1
|
Bangura U, Davis C, Lamin J, Bangura J, Soropogui B, Davison AJ, Nichols J, Vucak M, Dawson M, Ansumana R, Sondufu D, Cadar D, Rieger T, Thomson E, Sahr F, Magassouba N, Ghersi B, Bird BH, Fichet-Calvet E. Spatio-temporal spread of Lassa virus and a new rodent host in the Mano River Union area, West Africa. Emerg Microbes Infect 2024; 13:2290834. [PMID: 38047354 PMCID: PMC10919312 DOI: 10.1080/22221751.2023.2290834] [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: 09/13/2023] [Accepted: 11/29/2023] [Indexed: 12/05/2023]
Abstract
The spread of Lassa virus (LASV) in Guinea, Liberia and Sierra Leone, which together are named the Mano River Union (MRU) area, was examined phylogeographically. To provide a reliable evolutionary scenario, new rodent-derived, whole LASV sequences were included. These were generated by metatranscriptomic next-generation sequencing from rodents sampled between 2003 and 2020 in 21 localities of Guinea and Sierra Leone. An analysis was performed using BEAST to perform continuous phylogeographic inference and EvoLaps v36 to visualize spatio-temporal spread. LASV was identified as expected in its primary host reservoir, the Natal multimammate mouse (Mastomys natalensis), and also in two Guinean multimammate mice (Mastomys erythroleucus) in northern Sierra Leone and two rusty-bellied brush-furred mice (Lophuromys sikapusi) in southern Sierra Leone. This finding is consistent with the latter two species being secondary host reservoirs. The strains in these three species were very closely related in LASV lineage IV. Phylogenetic analysis indicated that the most recent common ancestor of lineage IV existed 316-374 years ago and revealed distinct, well-supported clades from Sierra Leone (Bo, Kabala and Kenema), Guinea (Faranah, Kissidougou-Guekedou and Macenta) and Liberia (Phebe-Ganta). The phylogeographic scenario suggests southern Guinea as the point of origin of LASV in the MRU area, with subsequent spread to towards Mali, Liberia and Sierra Leone at a mean speed of 1.6 to 1.1 km/year.
Collapse
Affiliation(s)
- Umaru Bangura
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, Hamburg, Germany
| | | | - Joyce Lamin
- Mercy Hospital Research Laboratory, Bo, Sierra Leone
| | - James Bangura
- University of Makeni and University of California, Davis One Health Program, Makeni, Sierra Leone
| | - Barré Soropogui
- Laboratoire des Fièvres Hémorragiques en Guinée, Conakry, Guinea
| | | | - Jenna Nichols
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Matej Vucak
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | | | | | - Dániel Cadar
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, Hamburg, Germany
| | - Toni Rieger
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, Hamburg, Germany
| | - Emma Thomson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Foday Sahr
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | | | - Bruno Ghersi
- One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Brian H. Bird
- One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Elisabeth Fichet-Calvet
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, Hamburg, Germany
| |
Collapse
|
2
|
Franzo G, Faustini G, Tucciarone CM, Pasotto D, Legnardi M, Cecchinato M. Conflicting Evidence between Clinical Perception and Molecular Epidemiology: The Case of Fowl Adenovirus D. Animals (Basel) 2023; 13:3851. [PMID: 38136888 PMCID: PMC10741239 DOI: 10.3390/ani13243851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Fowl adenoviruses (FAdVs, species FAdV-A/-E) are responsible for several clinical syndromes reported with increasing frequency in poultry farms in the last decades. In the present study, a phylodynamic analysis was performed on a group of FAdV-D Hexon sequences with adequate available metadata. The obtained results demonstrated the long-term circulation of this species, at least several decades before the first identification of the disease. After a period of progressive increase, the viral population showed a high-level circulation from approximately the 1960s to the beginning of the new millennium, mirroring the expansion of intensive poultry production and animal trade. At the same time, strain migration occurred mainly from Europe to other continents, although other among-continent connections were estimated. Thereafter, the viral population declined progressively, likely due to the improved control measures, potentially including the development and application of FAdV vaccines. An increase in the viral evolutionary rate featured this phase. A role of vaccine-induced immunity in shaping viral evolution could thus be hypothesized. Accordingly, several sites of the Hexon, especially those targeted by the host response were proven under a significant pervasive or episodic diversifying selection. The present study results demonstrate the role of intensive poultry production and market globalization in the rise of FAdV. The applied control strategies, on the other hand, were effective in limiting viral circulation and shaping its evolution.
