medellin
- Institute of Ecology, National Autonomous University of Mexico, Mexico City, Mexico
| | | | - Samira Mubareka
- Sunnybrook Research Institute and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | | | - M. Teague O'Mara
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
- Bat Conservation International Austin, TX, USA
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, LA, USA
| | - Paul A. Racey
- Centre for Ecology and Conservation, University of Exeter, Exeter, UK
| | - Merlin Tuttle
- Merlin Tuttle's Bat Conservation, Austin, TX USA
- Department of Integrative Biology, University of Texas, Austin, USA
| | | | - Amanda Vicente-Santos
- Graduate Program in Population Biology, Ecology and Emory University, Atlanta, GA, USA
- Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Marco Tschapka
- University of Ulm, Institute of Evolutionary Ecology and Conservation Genomics, Ulm, Germany
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
| | | | - Martin Wikelski
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Dina K.N. Dechmann
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
- Department of Biology, University of Konstanz, Konstanz, Germany
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11
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Muylaert RL, Wilkinson DA, Kingston T, D'Odorico P, Rulli MC, Galli N, John RS, Alviola P, Hayman DTS. Using drivers and transmission pathways to identify SARS-like coronavirus spillover risk hotspots. Nat Commun 2023; 14:6854. [PMID: 37891177 PMCID: PMC10611769 DOI: 10.1038/s41467-023-42627-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
The emergence of SARS-like coronaviruses is a multi-stage process from wildlife reservoirs to people. Here we characterize multiple drivers-landscape change, host distribution, and human exposure-associated with the risk of spillover of zoonotic SARS-like coronaviruses to help inform surveillance and mitigation activities. We consider direct and indirect transmission pathways by modeling four scenarios with livestock and mammalian wildlife as potential and known reservoirs before examining how access to healthcare varies within clusters and scenarios. We found 19 clusters with differing risk factor contributions within a single country (N = 9) or transboundary (N = 10). High-risk areas were mainly closer (11-20%) rather than far ( < 1%) from healthcare. Areas far from healthcare reveal healthcare access inequalities, especially Scenario 3, which includes wild mammals and not livestock as secondary hosts. China (N = 2) and Indonesia (N = 1) had clusters with the highest risk. Our findings can help stakeholders in land use planning, integrating healthcare implementation and One Health actions.
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Affiliation(s)
- Renata L Muylaert
- School of Veterinary Science, Massey University, Palmerston North, New Zealand.
| | - David A Wilkinson
- UMR ASTRE, CIRAD, INRAE, Université de Montpellier, Plateforme Technologique CYROI, Sainte-Clotilde, La Réunion, France
| | - Tigga Kingston
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Paolo D'Odorico
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA
| | - Maria Cristina Rulli
- Department of Civil and Environmental Engineering, Politecnico di Milano, Milan, Italy
| | - Nikolas Galli
- Department of Civil and Environmental Engineering, Politecnico di Milano, Milan, Italy
| | - Reju Sam John
- Department of Physics, Faculty of Science, University of Auckland, Auckland, New Zealand
| | - Phillip Alviola
- Institute of Biological Sciences, University of the Philippines- Los Banos, Laguna, Philippines
| | - David T S Hayman
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
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12
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Gamble A, Olarte-Castillo XA, Whittaker GR. Backyard zoonoses: The roles of companion animals and peri-domestic wildlife. Sci Transl Med 2023; 15:eadj0037. [PMID: 37851821 DOI: 10.1126/scitranslmed.adj0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/28/2023] [Indexed: 10/20/2023]
Abstract
The spillover of human infectious diseases from animal reservoirs is now well appreciated. However, societal and climate-related changes are affecting the dynamics of such interfaces. In addition to the disruption of traditional wildlife habitats, in part because of climate change and human demographics and behavior, there is an increasing zoonotic disease risk from companion animals. This includes such factors as the awareness of animals kept as domestic pets and increasing populations of free-ranging animals in peri-domestic environments. This review presents background and commentary focusing on companion and peri-domestic animals as disease risk for humans, taking into account the human-animal interface and population dynamics between the animals themselves.
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Affiliation(s)
- Amandine Gamble
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, UK
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Ximena A Olarte-Castillo
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Gary R Whittaker
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
- Atkinson Center for Sustainability, Cornell University, Ithaca, NY, USA
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13
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Si Y, Wu W, Xue X, Sun X, Qin Y, Li Y, Qiu C, Li Y, Zhuo Z, Mi Y, Zheng P. The evolution of SARS-CoV-2 and the COVID-19 pandemic. PeerJ 2023; 11:e15990. [PMID: 37701824 PMCID: PMC10493083 DOI: 10.7717/peerj.15990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 08/08/2023] [Indexed: 09/14/2023] Open
Abstract
Scientists have made great efforts to understand the evolution of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) to provide crucial information to public health experts on strategies to control this viral pathogen. The pandemic of the coronavirus disease that began in 2019, COVID-19, lasted nearly three years, and nearly all countries have set different epidemic prevention policies for this virus. The continuous evolution of SARS-CoV-2 alters its pathogenicity and infectivity in human hosts, thus the policy and treatments have been continually adjusted. Based on our previous study on the dynamics of binding ability prediction between the COVID-19 spike protein and human ACE2, the present study mined over 10 million sequences and epidemiological data of SARS-CoV-2 during 2020-2022 to understand the evolutionary path of SARS-CoV-2. We analyzed and predicted the mutation rates of the whole genome and main proteins of SARS-CoV-2 from different populations to understand the adaptive relationship between humans and COVID-19. Our study identified a correlation of the mutation rates from each protein of SARS-CoV-2 and various human populations. Overall, this analysis provides a scientific basis for developing data-driven strategies to confront human pathogens.
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Affiliation(s)
- Yuanfang Si
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Weidong Wu
- BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Xia Xue
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Xiangdong Sun
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Yaping Qin
- School of Basic Medical Sciences, Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Ya Li
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Chunjing Qiu
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Yingying Li
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Ziran Zhuo
- BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yang Mi
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Pengyuan Zheng
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
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14
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Sessions Z, Bobrowski T, Martin HJ, Beasley JMT, Kothari A, Phares T, Li M, Alves VM, Scotti MT, Moorman NJ, Baric R, Tropsha A, Muratov EN. Praemonitus praemunitus: can we forecast and prepare for future viral disease outbreaks? FEMS Microbiol Rev 2023; 47:fuad048. [PMID: 37596064 PMCID: PMC10532129 DOI: 10.1093/femsre/fuad048] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 07/04/2023] [Accepted: 08/17/2023] [Indexed: 08/20/2023] Open
Abstract
Understanding the origins of past and present viral epidemics is critical in preparing for future outbreaks. Many viruses, including SARS-CoV-2, have led to significant consequences not only due to their virulence, but also because we were unprepared for their emergence. We need to learn from large amounts of data accumulated from well-studied, past pandemics and employ modern informatics and therapeutic development technologies to forecast future pandemics and help minimize their potential impacts. While acknowledging the complexity and difficulties associated with establishing reliable outbreak predictions, herein we provide a perspective on the regions of the world that are most likely to be impacted by future outbreaks. We specifically focus on viruses with epidemic potential, namely SARS-CoV-2, MERS-CoV, DENV, ZIKV, MAYV, LASV, noroviruses, influenza, Nipah virus, hantaviruses, Oropouche virus, MARV, and Ebola virus, which all require attention from both the public and scientific community to avoid societal catastrophes like COVID-19. Based on our literature review, data analysis, and outbreak simulations, we posit that these future viral epidemics are unavoidable, but that their societal impacts can be minimized by strategic investment into basic virology research, epidemiological studies of neglected viral diseases, and antiviral drug discovery.
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Affiliation(s)
- Zoe Sessions
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, 301 Pharmacy Ln, Chapel Hill, NC 27599, United States
| | - Tesia Bobrowski
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, 301 Pharmacy Ln, Chapel Hill, NC 27599, United States
| | - Holli-Joi Martin
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, 301 Pharmacy Ln, Chapel Hill, NC 27599, United States
| | - Jon-Michael T Beasley
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, 301 Pharmacy Ln, Chapel Hill, NC 27599, United States
| | - Aneri Kothari
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, 301 Pharmacy Ln, Chapel Hill, NC 27599, United States
| | - Trevor Phares
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, 301 Pharmacy Ln, Chapel Hill, NC 27599, United States
- School of Chemistry, University of Louisville, 2320 S Brook St, Louisville, KY 40208, United States
| | - Michael Li
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, 301 Pharmacy Ln, Chapel Hill, NC 27599, United States
| | - Vinicius M Alves
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, 301 Pharmacy Ln, Chapel Hill, NC 27599, United States
| | - Marcus T Scotti
- Department of Pharmaceutical Sciences, Federal University of Paraiba, Campus I Lot. Cidade Universitaria, PB, 58051-900, Brazil
| | - Nathaniel J Moorman
- Department of Microbiology and Immunology, University of North Carolina, 116 Manning Drive, Chapel Hill, NC 27599, United States
| | - Ralph Baric
- Department of Epidemiology, University of North Carolina, 401 Pittsboro St, Chapel Hill, NC 27599, United States
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, 301 Pharmacy Ln, Chapel Hill, NC 27599, United States
| | - Eugene N Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, 301 Pharmacy Ln, Chapel Hill, NC 27599, United States
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15
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Dundarova H, Ivanova-Aleksandrova N, Bednarikova S, Georgieva I, Kirov K, Miteva K, Neov B, Ostoich P, Pikula J, Zukal J, Hristov P. Phylogeographic Aspects of Bat Lyssaviruses in Europe: A Review. Pathogens 2023; 12:1089. [PMID: 37764897 PMCID: PMC10534866 DOI: 10.3390/pathogens12091089] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/08/2023] [Accepted: 08/22/2023] [Indexed: 09/29/2023] Open
Abstract
During the last few decades, bat lyssaviruses have become the topic of intensive molecular and epidemiological investigations. Since ancient times, rhabdoviruses have caused fatal encephalitis in humans which has led to research into effective strategies for their eradication. Modelling of potential future cross-species virus transmissions forms a substantial component of the recent infection biology of rabies. In this article, we summarise the available data on the phylogeography of both bats and lyssaviruses in Europe and the adjacent reg ions, especially in the contact zone between the Palearctic and Ethiopian realms. Within these zones, three bat families are present with high potential for cross-species transmission and the spread of lyssaviruses in Phylogroup II to Europe (part of the western Palearctic). The lack of effective therapies for rabies viruses in Phylogroup II and the most divergent lyssaviruses generates impetus for additional phylogenetic and virological research within this geographical region.