Collapse
Affiliation(s)
- Giovanni Franzo
- Department of Animal Medicine, Production and Health, University of Padua, Viale dell’Università, 16, 35020 Legnaro, Italy; (G.F.); (C.M.T.); (D.P.); (M.L.); (M.C.)
| | | | | | | | | | | |
Collapse
|
3
|
Fitzmeyer EA, Gallichotte EN, Weger-Lucarelli J, Kapuscinski ML, Abdo Z, Pyron K, Young MC, Ebel GD. Loss of West Nile virus genetic diversity during mosquito infection due to species-dependent population bottlenecks. iScience 2023; 26:107711. [PMID: 37701570 PMCID: PMC10494182 DOI: 10.1016/j.isci.2023.107711] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/13/2023] [Accepted: 08/23/2023] [Indexed: 09/14/2023] Open
Abstract
Vector competence (VC) refers to the efficiency of pathogen transmission by vectors. Each step in the infection of a mosquito vector constitutes a barrier to transmission that may impose bottlenecks on virus populations. West Nile virus (WNV) is maintained by multiple mosquito species with varying VC. However, the extent to which bottlenecks and VC are linked is poorly understood. Similarly, quantitative analyses of mosquito-imposed bottlenecks on virus populations are limited. We used molecularly barcoded WNV to quantify tissue-associated population bottlenecks in three variably competent WNV vectors. Our results confirm strong population bottlenecks during mosquito infection that are capable of dramatically reshaping virus population structure in a non-selective manner. In addition, we found that mosquitoes with differing VC uniquely shape WNV population structure: highly competent vectors are more likely to contribute to the maintenance of rare viral genotypes. These findings have important implications for arbovirus emergence and evolution.
Collapse
Affiliation(s)
- Emily A. Fitzmeyer
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Emily N. Gallichotte
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
| | - Marylee L. Kapuscinski
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Zaid Abdo
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Kyra Pyron
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Michael C. Young
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Gregory D. Ebel
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| |
Collapse
|
4
|
Rothstein AP, Jesser KJ, Feistel DJ, Konstantinidis KT, Trueba G, Levy K. Population genomics of diarrheagenic Escherichia coli uncovers high connectivity between urban and rural communities in Ecuador. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 113:105476. [PMID: 37392822 PMCID: PMC10599324 DOI: 10.1016/j.meegid.2023.105476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 05/11/2023] [Accepted: 06/28/2023] [Indexed: 07/03/2023]
Abstract
Human movement may be an important driver of transmission dynamics for enteric pathogens but has largely been underappreciated except for international 'travelers' diarrhea or cholera. Phylodynamic methods, which combine genomic and epidemiological data, are used to examine rates and dynamics of disease matching underlying evolutionary history and biogeographic distributions, but these methods often are not applied to enteric bacterial pathogens. We used phylodynamics to explore the phylogeographic and evolutionary patterns of diarrheagenic E. coli in northern Ecuador to investigate the role of human travel in the geographic distribution of strains across the country. Using whole genome sequences of diarrheagenic E. coli isolates, we built a core genome phylogeny, reconstructed discrete ancestral states across urban and rural sites, and estimated migration rates between E. coli populations. We found minimal structuring based on site locations, urban vs. rural locality, pathotype, or clinical status. Ancestral states of phylogenomic nodes and tips were inferred to have 51% urban ancestry and 49% rural ancestry. Lack of structuring by location or pathotype E. coli isolates imply highly connected communities and extensive sharing of genomic characteristics across isolates. Using an approximate structured coalescent model, we estimated rates of migration among circulating isolates were 6.7 times larger for urban towards rural populations compared to rural towards urban populations. This suggests increased inferred migration rates of diarrheagenic E. coli from urban populations towards rural populations. Our results indicate that investments in water and sanitation prevention in urban areas could limit the spread of enteric bacterial pathogens among rural populations.
Collapse
Affiliation(s)
- Andrew P. Rothstein
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Kelsey J. Jesser
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Dorian J. Feistel
- School of a Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Konstantinos T. Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- School of a Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Gabriel Trueba
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Karen Levy
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| |
Collapse
|
5
|
Cellular Landscaping of COVID-19 and Gynaecological Cancers: An Infrequent Correlation. JOURNAL OF ONCOLOGY 2022; 2022:5231022. [PMID: 36299504 PMCID: PMC9592241 DOI: 10.1155/2022/5231022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 07/16/2022] [Indexed: 01/08/2023]
Abstract
COVID-19 resulted in a mortality rate of 3–6% caused by SARS-CoV-2 and its variant leading to unprecedented consequences of acute respiratory distress septic shock and multiorgan failure. In such a situation, evaluation, diagnosis, treatment, and care for cancer patients are difficult tasks faced by medical staff. Moreover, patients with gynaecological cancer appear to be more prone to severe infection and mortality from COVID-19 due to immunosuppression by chemotherapy and coexisting medical disorders. To deal with such a circumtances oncologists have been obliged to reconsider the entire diagnostic, treatment, and management approach. This review will provide and discuss the molecular link with gynaecological cancer under COVID-19 infection, providing a novel bilateral relationship between the two infections. Moreover, the authors have provided insights to discuss the pathobiology of COVID-19 in gynaecological cancer and their risks associated with such comorbidity. Furthermore, we have depicted the overall impact of host immunity along with guidelines for the treatment of patients with gynaecological cancer under COVID-19 infection. We have also discussed the feasible scope for the management of COVID-19 and gynaecological cancer.
Collapse
|
6
|
Jolly RJ. Decolonising 'man', resituating pandemic: an intervention in the pathogenesis of colonial capitalism. MEDICAL HUMANITIES 2022; 48:221-229. [PMID: 35296541 PMCID: PMC9185822 DOI: 10.1136/medhum-2021-012267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
This paper brings together fifth-wave public health theory and a decolonised approach to the human informed by the Caribbean thinker, Sylvia Wynter, and the primary exponent of African Humanism, Es'kia Mpahlele. Sub-Saharan indigenous ways of thinking the human as co-constitutive in a subject we might call human-animal-'environment', in conjunction with the subcontinent's experiences of colonial damage in disease 'prevention' and 'treatment', demonstrate the lack of genuine engagement with Indigenous wisdom in Western medical practice.The paper offers a decolonial reading of pandemic history, focused primarily on the human immunodefiency virus (HIV), the severe acute respiratory syndrome of 2003 caused by the SARS Covid 1 virus (SARS-CoV1) and COVID-19, caused by the SARS COVID 2 virus (SARS-CoV2) to demonstrate the importance of the co-constitutive subject in understanding the genesis of these pandemics as driven by colonial-capitalism. I emphasise that prevention will indeed take the kinds of massive changes proposed by fifth-wave public health theory. However, I differ from the proponents of that theory in an insistence that the new kind of thinking of the human Hanlon et al call for, has already been conceived: just not within the confines of the normative human of Western culture.I illustrate that Western Global Health approaches remain constitutionally 'deaf' to approaches that, although the West may not understand this to be the case, arise from fundamentally different-and extra-anthropocentric-notions of the human. In this context, Man as Wynter names Him is a subject ripe for decolonisation, rather than a premier site of capitalist development, including that of healthcare provision.Recognising that most of us are not individually able to change the structural violence of the colonial capitalist system in which Global Health practices are embedded, I conclude with implications drawn from my argument for quotidian practices that enable healthcare providers see their actions within a harm reduction paradigm, in the context of communities experiencing intergenerational impoverishment consequent on colonial violence.