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Affiliation(s)
- Heliana Dundarova
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd., 1000 Sofia, Bulgaria
| | | | - Sarka Bednarikova
- Department of Ecology and Diseases of Zoo Animals, Game, Fish and Bees, University of Veterinary Sciences Brno, Palackého tř. 1946/1, 612 42 Brno, Czech Republic
| | - Irina Georgieva
- National Centre of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Krasimir Kirov
- Faculty of Biology, University of Plovdiv “Paisii Hilendarski”, 24 Tzar Assen Str., 4000 Plovdiv, Bulgaria
| | - Kalina Miteva
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd., 1000 Sofia, Bulgaria
| | - Boyko Neov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd., 1000 Sofia, Bulgaria
| | - Peter Ostoich
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd., 1000 Sofia, Bulgaria
| | - Jiri Pikula
- Department of Ecology and Diseases of Zoo Animals, Game, Fish and Bees, University of Veterinary Sciences Brno, Palackého tř. 1946/1, 612 42 Brno, Czech Republic
| | - Jan Zukal
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic
| | - Peter Hristov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd., 1000 Sofia, Bulgaria
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16
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Urban L, Perlas A, Francino O, Martí‐Carreras J, Muga BA, Mwangi JW, Boykin Okalebo L, Stanton JL, Black A, Waipara N, Fontsere C, Eccles D, Urel H, Reska T, Morales HE, Palmada‐Flores M, Marques‐Bonet T, Watsa M, Libke Z, Erkenswick G, van Oosterhout C. Real-time genomics for One Health. Mol Syst Biol 2023; 19:e11686. [PMID: 37325891 PMCID: PMC10407731 DOI: 10.15252/msb.202311686] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/17/2023] Open
Abstract
The ongoing degradation of natural systems and other environmental changes has put our society at a crossroad with respect to our future relationship with our planet. While the concept of One Health describes how human health is inextricably linked with environmental health, many of these complex interdependencies are still not well-understood. Here, we describe how the advent of real-time genomic analyses can benefit One Health and how it can enable timely, in-depth ecosystem health assessments. We introduce nanopore sequencing as the only disruptive technology that currently allows for real-time genomic analyses and that is already being used worldwide to improve the accessibility and versatility of genomic sequencing. We showcase real-time genomic studies on zoonotic disease, food security, environmental microbiome, emerging pathogens, and their antimicrobial resistances, and on environmental health itself - from genomic resource creation for wildlife conservation to the monitoring of biodiversity, invasive species, and wildlife trafficking. We stress why equitable access to real-time genomics in the context of One Health will be paramount and discuss related practical, legal, and ethical limitations.
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Affiliation(s)
- Lara Urban
- Helmholtz AI, Helmholtz Zentrum MuenchenNeuherbergGermany
- Helmholtz Pioneer Campus, Helmholtz Zentrum MuenchenNeuherbergGermany
- School of Life Sciences, Technical University of MunichFreisingGermany
| | - Albert Perlas
- Helmholtz AI, Helmholtz Zentrum MuenchenNeuherbergGermany
- Helmholtz Pioneer Campus, Helmholtz Zentrum MuenchenNeuherbergGermany
| | - Olga Francino
- Nano1Health SL, Parc de Recerca UABCampus Universitat Autònoma de BarcelonaBarcelonaSpain
| | - Joan Martí‐Carreras
- Nano1Health SL, Parc de Recerca UABCampus Universitat Autònoma de BarcelonaBarcelonaSpain
| | - Brenda A Muga
- Department of AnatomyUniversity of OtagoDunedinNew Zealand
| | | | | | | | - Amanda Black
- Bioprotection AotearoaLincoln UniversityLincolnNew Zealand
| | | | - Claudia Fontsere
- Center for Evolutionary HologenomicsThe Globe Institute, University of CopenhagenCopenhagenDenmark
| | - David Eccles
- Hugh Green Cytometry CentreMalaghan Institute of Medical ResearchWellingtonNew Zealand
| | - Harika Urel
- Helmholtz AI, Helmholtz Zentrum MuenchenNeuherbergGermany
- Helmholtz Pioneer Campus, Helmholtz Zentrum MuenchenNeuherbergGermany
- School of Life Sciences, Technical University of MunichFreisingGermany
| | - Tim Reska
- Helmholtz AI, Helmholtz Zentrum MuenchenNeuherbergGermany
- Helmholtz Pioneer Campus, Helmholtz Zentrum MuenchenNeuherbergGermany
- School of Life Sciences, Technical University of MunichFreisingGermany
| | - Hernán E Morales
- Center for Evolutionary HologenomicsThe Globe Institute, University of CopenhagenCopenhagenDenmark
- Department of Biology, Ecology BuildingLund UniversityLundSweden
| | - Marc Palmada‐Flores
- Institute of Evolutionary BiologyUniversitat Pompeu Fabra‐CSIC, PRBBBarcelonaSpain
| | - Tomas Marques‐Bonet
- Institute of Evolutionary BiologyUniversitat Pompeu Fabra‐CSIC, PRBBBarcelonaSpain
- Catalan Institution of Research and Advanced Studies (ICREA)BarcelonaSpain
- CNAGCentre of Genomic AnalysisBarcelonaSpain
- Institut Català de Paleontologia Miquel CrusafontUniversitat Autònoma de BarcelonaBarcelonaSpain
| | | | - Zane Libke
- Instituto Nacional de BiodiversidadQuitoEcuador
- Fundación Sumak Kawsay In SituCantón MeraEcuador
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17
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Gupte PR, Albery GF, Gismann J, Sweeny A, Weissing FJ. Novel pathogen introduction triggers rapid evolution in animal social movement strategies. eLife 2023; 12:e81805. [PMID: 37548365 PMCID: PMC10449382 DOI: 10.7554/elife.81805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/04/2023] [Indexed: 08/08/2023] Open
Abstract
Animal sociality emerges from individual decisions on how to balance the costs and benefits of being sociable. Novel pathogens introduced into wildlife populations should increase the costs of sociality, selecting against gregariousness. Using an individual-based model that captures essential features of pathogen transmission among social hosts, we show how novel pathogen introduction provokes the rapid evolutionary emergence and coexistence of distinct social movement strategies. These strategies differ in how they trade the benefits of social information against the risk of infection. Overall, pathogen-risk-adapted populations move more and have fewer associations with other individuals than their pathogen-risk-naive ancestors, reducing disease spread. Host evolution to be less social can be sufficient to cause a pathogen to be eliminated from a population, which is followed by a rapid recovery in social tendency. Our conceptual model is broadly applicable to a wide range of potential host-pathogen introductions and offers initial predictions for the eco-evolutionary consequences of wildlife pathogen spillover scenarios and a template for the development of theory in the ecology and evolution of animals' movement decisions.
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Affiliation(s)
- Pratik Rajan Gupte
- Groningen Institute for Evolutionary Life Sciences, University of GroningenGroningenNetherlands
| | - Gregory F Albery
- Georgetown UniversityWashingtonUnited States
- Wissenschaftskolleg zu BerlinBerlinGermany
| | - Jakob Gismann
- Groningen Institute for Evolutionary Life Sciences, University of GroningenGroningenNetherlands
| | - Amy Sweeny
- Institute of Evolutionary Biology, University of EdinburghEdinburghUnited Kingdom
| | - Franz J Weissing
- Groningen Institute for Evolutionary Life Sciences, University of GroningenGroningenNetherlands
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18
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Zhai J, Wang Y, Tang B, Zheng S, He S, Zhao W, Chen H, Lin J, Li F, Bao Y, Lancuo Z, Sharshov K, Liu C, Wang W. Comparative analysis of gut DNA viromes in wild and captive Himalayan vultures. Front Microbiol 2023; 14:1120838. [PMID: 37601346 PMCID: PMC10433386 DOI: 10.3389/fmicb.2023.1120838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 07/21/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction Himalayan vultures (Gyps hinalayensis) are widely distributed on the Qinghai-Tibetan Plateau and play a crucial role in maintaining the ecological balance by feeding on decayed corpses of wild and domestic animals. Large-scale culture and metagenomics studies have broadened our understanding of viral diversity in animals' gastrointestinal tracts. However, despite the importance of gut viral communities in regulating bacterial diversity and performing symbiotic functions, no gut viral study has been conducted on Himalayan vultures. Furthermore, the impact of captivity on the gut virome of these vultures remains unknown. Methods In this study, metagenomic sequencing methods targeting DNA of virus-like particles enriched from feces were used to characterize the gut DNA viromes of wild and captive Himalayan vultures. Results In total, 22,938 unique viral operational taxonomic units (vOTUs) were identified and assigned to 140 viral genera in 41 viral families. These families included viruses associated with bacteria, animals, plants, insects, and archaea. Phage communities, including Siphoviridae, Microviridae, Myoviridae, Inoviridae, and Herelleviridae, dominated the gut virome of Himalayan vultures. Wild vultures exhibited higher viral richness and diversity compared with those in captivity. The functional capacity of the gut virome was characterized by identifying 93 KEGG pathways, which were significantly enriched in metabolism and genetic information processing. Abundant auxiliary metabolic genes, such as carbohydrate-active enzyme, and antibiotic resistance genes, were also found in the vultures' gut virome. Discussion Our findings reveal the complex and diverse viral community present in the gut virome of Himalayan vultures, which varies between wild, and captive states. The DNA virome dataset establishes a baseline for the vultures' gut virome and will serve as a reference for future virus isolation and cultivation. Understanding the impact of captivity on the gut virome contributes to our knowledge of vultures' response to captivity and aids in optimizing their rehabilitation and implementing protective measures.
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Affiliation(s)
- Jundie Zhai
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - You Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Boyu Tang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Sisi Zheng
- Animal Disease Prevention and Control Center of Qinghai Province, Xining, Qinghai, China
| | - Shunfu He
- Xining Wildlife Park of Qinghai Province, Xining, Qinghai, China
| | - Wenxin Zhao
- Xining Wildlife Park of Qinghai Province, Xining, Qinghai, China
| | - Hanxi Chen
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Jun Lin
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Feng Li
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Yuzi Bao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Zhuoma Lancuo
- College of Finance and Economics, Qinghai University, Xining, Qinghai, China
| | - Kirill Sharshov
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
| | - Chuanfa Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wen Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
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19
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Salve BG, Kurian AM, Vijay N. Concurrent loss of ciliary genes WDR93 and CFAP46 in phylogenetically distant birds. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230801. [PMID: 37621660 PMCID: PMC10445033 DOI: 10.1098/rsos.230801] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/01/2023] [Indexed: 08/26/2023]
Abstract
The respiratory system is the primary route of infection for many contagious pathogens. Mucociliary clearance of inhaled pathogens is an important innate defence mechanism sustained by the rhythmic movement of epithelial cilia. To counter host defences, viral pathogens target epithelial cells and cilia. For instance, the avian influenza virus that targets ciliated cells modulates the expression of WDR93, a central ciliary apparatus C1d projection component. Lineage-specific prevalence of such host defence genes results in differential susceptibility. In this study, the comparative analysis of approximately 500 vertebrate genomes from seven taxonomic classes spanning 73 orders confirms the widespread conservation of WDR93 across these different vertebrate groups. However, we established loss of the WDR93 in landfowl, geese and other phylogenetically independent bird species due to gene-disrupting changes. The lack of WDR93 transcripts in species with gene loss in contrast to its expression in species with an intact gene confirms gene loss. Notably, species with WDR93 loss have concurrently lost another C1d component, CFAP46, through large segmental deletions. Understanding the consequences of such gene loss may provide insight into their role in host-pathogen interactions and benefit global pathogen surveillance efforts by prioritizing species missing host defence genes and identifying putative zoonotic reservoirs.
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Affiliation(s)
- Buddhabhushan Girish Salve
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India
| | - Amia Miriam Kurian
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India
| | - Nagarjun Vijay
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India
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20
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Poisot T, Ouellet MA, Mollentze N, Farrell MJ, Becker DJ, Brierley L, Albery GF, Gibb RJ, Seifert SN, Carlson CJ. Network embedding unveils the hidden interactions in the mammalian virome. PATTERNS (NEW YORK, N.Y.) 2023; 4:100738. [PMID: 37409053 PMCID: PMC10318366 DOI: 10.1016/j.patter.2023.100738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 01/19/2023] [Accepted: 03/31/2023] [Indexed: 07/07/2023]
Abstract
Predicting host-virus interactions is fundamentally a network science problem. We develop a method for bipartite network prediction that combines a recommender system (linear filtering) with an imputation algorithm based on low-rank graph embedding. We test this method by applying it to a global database of mammal-virus interactions and thus show that it makes biologically plausible predictions that are robust to data biases. We find that the mammalian virome is under-characterized anywhere in the world. We suggest that future virus discovery efforts could prioritize the Amazon Basin (for its unique coevolutionary assemblages) and sub-Saharan Africa (for its poorly characterized zoonotic reservoirs). Graph embedding of the imputed network improves predictions of human infection from viral genome features, providing a shortlist of priorities for laboratory studies and surveillance. Overall, our study indicates that the global structure of the mammal-virus network contains a large amount of information that is recoverable, and this provides new insights into fundamental biology and disease emergence.
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Affiliation(s)
- Timothée Poisot
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC, Canada
| | - Marie-Andrée Ouellet
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC, Canada
| | - Nardus Mollentze
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
- MRC – University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Maxwell J. Farrell
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | | | - Liam Brierley
- Department of Health Data Science, University of Liverpool, Liverpool, UK
| | | | - Rory J. Gibb
- Center for Biodiversity & Environment Research, University College, London, UK
| | - Stephanie N. Seifert
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA, USA
| | - Colin J. Carlson
- Center for Global Health Science and Security, Georgetown University, Washington, DC, USA
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21
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Shi H, Wang J, Cheng J, Qi X, Ji H, Struchiner CJ, Villela DAM, Karamov EV, Turgiev AS. Big data technology in infectious diseases modeling, simulation, and prediction after the COVID-19 outbreak. INTELLIGENT MEDICINE 2023; 3:85-96. [PMID: 36694623 PMCID: PMC9851724 DOI: 10.1016/j.imed.2023.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 12/06/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
After the outbreak of COVID-19, the interaction of infectious disease systems and social systems has challenged traditional infectious disease modeling methods. Starting from the research purpose and data, researchers improved the structure and data of the compartment model or used agents and artificial intelligence based models to solve epidemiological problems. In terms of modeling methods, the researchers use compartment subdivision, dynamic parameters, agent-based model methods, and artificial intelligence related methods. In terms of factors studied, the researchers studied 6 categories: human mobility, nonpharmaceutical interventions (NPIs), ages, medical resources, human response, and vaccine. The researchers completed the study of factors through modeling methods to quantitatively analyze the impact of social systems and put forward their suggestions for the future transmission status of infectious diseases and prevention and control strategies. This review started with a research structure of research purpose, factor, data, model, and conclusion. Focusing on the post-COVID-19 infectious disease prediction simulation research, this study summarized various improvement methods and analyzes matching improvements for various specific research purposes.
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Affiliation(s)
- Honghao Shi
- School of Computer Science and Engineering, Beihang University, Beijing 100191, China
| | - Jingyuan Wang
- School of Computer Science and Engineering, Beihang University, Beijing 100191, China
| | - Jiawei Cheng
- School of Computer Science and Engineering, Beihang University, Beijing 100191, China
| | - Xiaopeng Qi
- Center for Global Public Health, Chinese Center for Disease Control and Prevention, Beijing 102211, China
| | - Hanran Ji
- Center for Global Public Health, Chinese Center for Disease Control and Prevention, Beijing 102211, China
| | - Claudio J Struchiner
- Fundação Getúlio Vargas, Rio de Janeiro, Brazil
- Instituto de Medicina Social Hesio Cordeiro, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Daniel AM Villela
- Programa de Computação Científica, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Eduard V Karamov
- Gamaleya National Research Center for Epidemiology and Microbiology of the Russian Ministry of Health, Russia
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases of the Russian Ministry of Health, Russia
| | - Ali S Turgiev
- Gamaleya National Research Center for Epidemiology and Microbiology of the Russian Ministry of Health, Russia
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases of the Russian Ministry of Health, Russia
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22
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Alwine JC, Casadevall A, Enquist LW, Goodrum FD, Imperiale MJ. A Critical Analysis of the Evidence for the SARS-CoV-2 Origin Hypotheses. mSphere 2023; 8:e0011923. [PMID: 36897078 PMCID: PMC10117112 DOI: 10.1128/msphere.00119-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
When humans experience a new, devastating viral infection such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), significant challenges arise. How should individuals as well as societies respond to the situation? One of the primary questions concerns the origin of the SARS-CoV-2 virus that infected and was transmitted efficiently among humans, resulting in a pandemic. At first glance, the question appears straightforward to answer. However, the origin of SARS-CoV-2 has been the topic of substantial debate primarily because we do not have access to some relevant data. At least two major hypotheses have been suggested: a natural origin through zoonosis followed by sustained human-to-human spread or the introduction of a natural virus into humans from a laboratory source. Here, we summarize the scientific evidence that informs this debate to provide our fellow scientists and the public with the tools to join the discussion in a constructive and informed manner. Our goal is to dissect the evidence to make it more accessible to those interested in this important problem. The engagement of a broad representation of scientists is critical to ensure that the public and policy-makers can draw on relevant expertise in navigating this controversy.
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Affiliation(s)
- James C. Alwine
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
| | - Arturo Casadevall
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Lynn W. Enquist
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Felicia D. Goodrum
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
- BIO5 Institute, University of Arizona, Tucson, Arizona, USA
| | - Michael J. Imperiale
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
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23
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Goodrum F, Lowen AC, Lakdawala S, Alwine J, Casadevall A, Imperiale MJ, Atwood W, Avgousti D, Baines J, Banfield B, Banks L, Bhaduri-McIntosh S, Bhattacharya D, Blanco-Melo D, Bloom D, Boon A, Boulant S, Brandt C, Broadbent A, Brooke C, Cameron C, Campos S, Caposio P, Chan G, Cliffe A, Coffin J, Collins K, Damania B, Daugherty M, Debbink K, DeCaprio J, Dermody T, Dikeakos J, DiMaio D, Dinglasan R, Duprex WP, Dutch R, Elde N, Emerman M, Enquist L, Fane B, Fernandez-Sesma A, Flenniken M, Frappier L, Frieman M, Frueh K, Gack M, Gaglia M, Gallagher T, Galloway D, García-Sastre A, Geballe A, Glaunsinger B, Goff S, Greninger A, Hancock M, Harris E, Heaton N, Heise M, Heldwein E, Hogue B, Horner S, Hutchinson E, Hyser J, Jackson W, Kalejta R, Kamil J, Karst S, Kirchhoff F, Knipe D, Kowalik T, Lagunoff M, Laimins L, Langlois R, Lauring A, Lee B, Leib D, Liu SL, Longnecker R, Lopez C, Luftig M, Lund J, Manicassamy B, McFadden G, McIntosh M, Mehle A, Miller WA, Mohr I, Moody C, Moorman N, Moscona A, Mounce B, Munger J, Münger K, Murphy E, Naghavi M, Nelson J, Neufeldt C, Nikolich J, O'Connor C, Ono A, Orenstein W, Ornelles D, Ou JH, Parker J, Parrish C, Pekosz A, Pellett P, Pfeiffer J, Plemper R, Polyak S, Purdy J, Pyeon D, Quinones-Mateu M, Renne R, Rice C, Schoggins J, Roller R, Russell C, Sandri-Goldin R, Sapp M, Schang L, Schmid S, Schultz-Cherry S, Semler B, Shenk T, Silvestri G, Simon V, Smith G, Smith J, Spindler K, Stanifer M, Subbarao K, Sundquist W, Suthar M, Sutton T, Tai A, Tarakanova V, tenOever B, Tibbetts S, Tompkins S, Toth Z, van Doorslaer K, Vignuzzi M, Wallace N, Walsh D, Weekes M, Weinberg J, Weitzman M, Weller S, Whelan S, White E, Williams B, Wobus C, Wong S, Yurochko A. Virology under the Microscope-a Call for Rational Discourse. mSphere 2023; 8:e0003423. [PMID: 36700653 PMCID: PMC10117089 DOI: 10.1128/msphere.00034-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Viruses have brought humanity many challenges: respiratory infection, cancer, neurological impairment and immunosuppression to name a few. Virology research over the last 60+ years has responded to reduce this disease burden with vaccines and antivirals. Despite this long history, the COVID-19 pandemic has brought unprecedented attention to the field of virology. Some of this attention is focused on concern about the safe conduct of research with human pathogens. A small but vocal group of individuals has seized upon these concerns - conflating legitimate questions about safely conducting virus-related research with uncertainties over the origins of SARS-CoV-2. The result has fueled public confusion and, in many instances, ill-informed condemnation of virology. With this article, we seek to promote a return to rational discourse. We explain the use of gain-of-function approaches in science, discuss the possible origins of SARS-CoV-2 and outline current regulatory structures that provide oversight for virological research in the United States. By offering our expertise, we - a broad group of working virologists - seek to aid policy makers in navigating these controversial issues. Balanced, evidence-based discourse is essential to addressing public concern while maintaining and expanding much-needed research in virology.
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Affiliation(s)
- Felicia Goodrum
- Department of Immunobiology, BIO5 Institute, University of Arizona, Tucson, Arizona, USA
| | - Anice C Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Seema Lakdawala
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - James Alwine
- Department of Immunobiology, BIO5 Institute, University of Arizona, Tucson, Arizona, USA
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Michael J Imperiale
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Daphne Avgousti
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | - Lawrence Banks
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | | | | | | | - David Bloom
- University of Florida, Gainesville, Florida, USA
| | - Adrianus Boon
- University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | | | - Curtis Brandt
- University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | | | - Craig Cameron
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | - Gary Chan
- SUNY Upstate Medical University, Syracuse, New York, USA
| | - Anna Cliffe
- University of Virginia, Charlottesville, Virginia, USA
| | - John Coffin
- Tufts University, Boston, Massachusetts, USA
| | | | - Blossom Damania
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Kari Debbink
- Johns Hopkins University, Baltimore, Maryland, USA
| | | | | | | | | | | | - W Paul Duprex
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - Nels Elde
- University of Utah, Salt Lake City, Utah, USA
| | - Michael Emerman
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Lynn Enquist
- Princeton University, Princeton, New Jersey, USA
| | | | | | | | | | | | - Klaus Frueh
- Oregon Health and Science University, Beaverton, Oregon, USA
| | - Michaela Gack
- Florida Research and Innovation Center, Port Saint Lucie, Florida, USA
| | - Marta Gaglia
- University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Denise Galloway
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Adam Geballe
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | | | - Meaghan Hancock
- Oregon Health and Science University, Beaverton, Oregon, USA
| | - Eva Harris
- University of California, Berkeley, Berkeley, California, USA
| | | | - Mark Heise
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | | | | | | | | | | | - Jeremy Kamil
- Louisiana State University, Shreveport, Louisiana, USA
| | | | | | - David Knipe
- Harvard Medical School, Boston, Massachusetts, USA
| | | | | | | | - Ryan Langlois
- University of Minnesota, Minneapolis, Minnesota, USA
| | - Adam Lauring
- University of Michigan, Ann Arbor, Michigan, USA
| | - Benhur Lee
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - David Leib
- Dartmouth College, Lebanon, New Hampshire, USA
| | - Shan-Lu Liu
- The Ohio State University, Columbus, Ohio, USA
| | | | | | | | - Jennifer Lund
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | | | - Andrew Mehle
- University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Ian Mohr
- New York University, New York, New York, USA
| | - Cary Moody
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | | | | | - Karl Münger
- Tufts University, Boston, Massachusetts, USA
| | - Eain Murphy
- SUNY Upstate Medical University, Syracuse, New York, USA
| | | | - Jay Nelson
- Oregon Health and Science University, Beaverton, Oregon, USA
| | | | | | | | - Akira Ono
- University of Michigan, Ann Arbor, Michigan, USA
| | | | - David Ornelles
- Wake Forest University, Winston-Salem, North Carolina, USA
| | - Jing-Hsiung Ou
- University of Southern California, Los Angeles, California, USA
| | | | | | | | | | | | | | | | - John Purdy
- University of Arizona, Tucson, Arizona, USA
| | - Dohun Pyeon
- Michigan State University, East Lansing, Michigan, USA
| | | | - Rolf Renne
- University of Florida, Gainesville, Florida, USA
| | - Charles Rice
- The Rockefeller University, New York, New York, USA
| | | | | | - Charles Russell
- St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - Martin Sapp
- Louisiana State University, Shreveport, Louisiana, USA
| | | | | | | | - Bert Semler
- University of California, Irvine, Irvine, California, USA
| | - Thomas Shenk
- Princeton University, Princeton, New Jersey, USA
| | | | - Viviana Simon
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Jason Smith
- University of Washington, Seattle, Washington, USA
| | | | | | - Kanta Subbarao
- The Peter Doherty Institute, Melbourne, Victoria, Australia
| | | | | | - Troy Sutton
- The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Andrew Tai
- University of Michigan, Ann Arbor, Michigan, USA
| | | | | | | | | | - Zsolt Toth
- University of Florida, Gainesville, Florida, USA
| | | | | | | | - Derek Walsh
- Northwestern University, Chicago, Illinois, USA
| | | | | | | | - Sandra Weller
- University of Connecticut, Farmington, Connecticut, USA
| | - Sean Whelan
- Washington University, St. Louis, Missouri, USA
| | | | | | | | - Scott Wong
- Oregon Health and Science University, Beaverton, Oregon, USA
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24
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Herrera JP, Moody J, Nunn CL. Predicting primate-parasite associations using exponential random graph models. J Anim Ecol 2023; 92:710-722. [PMID: 36633380 DOI: 10.1111/1365-2656.13883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 12/07/2022] [Indexed: 01/13/2023]
Abstract
Ecological associations between hosts and parasites are influenced by host exposure and susceptibility to parasites, and by parasite traits, such as transmission mode. Advances in network analysis allow us to answer questions about the causes and consequences of traits in ecological networks in ways that could not be addressed in the past. We used a network-based framework (exponential random graph models or ERGMs) to investigate the biogeographic, phylogenetic and ecological characteristics of hosts and parasites that affect the probability of interactions among nonhuman primates and their parasites. Parasites included arthropods, bacteria, fungi, protozoa, viruses and helminths. We investigated existing hypotheses, along with new predictors and an expanded host-parasite database that included 213 primate nodes, 763 parasite nodes and 2319 edges among them. Analyses also investigated phylogenetic relatedness, sampling effort and spatial overlap among hosts. In addition to supporting some previous findings, our ERGM approach demonstrated that more threatened hosts had fewer parasites, and notably, that this effect was independent of hosts also having a smaller geographic range. Despite having fewer parasites, threatened host species shared more parasites with other hosts, consistent with loss of specialist parasites and threat arising from generalist parasites that can be maintained in other, non-threatened hosts. Viruses, protozoa and helminths had broader host ranges than bacteria, or fungi, and parasites that infect non-primates had a higher probability of infecting more primate species. The value of the ERGM approach for investigating the processes structing host-parasite networks provided a more complete view on the biogeographic, phylogenetic and ecological traits that influence parasite species richness and parasite sharing among hosts. The results supported some previous analyses and revealed new associations that warrant future research, thus revealing how hosts and parasites interact to form ecological networks.
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Affiliation(s)
- James P Herrera
- Duke Lemur Center SAVA Conservation, Duke University, Durham, North Carolina, USA
| | - James Moody
- Department of Sociology, Duke University, Durham, North Carolina, USA
| | - Charles L Nunn
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA.,Duke Global Health Institute, Duke University, Durham, North Carolina, USA
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25
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Goodrum F, Lowen AC, Lakdawala S, Alwine J, Casadevall A, Imperiale MJ, Atwood W, Avgousti D, Baines J, Banfield B, Banks L, Bhaduri-McIntosh S, Bhattacharya D, Blanco-Melo D, Bloom D, Boon A, Boulant S, Brandt C, Broadbent A, Brooke C, Cameron C, Campos S, Caposio P, Chan G, Cliffe A, Coffin J, Collins K, Damania B, Daugherty M, Debbink K, DeCaprio J, Dermody T, Dikeakos J, DiMaio D, Dinglasan R, Duprex WP, Dutch R, Elde N, Emerman M, Enquist L, Fane B, Fernandez-Sesma A, Flenniken M, Frappier L, Frieman M, Frueh K, Gack M, Gaglia M, Gallagher T, Galloway D, García-Sastre A, Geballe A, Glaunsinger B, Goff S, Greninger A, Hancock M, Harris E, Heaton N, Heise M, Heldwein E, Hogue B, Horner S, Hutchinson E, Hyser J, Jackson W, Kalejta R, Kamil J, Karst S, Kirchhoff F, Knipe D, Kowalik T, Lagunoff M, Laimins L, Langlois R, Lauring A, Lee B, Leib D, Liu SL, Longnecker R, Lopez C, Luftig M, Lund J, Manicassamy B, McFadden G, McIntosh M, Mehle A, Miller WA, Mohr I, Moody C, Moorman N, Moscona A, Mounce B, Munger J, Münger K, Murphy E, Naghavi M, Nelson J, Neufeldt C, Nikolich J, O'Connor C, Ono A, Orenstein W, Ornelles D, Ou JH, Parker J, Parrish C, Pekosz A, Pellett P, Pfeiffer J, Plemper R, Polyak S, Purdy J, Pyeon D, Quinones-Mateu M, Renne R, Rice C, Schoggins J, Roller R, Russell C, Sandri-Goldin R, Sapp M, Schang L, Schmid S, Schultz-Cherry S, Semler B, Shenk T, Silvestri G, Simon V, Smith G, Smith J, Spindler K, Stanifer M, Subbarao K, Sundquist W, Suthar M, Sutton T, Tai A, Tarakanova V, tenOever B, Tibbetts S, Tompkins S, Toth Z, van Doorslaer K, Vignuzzi M, Wallace N, Walsh D, Weekes M, Weinberg J, Weitzman M, Weller S, Whelan S, White E, Williams B, Wobus C, Wong S, Yurochko A. Virology under the Microscope-a Call for Rational Discourse. mBio 2023; 14:e0018823. [PMID: 36700642 PMCID: PMC9973315 DOI: 10.1128/mbio.00188-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Viruses have brought humanity many challenges: respiratory infection, cancer, neurological impairment and immunosuppression to name a few. Virology research over the last 60+ years has responded to reduce this disease burden with vaccines and antivirals. Despite this long history, the COVID-19 pandemic has brought unprecedented attention to the field of virology. Some of this attention is focused on concern about the safe conduct of research with human pathogens. A small but vocal group of individuals has seized upon these concerns - conflating legitimate questions about safely conducting virus-related research with uncertainties over the origins of SARS-CoV-2. The result has fueled public confusion and, in many instances, ill-informed condemnation of virology. With this article, we seek to promote a return to rational discourse. We explain the use of gain-of-function approaches in science, discuss the possible origins of SARS-CoV-2 and outline current regulatory structures that provide oversight for virological research in the United States. By offering our expertise, we - a broad group of working virologists - seek to aid policy makers in navigating these controversial issues. Balanced, evidence-based discourse is essential to addressing public concern while maintaining and expanding much-needed research in virology.
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Affiliation(s)
- Felicia Goodrum
- Department of Immunobiology, BIO5 Institute, University of Arizona, Tucson, Arizona, USA
| | - Anice C. Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Seema Lakdawala
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - James Alwine
- Department of Immunobiology, BIO5 Institute, University of Arizona, Tucson, Arizona, USA
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Michael J. Imperiale
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Daphne Avgousti
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | - Lawrence Banks
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | | | | | | | - David Bloom
- University of Florida, Gainesville, Florida, USA
| | - Adrianus Boon
- University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | | | - Curtis Brandt
- University of Wisconsin—Madison, Madison, Wisconsin, USA
| | | | | | - Craig Cameron
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | - Gary Chan
- SUNY Upstate Medical University, Syracuse, New York, USA
| | - Anna Cliffe
- University of Virginia, Charlottesville, Virginia, USA
| | - John Coffin
- Tufts University, Boston, Massachusetts, USA
| | | | - Blossom Damania
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Kari Debbink
- Johns Hopkins University, Baltimore, Maryland, USA
| | | | | | | | | | | | | | | | - Nels Elde
- University of Utah, Salt Lake City, Utah, USA
| | - Michael Emerman
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Lynn Enquist
- Princeton University, Princeton, New Jersey, USA
| | | | | | | | | | | | - Klaus Frueh
- Oregon Health and Science University, Beaverton, Oregon, USA
| | - Michaela Gack
- Florida Research and Innovation Center, Port Saint Lucie, Florida, USA
| | - Marta Gaglia
- University of Wisconsin—Madison, Madison, Wisconsin, USA
| | | | - Denise Galloway
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Adam Geballe
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | | | - Meaghan Hancock
- Oregon Health and Science University, Beaverton, Oregon, USA
| | - Eva Harris
- University of California, Berkeley, Berkeley, California, USA
| | | | - Mark Heise
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | | | | | | | | | | | - Jeremy Kamil
- Louisiana State University, Shreveport, Louisiana, USA
| | | | | | - David Knipe
- Harvard Medical School, Boston, Massachusetts, USA
| | | | | | | | - Ryan Langlois
- University of Minnesota, Minneapolis, Minnesota, USA
| | - Adam Lauring
- University of Michigan, Ann Arbor, Michigan, USA
| | - Benhur Lee
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - David Leib
- Dartmouth College, Lebanon, New Hampshire, USA
| | - Shan-Lu Liu
- The Ohio State University, Columbus, Ohio, USA
| | | | | | | | - Jennifer Lund
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | | | - Andrew Mehle
- University of Wisconsin—Madison, Madison, Wisconsin, USA
| | | | - Ian Mohr
- New York University, New York, New York, USA
| | - Cary Moody
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | | | | | - Karl Münger
- Tufts University, Boston, Massachusetts, USA
| | - Eain Murphy
- SUNY Upstate Medical University, Syracuse, New York, USA
| | | | - Jay Nelson
- Oregon Health and Science University, Beaverton, Oregon, USA
| | | | | | | | - Akira Ono
- University of Michigan, Ann Arbor, Michigan, USA
| | | | - David Ornelles
- Wake Forest University, Winston-Salem, North Carolina, USA
| | - Jing-hsiung Ou
- University of Southern California, Los Angeles, California, USA
| | | | | | | | | | | | | | | | - John Purdy
- University of Arizona, Tucson, Arizona, USA
| | - Dohun Pyeon
- Michigan State University, East Lansing, Michigan, USA
| | | | - Rolf Renne
- University of Florida, Gainesville, Florida, USA
| | - Charles Rice
- The Rockefeller University, New York, New York, USA
| | | | | | - Charles Russell
- St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - Martin Sapp
- Louisiana State University, Shreveport, Louisiana, USA
| | | | | | | | - Bert Semler
- University of California, Irvine, Irvine, California, USA
| | - Thomas Shenk
- Princeton University, Princeton, New Jersey, USA
| | | | - Viviana Simon
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Jason Smith
- University of Washington, Seattle, Washington, USA
| | | | | | - Kanta Subbarao
- The Peter Doherty Institute, Melbourne, Victoria, Australia
| | | | | | - Troy Sutton
- The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Andrew Tai
- University of Michigan, Ann Arbor, Michigan, USA
| | | | | | | | | | - Zsolt Toth
- University of Florida, Gainesville, Florida, USA
| | | | | | | | - Derek Walsh
- Northwestern University, Chicago, Illinois, USA
| | | | | | | | - Sandra Weller
- University of Connecticut, Farmington, Connecticut, USA
| | - Sean Whelan
- Washington University, St. Louis, Missouri, USA
| | | | | | | | - Scott Wong
- Oregon Health and Science University, Beaverton, Oregon, USA
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26
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Goodrum F, Lowen AC, Lakdawala S, Alwine J, Casadevall A, Imperiale MJ, Atwood W, Avgousti D, Baines J, Banfield B, Banks L, Bhaduri-McIntosh S, Bhattacharya D, Blanco-Melo D, Bloom D, Boon A, Boulant S, Brandt C, Broadbent A, Brooke C, Cameron C, Campos S, Caposio P, Chan G, Cliffe A, Coffin J, Collins K, Damania B, Daugherty M, Debbink K, DeCaprio J, Dermody T, Dikeakos J, DiMaio D, Dinglasan R, Duprex WP, Dutch R, Elde N, Emerman M, Enquist L, Fane B, Fernandez-Sesma A, Flenniken M, Frappier L, Frieman M, Frueh K, Gack M, Gaglia M, Gallagher T, Galloway D, García-Sastre A, Geballe A, Glaunsinger B, Goff S, Greninger A, Hancock M, Harris E, Heaton N, Heise M, Heldwein E, Hogue B, Horner S, Hutchinson E, Hyser J, Jackson W, Kalejta R, Kamil J, Karst S, Kirchhoff F, Knipe D, Kowalik T, Lagunoff M, Laimins L, Langlois R, Lauring A, Lee B, Leib D, Liu SL, Longnecker R, Lopez C, Luftig M, Lund J, Manicassamy B, McFadden G, McIntosh M, Mehle A, Miller WA, Mohr I, Moody C, Moorman N, Moscona A, Mounce B, Munger J, Münger K, Murphy E, Naghavi M, Nelson J, Neufeldt C, Nikolich J, O'Connor C, Ono A, Orenstein W, Ornelles D, Ou JH, Parker J, Parrish C, Pekosz A, Pellett P, Pfeiffer J, Plemper R, Polyak S, Purdy J, Pyeon D, Quinones-Mateu M, Renne R, Rice C, Schoggins J, Roller R, Russell C, Sandri-Goldin R, Sapp M, Schang L, Schmid S, Schultz-Cherry S, Semler B, Shenk T, Silvestri G, Simon V, Smith G, Smith J, Spindler K, Stanifer M, Subbarao K, Sundquist W, Suthar M, Sutton T, Tai A, Tarakanova V, tenOever B, Tibbetts S, Tompkins S, Toth Z, van Doorslaer K, Vignuzzi M, Wallace N, Walsh D, Weekes M, Weinberg J, Weitzman M, Weller S, Whelan S, White E, Williams B, Wobus C, Wong S, Yurochko A. Virology under the Microscope-a Call for Rational Discourse. J Virol 2023; 97:e0008923. [PMID: 36700640 PMCID: PMC9972907 DOI: 10.1128/jvi.00089-23] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Viruses have brought humanity many challenges: respiratory infection, cancer, neurological impairment and immunosuppression to name a few. Virology research over the last 60+ years has responded to reduce this disease burden with vaccines and antivirals. Despite this long history, the COVID-19 pandemic has brought unprecedented attention to the field of virology. Some of this attention is focused on concern about the safe conduct of research with human pathogens. A small but vocal group of individuals has seized upon these concerns - conflating legitimate questions about safely conducting virus-related research with uncertainties over the origins of SARS-CoV-2. The result has fueled public confusion and, in many instances, ill-informed condemnation of virology. With this article, we seek to promote a return to rational discourse. We explain the use of gain-of-function approaches in science, discuss the possible origins of SARS-CoV-2 and outline current regulatory structures that provide oversight for virological research in the United States. By offering our expertise, we - a broad group of working virologists - seek to aid policy makers in navigating these controversial issues. Balanced, evidence-based discourse is essential to addressing public concern while maintaining and expanding much-needed research in virology.
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Affiliation(s)
- Felicia Goodrum
- Department of Immunobiology, BIO5 Institute, University of Arizona, Tucson, Arizona, USA
| | - Anice C. Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Seema Lakdawala
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - James Alwine
- Department of Immunobiology, BIO5 Institute, University of Arizona, Tucson, Arizona, USA
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Michael J. Imperiale
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Daphne Avgousti
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | - Lawrence Banks
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | | | | | | | - David Bloom
- University of Florida, Gainesville, Florida, USA
| | - Adrianus Boon
- University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | | | - Curtis Brandt
- University of Wisconsin—Madison, Madison, Wisconsin, USA
| | | | | | - Craig Cameron
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | - Gary Chan
- SUNY Upstate Medical University, Syracuse, New York, USA
| | - Anna Cliffe
- University of Virginia, Charlottesville, Virginia, USA
| | - John Coffin
- Tufts University, Boston, Massachusetts, USA
| | | | - Blossom Damania
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Kari Debbink
- Johns Hopkins University, Baltimore, Maryland, USA
| | | | | | | | | | | | | | | | - Nels Elde
- University of Utah, Salt Lake City, Utah, USA
| | - Michael Emerman
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Lynn Enquist
- Princeton University, Princeton, New Jersey, USA
| | | | | | | | | | | | - Klaus Frueh
- Oregon Health and Science University, Beaverton, Oregon, USA
| | - Michaela Gack
- Florida Research and Innovation Center, Port Saint Lucie, Florida, USA
| | - Marta Gaglia
- University of Wisconsin—Madison, Madison, Wisconsin, USA
| | | | - Denise Galloway
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Adam Geballe
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | | | - Meaghan Hancock
- Oregon Health and Science University, Beaverton, Oregon, USA
| | - Eva Harris
- University of California, Berkeley, Berkeley, California, USA
| | | | - Mark Heise
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | | | | | | | | | | | - Jeremy Kamil
- Louisiana State University, Shreveport, Louisiana, USA
| | | | | | - David Knipe
- Harvard Medical School, Boston, Massachusetts, USA
| | | | | | | | - Ryan Langlois
- University of Minnesota, Minneapolis, Minnesota, USA
| | - Adam Lauring
- University of Michigan, Ann Arbor, Michigan, USA
| | - Benhur Lee
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - David Leib
- Dartmouth College, Lebanon, New Hampshire, USA
| | - Shan-Lu Liu
- The Ohio State University, Columbus, Ohio, USA
| | | | | | | | - Jennifer Lund
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | | | - Andrew Mehle
- University of Wisconsin—Madison, Madison, Wisconsin, USA
| | | | - Ian Mohr
- New York University, New York, New York, USA
| | - Cary Moody
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | | | | | - Karl Münger
- Tufts University, Boston, Massachusetts, USA
| | - Eain Murphy
- SUNY Upstate Medical University, Syracuse, New York, USA
| | | | - Jay Nelson
- Oregon Health and Science University, Beaverton, Oregon, USA
| | | | | | | | - Akira Ono
- University of Michigan, Ann Arbor, Michigan, USA
| | | | - David Ornelles
- Wake Forest University, Winston-Salem, North Carolina, USA
| | - Jing-hsiung Ou
- University of Southern California, Los Angeles, California, USA
| | | | | | | | | | | | | | | | - John Purdy
- University of Arizona, Tucson, Arizona, USA
| | - Dohun Pyeon
- Michigan State University, East Lansing, Michigan, USA
| | | | - Rolf Renne
- University of Florida, Gainesville, Florida, USA
| | - Charles Rice
- The Rockefeller University, New York, New York, USA
| | | | | | - Charles Russell
- St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - Martin Sapp
- Louisiana State University, Shreveport, Louisiana, USA
| | | | | | | | - Bert Semler
- University of California, Irvine, Irvine, California, USA
| | - Thomas Shenk
- Princeton University, Princeton, New Jersey, USA
| | | | - Viviana Simon
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Jason Smith
- University of Washington, Seattle, Washington, USA
| | | | | | - Kanta Subbarao
- The Peter Doherty Institute, Melbourne, Victoria, Australia
| | | | | | - Troy Sutton
- The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Andrew Tai
- University of Michigan, Ann Arbor, Michigan, USA
| | | | | | | | | | - Zsolt Toth
- University of Florida, Gainesville, Florida, USA
| | | | | | | | - Derek Walsh
- Northwestern University, Chicago, Illinois, USA
| | | | | | | | - Sandra Weller
- University of Connecticut, Farmington, Connecticut, USA
| | - Sean Whelan
- Washington University, St. Louis, Missouri, USA
| | | | | | | | - Scott Wong
- Oregon Health and Science University, Beaverton, Oregon, USA
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27
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Zhang HP, Sun YL, Wang YF, Yazici D, Azkur D, Ogulur I, Azkur AK, Yang ZW, Chen XX, Zhang AZ, Hu JQ, Liu GH, Akdis M, Akdis CA, Gao YD. Recent developments in the immunopathology of COVID-19. Allergy 2023; 78:369-388. [PMID: 36420736 PMCID: PMC10108124 DOI: 10.1111/all.15593] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 11/01/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022]
Abstract
There has been an important change in the clinical characteristics and immune profile of Coronavirus disease 2019 (COVID-19) patients during the pandemic thanks to the extensive vaccination programs. Here, we highlight recent studies on COVID-19, from the clinical and immunological characteristics to the protective and risk factors for severity and mortality of COVID-19. The efficacy of the COVID-19 vaccines and potential allergic reactions after administration are also discussed. The occurrence of new variants of concerns such as Omicron BA.2, BA.4, and BA.5 and the global administration of COVID-19 vaccines have changed the clinical scenario of COVID-19. Multisystem inflammatory syndrome in children (MIS-C) may cause severe and heterogeneous disease but with a lower mortality rate. Perturbations in immunity of T cells, B cells, and mast cells, as well as autoantibodies and metabolic reprogramming may contribute to the long-term symptoms of COVID-19. There is conflicting evidence about whether atopic diseases, such as allergic asthma and rhinitis, are associated with a lower susceptibility and better outcomes of COVID-19. At the beginning of pandemic, the European Academy of Allergy and Clinical Immunology (EAACI) developed guidelines that provided timely information for the management of allergic diseases and preventive measures to reduce transmission in the allergic clinics. The global distribution of COVID-19 vaccines and emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with reduced pathogenic potential dramatically decreased the morbidity, severity, and mortality of COVID-19. Nevertheless, breakthrough infection remains a challenge for disease control. Hypersensitivity reactions (HSR) to COVID-19 vaccines are low compared to other vaccines, and these were addressed in EAACI statements that provided indications for the management of allergic reactions, including anaphylaxis to COVID-19 vaccines. We have gained a depth knowledge and experience in the over 2 years since the start of the pandemic, and yet a full eradication of SARS-CoV-2 is not on the horizon. Novel strategies are warranted to prevent severe disease in high-risk groups, the development of MIS-C and long COVID-19.
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Affiliation(s)
- Huan-Ping Zhang
- Department of Allergology, Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Yuan-Li Sun
- Department of Allergology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yan-Fen Wang
- Department of Pediatrics, Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Duygu Yazici
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Dilek Azkur
- Division of Pediatric Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, University of Kirikkale, Kirikkale, Turkey
| | - Ismail Ogulur
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Ahmet Kursat Azkur
- Department of Virology, Faculty of Veterinary Medicine, University of Kirikkale, Kirikkale, Turkey
| | - Zhao-Wei Yang
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiao-Xue Chen
- Department of Allergology, Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Ai-Zhi Zhang
- Intensive Care Unit, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Jia-Qian Hu
- Department of Allergology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Guang-Hui Liu
- Department of Allergology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Mübeccel Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Cezmi A Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Ya-Dong Gao
- Department of Allergology, Zhongnan Hospital of Wuhan University, Wuhan, China
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28
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Worldwide transmission and infection risk of mosquito vectors of West Nile, St. Louis encephalitis, Usutu and Japanese encephalitis viruses: a systematic review. Sci Rep 2023; 13:308. [PMID: 36609450 PMCID: PMC9822987 DOI: 10.1038/s41598-022-27236-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/28/2022] [Indexed: 01/07/2023] Open
Abstract
The increasing trend of mosquito-borne pathogens demands more accurate global estimations of infection and transmission risks between mosquitoes. Here, we systematically review field and laboratory studies to assess the natural field infection and experimental laboratory transmission risk in Culex mosquitoes. We studied four worldwide flaviviruses: West Nile, Usutu, Japanese encephalitis, and St. Louis encephalitis, belonging to the Japanese encephalitis Serocomplex (JES). The PRISMA statement was carried out for both approaches. The Transmission-Infection Risk of the diverse mosquito species for the different viruses was estimated through seven variables. We considered 130 and 95 articles for field and experimental approach, respectively. We identified 30 species naturally infected, and 23 species capable to transmit some of the four flaviviruses. For the JES, the highest Transmission-Infection Risk estimate was recorded in Culex quinquefasciatus (North America). The maximum Infection-Transmission Risk values for West Nile was Culex restuans, for Usutu it was Culex pipiens (Europe), for St. Louis encephalitis Culex quinquefasciatus (North America), and for Japanese encephalitis Culex gelidus (Oceania). We conclude that on a worldwide scale, a combination of field and experimental data offers a better way of understanding natural infection and transmission risks between mosquito populations.
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29
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Li Q, Shah T, Wang B, Qu L, Wang R, Hou Y, Baloch Z, Xia X. Cross-species transmission, evolution and zoonotic potential of coronaviruses. Front Cell Infect Microbiol 2023; 12:1081370. [PMID: 36683695 PMCID: PMC9853062 DOI: 10.3389/fcimb.2022.1081370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/19/2022] [Indexed: 01/09/2023] Open
Abstract
Coronaviruses (CoVs) continuously evolve, crossing species barriers and spreading across host ranges. Over the last two decades, several CoVs (HCoV-229E, HCoV-NL63, HCoV-HKU1, HCoV-OC43, SARS-CoV, MERS-CoV, and SARS-CoV-2) have emerged in animals and mammals, causing significant economic and human life losses. Due to CoV cross-species transmission and the evolution of novel viruses, it is critical to identify their natural reservoiurs and the circumstances under which their transmission occurs. In this review, we use genetic and ecological data to disentangle the evolution of various CoVs in wildlife, humans, and domestic mammals. We thoroughly investigate several host species and outline the epidemiology of CoVs toward specific hosts. We also discuss the cross-species transmission of CoVs at the interface of wildlife, animals, and humans. Clarifying the epidemiology and diversity of species reservoirs will significantly impact our ability to respond to the future emergence of CoVs in humans and domestic animals.
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Affiliation(s)
- Qian Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China,The First Affiliated Hospital & Clinical Medical College, Dali University, Dali, Yunnan, China
| | - Taif Shah
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Binghui Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Linyu Qu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Rui Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Yutong Hou
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Zulqarnain Baloch
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China,*Correspondence: Xueshan Xia,
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30
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Moreno E, Ron R, Serrano-Villar S. The microbiota as a modulator of mucosal inflammation and HIV/HPV pathogenesis: From association to causation. Front Immunol 2023; 14:1072655. [PMID: 36756132 PMCID: PMC9900135 DOI: 10.3389/fimmu.2023.1072655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/06/2023] [Indexed: 01/24/2023] Open
Abstract
Although the microbiota has largely been associated with the pathogenesis of viral infections, most studies using omics techniques are correlational and hypothesis-generating. The mechanisms affecting the immune responses to viral infections are still being fully understood. Here we focus on the two most important sexually transmitted persistent viruses, HPV and HIV. Sophisticated omics techniques are boosting our ability to understand microbiota-pathogen-host interactions from a functional perspective by surveying the host and bacterial protein and metabolite production using systems biology approaches. However, while these strategies have allowed describing interaction networks to identify potential novel microbiota-associated biomarkers or therapeutic targets to prevent or treat infectious diseases, the analyses are typically based on highly dimensional datasets -thousands of features in small cohorts of patients-. As a result, we are far from getting to their clinical use. Here we provide a broad overview of how the microbiota influences the immune responses to HIV and HPV disease. Furthermore, we highlight experimental approaches to understand better the microbiota-host-virus interactions that might increase our potential to identify biomarkers and therapeutic agents with clinical applications.
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Affiliation(s)
- Elena Moreno
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal, Facultad de Medicina, Universidad de Alcalá, IRYCIS, Madrid, Spain.,CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
| | - Raquel Ron
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal, Facultad de Medicina, Universidad de Alcalá, IRYCIS, Madrid, Spain.,CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
| | - Sergio Serrano-Villar
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal, Facultad de Medicina, Universidad de Alcalá, IRYCIS, Madrid, Spain.,CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
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31
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Kawasaki J, Tomonaga K, Horie M. Large-scale investigation of zoonotic viruses in the era of high-throughput sequencing. Microbiol Immunol 2023; 67:1-13. [PMID: 36259224 DOI: 10.1111/1348-0421.13033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 09/28/2022] [Accepted: 10/16/2022] [Indexed: 01/10/2023]
Abstract
Zoonotic diseases considerably impact public health and socioeconomics. RNA viruses reportedly caused approximately 94% of zoonotic diseases documented from 1990 to 2010, emphasizing the importance of investigating RNA viruses in animals. Furthermore, it has been estimated that hundreds of thousands of animal viruses capable of infecting humans are yet to be discovered, warning against the inadequacy of our understanding of viral diversity. High-throughput sequencing (HTS) has enabled the identification of viral infections with relatively little bias. Viral searches using both symptomatic and asymptomatic animal samples by HTS have revealed hidden viral infections. This review introduces the history of viral searches using HTS, current analytical limitations, and future potentials. We primarily summarize recent research on large-scale investigations on viral infections reusing HTS data from public databases. Furthermore, considering the accumulation of uncultivated viruses, we discuss current studies and challenges for connecting viral sequences to their phenotypes using various approaches: performing data analysis, developing predictive modeling, or implementing high-throughput platforms of virological experiments. We believe that this article provides a future direction in large-scale investigations of potential zoonotic viruses using the HTS technology.
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Affiliation(s)
- Junna Kawasaki
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,Laboratory of RNA Viruses, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto, Japan.,Faculty of Science and Engineering, Waseda University, Tokyo, Japan
| | - Keizo Tomonaga
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,Laboratory of RNA Viruses, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto, Japan.,Department of Molecular Virology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masayuki Horie
- Division of Veterinary Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan.,Osaka International Research Center for Infectious Diseases, Osaka Prefecture University, Osaka, Japan
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32
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Iuchi H, Kawasaki J, Kubo K, Fukunaga T, Hokao K, Yokoyama G, Ichinose A, Suga K, Hamada M. Bioinformatics approaches for unveiling virus-host interactions. Comput Struct Biotechnol J 2023; 21:1774-1784. [PMID: 36874163 PMCID: PMC9969756 DOI: 10.1016/j.csbj.2023.02.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/22/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
The coronavirus disease-2019 (COVID-19) pandemic has elucidated major limitations in the capacity of medical and research institutions to appropriately manage emerging infectious diseases. We can improve our understanding of infectious diseases by unveiling virus-host interactions through host range prediction and protein-protein interaction prediction. Although many algorithms have been developed to predict virus-host interactions, numerous issues remain to be solved, and the entire network remains veiled. In this review, we comprehensively surveyed algorithms used to predict virus-host interactions. We also discuss the current challenges, such as dataset biases toward highly pathogenic viruses, and the potential solutions. The complete prediction of virus-host interactions remains difficult; however, bioinformatics can contribute to progress in research on infectious diseases and human health.
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Affiliation(s)
- Hitoshi Iuchi
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan.,Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 169-8555, Japan
| | - Junna Kawasaki
- Faculty of Science and Engineering, Waseda University, Okubo Shinjuku-ku, Tokyo 169-8555, Japan
| | - Kento Kubo
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 169-8555, Japan.,School of Advanced Science and Engineering, Waseda University, Okubo Shinjuku-ku, Tokyo 169-8555, Japan
| | - Tsukasa Fukunaga
- Waseda Institute for Advanced Study, Waseda University, Nishi Waseda, Shinjuku-ku, Tokyo 169-0051, Japan
| | - Koki Hokao
- School of Advanced Science and Engineering, Waseda University, Okubo Shinjuku-ku, Tokyo 169-8555, Japan
| | - Gentaro Yokoyama
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 169-8555, Japan.,School of Advanced Science and Engineering, Waseda University, Okubo Shinjuku-ku, Tokyo 169-8555, Japan
| | - Akiko Ichinose
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Kanta Suga
- School of Advanced Science and Engineering, Waseda University, Okubo Shinjuku-ku, Tokyo 169-8555, Japan
| | - Michiaki Hamada
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan.,Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 169-8555, Japan.,School of Advanced Science and Engineering, Waseda University, Okubo Shinjuku-ku, Tokyo 169-8555, Japan.,Graduate School of Medicine, Nippon Medical School, Tokyo 113-8602, Japan
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33
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Wang Z, Huang G, Huang M, Dai Q, Hu Y, Zhou J, Wei F. Global patterns of phylogenetic diversity and transmission of bat coronavirus. SCIENCE CHINA LIFE SCIENCES 2022; 66:861-874. [PMID: 36378474 PMCID: PMC9664035 DOI: 10.1007/s11427-022-2221-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/12/2022] [Indexed: 11/16/2022]
Abstract
Bats are reservoirs for multiple coronaviruses (CoVs). However, the phylogenetic diversity and transmission of global bat-borne CoVs remain poorly understood. Here, we performed a Bayesian phylogeographic analysis based on 3,594 bat CoV RdRp gene sequences to study the phylogenetic diversity and transmission of bat-borne CoVs and the underlying driving factors. We found that host-switching events occurred more frequently for α-CoVs than for β-CoVs, and the latter was highly constrained by bat phylogeny. Bat species in the families Molossidae, Rhinolophidae, Miniopteridae, and Vespertilionidae had larger contributions to the cross-species transmission of bat CoVs. Regions of eastern and southern Africa, southern South America, Western Europe, and Southeast Asia were more frequently involved in cross-region transmission events of bat CoVs than other regions. Phylogenetic and geographic distances were the most important factors limiting CoV transmission. Bat taxa and global geographic hotspots associated with bat CoV phylogenetic diversity were identified, and bat species richness, mean annual temperature, global agricultural cropland, and human population density were strongly correlated with the phylogenetic diversity of bat CoVs. These findings provide insight into bat CoV evolution and ecological transmission among bat taxa. The identified hotspots of bat CoV evolution and transmission will guide early warnings of bat-borne CoV zoonotic diseases.
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Affiliation(s)
- Zhilin Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guangping Huang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mingpan Huang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiang Dai
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yibo Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiang Zhou
- School of Karst Science, Guizhou Normal University, Guiyang, 550000, China
| | - Fuwen Wei
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
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34
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Wu VY, Chen B, Christofferson R, Ebel G, Fagre AC, Gallichotte EN, Sweeny AR, Carlson CJ, Ryan SJ. A minimum data standard for vector competence experiments. Sci Data 2022; 9:634. [PMID: 36261651 PMCID: PMC9582208 DOI: 10.1038/s41597-022-01741-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 10/05/2022] [Indexed: 11/25/2022] Open
Abstract
The growing threat of vector-borne diseases, highlighted by recent epidemics, has prompted increased focus on the fundamental biology of vector-virus interactions. To this end, experiments are often the most reliable way to measure vector competence (the potential for arthropod vectors to transmit certain pathogens). Data from these experiments are critical to understand outbreak risk, but – despite having been collected and reported for a large range of vector-pathogen combinations – terminology is inconsistent, records are scattered across studies, and the accompanying publications often share data with insufficient detail for reuse or synthesis. Here, we present a minimum data and metadata standard for reporting the results of vector competence experiments. Our reporting checklist strikes a balance between completeness and labor-intensiveness, with the goal of making these important experimental data easier to find and reuse in the future, without much added effort for the scientists generating the data. To illustrate the standard, we provide an example that reproduces results from a study of Aedes aegypti vector competence for Zika virus.
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Affiliation(s)
- Velen Yifei Wu
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, D.C., USA
| | - Binqi Chen
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, D.C., USA
| | | | - Gregory Ebel
- Center for Vector-borne Infectious Diseases, Colorado State University, Fort Collins, USA
| | - Anna C Fagre
- Center for Vector-borne Infectious Diseases, Colorado State University, Fort Collins, USA
| | - Emily N Gallichotte
- Center for Vector-borne Infectious Diseases, Colorado State University, Fort Collins, USA
| | - Amy R Sweeny
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, D.C., USA.,School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Colin J Carlson
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, D.C., USA. .,Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, D.C., USA. .,Department of Biology, Georgetown University, Washington, USA.
| | - Sadie J Ryan
- Department of Geography, University of Florida, Gainesville, USA. .,Emerging Pathogens Institute, University of Florida, Gainesville, USA. .,College of Life Sciences, University of KwaZulu Natal, Durban, South Africa.
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35
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Silk MJ, Wilber MQ, Fefferman NH. Capturing complex interactions in disease ecology with simplicial sets. Ecol Lett 2022; 25:2217-2231. [PMID: 36001469 DOI: 10.1111/ele.14079] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/21/2022] [Accepted: 06/29/2022] [Indexed: 11/28/2022]
Abstract
Network approaches have revolutionized the study of ecological interactions. Social, movement and ecological networks have all been integral to studying infectious disease ecology. However, conventional (dyadic) network approaches are limited in their ability to capture higher-order interactions. We present simplicial sets as a tool that addresses this limitation. First, we explain what simplicial sets are. Second, we explain why their use would be beneficial in different subject areas. Third, we detail where these areas are: social, transmission, movement/spatial and ecological networks and when using them would help most in each context. To demonstrate their application, we develop a novel approach to identify how pathogens persist within a host population. Fourth, we provide an overview of how to use simplicial sets, highlighting specific metrics, generative models and software. Finally, we synthesize key research questions simplicial sets will help us answer and draw attention to methodological developments that will facilitate this.
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Affiliation(s)
- Matthew J Silk
- NIMBioS, University of Tennessee, Knoxville, Tennessee, USA.,CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Mark Q Wilber
- Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, Tennessee, USA
| | - Nina H Fefferman
- NIMBioS, University of Tennessee, Knoxville, Tennessee, USA.,Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, USA.,Department of Mathematics, University of Tennessee, Knoxville, Tennessee, USA
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36
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Predicting the potential for zoonotic transmission and host associations for novel viruses. Commun Biol 2022; 5:844. [PMID: 35986178 PMCID: PMC9390964 DOI: 10.1038/s42003-022-03797-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 08/04/2022] [Indexed: 01/14/2023] Open
Abstract
Host-virus associations have co-evolved under ecological and evolutionary selection pressures that shape cross-species transmission and spillover to humans. Observed virus-host associations provide relevant context for newly discovered wildlife viruses to assess knowledge gaps in host-range and estimate pathways for potential human infection. Using models to predict virus-host networks, we predicted the likelihood of humans as hosts for 513 newly discovered viruses detected by large-scale wildlife surveillance at high-risk animal-human interfaces in Africa, Asia, and Latin America. Predictions indicated that novel coronaviruses are likely to infect a greater number of host species than viruses from other families. Our models further characterize novel viruses through prioritization scores and directly inform surveillance targets to identify host ranges for newly discovered viruses.
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37
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Chen D, Ou Z, Zhu J, Wang H, Ding P, Luo L, Ding X, Sun C, Lan T, Sahu SK, Wu W, Yuan Y, Wu W, Qiu J, Zhu Y, Yue Q, Jia Y, Wei Y, Qin Q, Li R, Zhao W, Lv Z, Pu M, Lv B, Yang S, Chang A, Wei X, Chen F, Yang T, Wei Z, Yang F, Zhang P, Guo G, Li Y, Hua Y, Liu H. Screening of cell-virus, cell-cell, gene-gene crosstalk among animal kingdom at single cell resolution. Clin Transl Med 2022; 12:e886. [PMID: 35917402 PMCID: PMC9345398 DOI: 10.1002/ctm2.886] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 04/20/2022] [Accepted: 05/05/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The exact animal origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains obscure and understanding its host range is vital for preventing interspecies transmission. METHODS Herein, we applied single-cell sequencing to multiple tissues of 20 species (30 data sets) and integrated them with public resources (45 data sets covering 26 species) to expand the virus receptor distribution investigation. While the binding affinity between virus and receptor is essential for viral infectivity, understanding the receptor distribution could predict the permissive organs and tissues when infection occurs. RESULTS Based on the transcriptomic data, the expression profiles of receptor or associated entry factors for viruses capable of causing respiratory, blood, and brain diseases were described in detail. Conserved cellular connectomes and regulomes were also identified, revealing fundamental cell-cell and gene-gene cross-talks from reptiles to humans. CONCLUSIONS Overall, our study provides a resource of the single-cell atlas of the animal kingdom which could help to identify the potential host range and tissue tropism of viruses and reveal the host-virus co-evolution.
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Affiliation(s)
- Dongsheng Chen
- BGI‐ShenzhenShenzhenChina,Suzhou Institute of Systems MedicineSuzhouJiangsuChina
| | - Zhihua Ou
- BGI‐ShenzhenShenzhenChina,Shenzhen Key Laboratory of Unknown Pathogen IdentificationBGI‐ShenzhenShenzhenChina
| | - Jiacheng Zhu
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Haoyu Wang
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Peiwen Ding
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Lihua Luo
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Xiangning Ding
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Chengcheng Sun
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | | | | | - Weiying Wu
- The MOE Frontier Science Center for Brain Research and Brain‐Machine IntegrationSchool of Brain Science and Brain MedicineZhejiang UniversityHangzhouChina
| | - Yuting Yuan
- Department of Physiology, School of Basic Medical SciencesBinzhou Medical UniversityYantaiChina
| | - Wendi Wu
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | - Jiaying Qiu
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Yixin Zhu
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Qizhen Yue
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | - Yi Jia
- BGI‐ShenzhenShenzhenChina
| | - Yanan Wei
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | - Qiuyu Qin
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | - Runchu Li
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | - Wandong Zhao
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | - Zhiyuan Lv
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | - Mingyi Pu
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | | | - Shangchen Yang
- College of Life SciencesZhejiang UniversityHangzhouChina
| | | | | | | | - Tao Yang
- China National GeneBankShenzhenChina
| | | | - Fan Yang
- China National GeneBankShenzhenChina
| | - Peijing Zhang
- Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouChina
| | - Guoji Guo
- Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouChina
| | | | - Yan Hua
- Guangdong Provincial Key Laboratory of SilvicultureProtection and UtilizationGuangdong Academy of ForestryGuangzhouChina
| | - Huan Liu
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
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38
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Carlson CJ, Albery GF, Merow C, Trisos CH, Zipfel CM, Eskew EA, Olival KJ, Ross N, Bansal S. Climate change increases cross-species viral transmission risk. Nature 2022; 607:555-562. [PMID: 35483403 DOI: 10.1101/2020.01.24.918755] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 04/21/2022] [Indexed: 05/28/2023]
Abstract
At least 10,000 virus species have the ability to infect humans but, at present, the vast majority are circulating silently in wild mammals1,2. However, changes in climate and land use will lead to opportunities for viral sharing among previously geographically isolated species of wildlife3,4. In some cases, this will facilitate zoonotic spillover-a mechanistic link between global environmental change and disease emergence. Here we simulate potential hotspots of future viral sharing, using a phylogeographical model of the mammal-virus network, and projections of geographical range shifts for 3,139 mammal species under climate-change and land-use scenarios for the year 2070. We predict that species will aggregate in new combinations at high elevations, in biodiversity hotspots, and in areas of high human population density in Asia and Africa, causing the cross-species transmission of their associated viruses an estimated 4,000 times. Owing to their unique dispersal ability, bats account for the majority of novel viral sharing and are likely to share viruses along evolutionary pathways that will facilitate future emergence in humans. Notably, we find that this ecological transition may already be underway, and holding warming under 2 °C within the twenty-first century will not reduce future viral sharing. Our findings highlight an urgent need to pair viral surveillance and discovery efforts with biodiversity surveys tracking the range shifts of species, especially in tropical regions that contain the most zoonoses and are experiencing rapid warming.
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Affiliation(s)
- Colin J Carlson
- Department of Biology, Georgetown University, Washington, DC, USA.
- Center for Global Health Science & Security, Georgetown University, Washington, DC, USA.
| | - Gregory F Albery
- Department of Biology, Georgetown University, Washington, DC, USA.
- EcoHealth Alliance, New York, NY, USA.
| | - Cory Merow
- Eversource Energy Center, University of Connecticut, Storrs, CT, USA
| | - Christopher H Trisos
- African Climate and Development Initiative, University of Cape Town, Cape Town, South Africa
| | - Casey M Zipfel
- Department of Biology, Georgetown University, Washington, DC, USA
| | - Evan A Eskew
- EcoHealth Alliance, New York, NY, USA
- Department of Biology, Pacific Lutheran University, Tacoma, WA, USA
| | | | - Noam Ross
- EcoHealth Alliance, New York, NY, USA
| | - Shweta Bansal
- Department of Biology, Georgetown University, Washington, DC, USA
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39
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Carlson CJ, Albery GF, Merow C, Trisos CH, Zipfel CM, Eskew EA, Olival KJ, Ross N, Bansal S. Climate change increases cross-species viral transmission risk. Nature 2022; 607:555-562. [PMID: 35483403 DOI: 10.1038/s41586-022-04788-w] [Citation(s) in RCA: 235] [Impact Index Per Article: 117.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 04/21/2022] [Indexed: 11/09/2022]
Abstract
At least 10,000 virus species have the ability to infect humans but, at present, the vast majority are circulating silently in wild mammals1,2. However, changes in climate and land use will lead to opportunities for viral sharing among previously geographically isolated species of wildlife3,4. In some cases, this will facilitate zoonotic spillover-a mechanistic link between global environmental change and disease emergence. Here we simulate potential hotspots of future viral sharing, using a phylogeographical model of the mammal-virus network, and projections of geographical range shifts for 3,139 mammal species under climate-change and land-use scenarios for the year 2070. We predict that species will aggregate in new combinations at high elevations, in biodiversity hotspots, and in areas of high human population density in Asia and Africa, causing the cross-species transmission of their associated viruses an estimated 4,000 times. Owing to their unique dispersal ability, bats account for the majority of novel viral sharing and are likely to share viruses along evolutionary pathways that will facilitate future emergence in humans. Notably, we find that this ecological transition may already be underway, and holding warming under 2 °C within the twenty-first century will not reduce future viral sharing. Our findings highlight an urgent need to pair viral surveillance and discovery efforts with biodiversity surveys tracking the range shifts of species, especially in tropical regions that contain the most zoonoses and are experiencing rapid warming.
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Affiliation(s)
- Colin J Carlson
- Department of Biology, Georgetown University, Washington, DC, USA. .,Center for Global Health Science & Security, Georgetown University, Washington, DC, USA.
| | - Gregory F Albery
- Department of Biology, Georgetown University, Washington, DC, USA. .,EcoHealth Alliance, New York, NY, USA.
| | - Cory Merow
- Eversource Energy Center, University of Connecticut, Storrs, CT, USA
| | - Christopher H Trisos
- African Climate and Development Initiative, University of Cape Town, Cape Town, South Africa
| | - Casey M Zipfel
- Department of Biology, Georgetown University, Washington, DC, USA
| | - Evan A Eskew
- EcoHealth Alliance, New York, NY, USA.,Department of Biology, Pacific Lutheran University, Tacoma, WA, USA
| | | | - Noam Ross
- EcoHealth Alliance, New York, NY, USA
| | - Shweta Bansal
- Department of Biology, Georgetown University, Washington, DC, USA
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40
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Abstract
The coronavirus disease 2019 (COVID-19) pandemic has had a profound impact on human health, economic well-being, and societal function. It is essential that we use this generational experience to better understand the processes that underpin the emergence of COVID-19 and other zoonotic diseases. Herein, I review the mechanisms that determine why and how viruses emerge in new hosts, as well as the barriers to this process. I show that traditional studies of virus emergence have an inherent anthropocentric bias, with disease in humans considered the inevitable outcome of virus emergence, when in reality viruses are integral components of a global ecosystem characterized by continual host jumping with humans also transmitting their viruses to other animals. I illustrate these points using coronaviruses, including severe acute respiratory syndrome coronavirus 2, as a case study. I also outline the potential steps that can be followed to help mitigate and prevent future pandemics, with combating climate change a central component. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia;
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41
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Muylaert RL, Kingston T, Luo J, Vancine MH, Galli N, Carlson CJ, John RS, Rulli MC, Hayman DTS. Present and future distribution of bat hosts of sarbecoviruses: implications for conservation and public health. Proc Biol Sci 2022; 289:20220397. [PMID: 35611534 PMCID: PMC9130791 DOI: 10.1098/rspb.2022.0397] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Global changes in response to human encroachment into natural habitats and carbon emissions are driving the biodiversity extinction crisis and increasing disease emergence risk. Host distributions are one critical component to identify areas at risk of viral spillover, and bats act as reservoirs of diverse viruses. We developed a reproducible ecological niche modelling pipeline for bat hosts of SARS-like viruses (subgenus Sarbecovirus), given that several closely related viruses have been discovered and sarbecovirus-host interactions have gained attention since SARS-CoV-2 emergence. We assessed sampling biases and modelled current distributions of bats based on climate and landscape relationships and project future scenarios for host hotspots. The most important predictors of species distributions were temperature seasonality and cave availability. We identified concentrated host hotspots in Myanmar and projected range contractions for most species by 2100. Our projections indicate hotspots will shift east in Southeast Asia in locations greater than 2°C hotter in a fossil-fuelled development future. Hotspot shifts have implications for conservation and public health, as loss of population connectivity can lead to local extinctions, and remaining hotspots may concentrate near human populations.
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Affiliation(s)
| | | | - Jinhong Luo
- Central China Normal University, Wuhan, People's Republic of China
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42
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Biological invasions facilitate zoonotic disease emergences. Nat Commun 2022; 13:1762. [PMID: 35365665 PMCID: PMC8975888 DOI: 10.1038/s41467-022-29378-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 03/14/2022] [Indexed: 12/27/2022] Open
Abstract
Outbreaks of zoonotic diseases are accelerating at an unprecedented rate in the current era of globalization, with substantial impacts on the global economy, public health, and sustainability. Alien species invasions have been hypothesized to be important to zoonotic diseases by introducing both existing and novel pathogens to invaded ranges. However, few studies have evaluated the generality of alien species facilitating zoonoses across multiple host and parasite taxa worldwide. Here, we simultaneously quantify the role of 795 established alien hosts on the 10,473 zoonosis events across the globe since the 14th century. We observe an average of ~5.9 zoonoses per alien zoonotic host. After accounting for species-, disease-, and geographic-level sampling biases, spatial autocorrelation, and the lack of independence of zoonosis events, we find that the number of zoonosis events increase with the richness of alien zoonotic hosts, both across space and through time. We also detect positive associations between the number of zoonosis events per unit space and climate change, land-use change, biodiversity loss, human population density, and PubMed citations. These findings suggest that alien host introductions have likely contributed to zoonosis emergences throughout recent history and that minimizing future zoonotic host species introductions could have global health benefits. Alien species invasions are thought to be important to zoonotic diseases through the introduction of both existing and novel pathogens to invaded ranges. Using data from 795 established alien animals and 10,473 zoonosis events worldwide, this study examines the role of alien zoonotic hosts on zoonosis emergences after accounting for climate, propagule pressure, global change and sampling bias.
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43
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Nocentini A, Capasso C, Supuran CT. Perspectives on the design and discovery of α-ketoamide inhibitors for the treatment of novel coronavirus: where do we stand and where do we go? Expert Opin Drug Discov 2022; 17:547-557. [DOI: 10.1080/17460441.2022.2052847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Alessio Nocentini
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Firenze, Italy
| | - Clemente Capasso
- Department of Biology, Agriculture and Food Sciences, Institute of Biosciences and Bioresources, Napoli, Italy
| | - Claudiu T. Supuran
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Firenze, Italy
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44
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Zhu W, Yang J, Lu S, Jin D, Pu J, Wu S, Luo XL, Liu L, Li Z, Xu J. RNA Virus Diversity in Birds and Small Mammals From Qinghai–Tibet Plateau of China. Front Microbiol 2022; 13:780651. [PMID: 35250920 PMCID: PMC8894885 DOI: 10.3389/fmicb.2022.780651] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 01/12/2022] [Indexed: 12/20/2022] Open
Abstract
Most emerging and re-emerging viruses causing infectious diseases in humans and domestic animals have originated from wildlife. However, current knowledge of the spectrum of RNA viruses in the Qinghai-Tibet Plateau in China is still limited. Here, we performed metatranscriptomic sequencing on fecal samples from 56 birds and 91 small mammals in Tibet and Qinghai Provinces, China, to delineate their viromes and focused on vertebrate RNA viruses. A total of 184 nearly complete genome RNA viruses belonging to 28 families were identified. Among these, 173 new viruses shared <90% amino acid identity with previously known viral sequences. Several of these viruses, such as those belonging to genera Orthonairovirus and Hepatovirus, could be zoonotic viruses. In addition, host taxonomy and geographical location of these viruses showed new hosts and distribution of several previously discovered viruses. Moreover, 12 invertebrate RNA viruses were identified with <40% amino acid identity to known viruses, indicating that they belong to potentially new taxa. The detection and characterization of RNA viruses from wildlife will broaden our knowledge of virus biodiversity and possible viral diseases in the Qinghai–Tibet Plateau.
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Affiliation(s)
- Wentao Zhu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Shusheng Wu
- Yushu Prefecture Center for Disease Control and Prevention, Yushu, China
| | - Xue-Lian Luo
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Zhenjun Li
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
- Research Institute of Public Heath, Nankai University, Tianjin, China
- *Correspondence: Jianguo Xu,
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Farrell MJ, Elmasri M, Stephens D, Davies TJ. Predicting missing links in global host‐parasite networks. J Anim Ecol 2022; 91:715-726. [DOI: 10.1111/1365-2656.13666] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 12/28/2021] [Indexed: 12/01/2022]
Affiliation(s)
- Maxwell J. Farrell
- Department of Biology McGill University
- Ecology & Evolutionary Biology Department University of Toronto
- Center for the Ecology of Infectious Diseases University of Georgia
| | | | - David Stephens
- Department of Mathematics & Statistics McGill University
| | - T. Jonathan Davies
- Botany, Forest & Conservation Sciences University of British Columbia
- African Centre for DNA Barcoding University of Johannesburg
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