Collapse
Affiliation(s)
- Rosemary J Jolly
- Comparative Literature, Pennsylvania State University, State College, PA 16801, USA
| |
Collapse
|
7
|
Avetyan D, Hakobyan S, Nikoghosyan M, Ghukasyan L, Khachatryan G, Sirunyan T, Muradyan N, Zakharyan R, Chavushyan A, Hayrapetyan V, Hovhannisyan A, Mohamed Bakhash SA, Jerome KR, Roychoudhury P, Greninger AL, Niazyan L, Davidyants M, Melik-Andreasyan G, Sargsyan S, Nersisyan L, Arakelyan A. Molecular Analysis of SARS-CoV-2 Lineages in Armenia. Viruses 2022; 14:v14051074. [PMID: 35632815 PMCID: PMC9142918 DOI: 10.3390/v14051074] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/04/2022] [Accepted: 05/13/2022] [Indexed: 12/11/2022] Open
Abstract
The sequencing of SARS-CoV-2 provides essential information on viral evolution, transmission, and epidemiology. In this paper, we performed the whole-genome sequencing of SARS-CoV-2 using nanopore and Illumina sequencing to describe the circulation of the virus lineages in Armenia. The analysis of 145 full genomes identified six clades (19A, 20A, 20B, 20I, 21J, and 21K) and considerable intra-clade PANGO lineage diversity. Phylodynamic and transmission analysis allowed to attribute specific clades as well as infer their importation routes. Thus, the first two waves of positive case increase were caused by the 20B clade, the third peak caused by the 20I (Alpha), while the last two peaks were caused by the 21J (Delta) and 21K (Omicron) variants. The functional analyses of mutations in sequences largely affected epitopes associated with protective HLA loci and did not cause the loss of the signal in PCR tests targeting ORF1ab and N genes as confirmed by RT-PCR. We also compared the performance of nanopore and Illumina short-read sequencing and showed the utility of nanopore sequencing as an efficient and affordable alternative for large-scale molecular epidemiology research. Thus, our paper describes new data on the genomic diversity of SARS-CoV-2 variants in Armenia in the global context of the virus molecular genomic surveillance.
Collapse
Affiliation(s)
- Diana Avetyan
- Laboratory of Human Genomics, Institute of Molecular Biology NAS RA, Yerevan 0014, Armenia; (L.G.); (G.K.); (T.S.); (N.M.); (R.Z.); (A.C.); (V.H.)
- Institute of Biomedicine and Pharmacy, Russian-Armenian University, Yerevan 0051, Armenia; (M.N.); (A.H.)
- Correspondence: (D.A.); (A.A.)
| | - Siras Hakobyan
- Bioinformatics Group, Institute of Molecular Biology NAS RA, Yerevan 0014, Armenia;
- Armenian Bioinformatics Institute, Yerevan 0014, Armenia;
| | - Maria Nikoghosyan
- Institute of Biomedicine and Pharmacy, Russian-Armenian University, Yerevan 0051, Armenia; (M.N.); (A.H.)
- Bioinformatics Group, Institute of Molecular Biology NAS RA, Yerevan 0014, Armenia;
| | - Lilit Ghukasyan
- Laboratory of Human Genomics, Institute of Molecular Biology NAS RA, Yerevan 0014, Armenia; (L.G.); (G.K.); (T.S.); (N.M.); (R.Z.); (A.C.); (V.H.)
| | - Gisane Khachatryan
- Laboratory of Human Genomics, Institute of Molecular Biology NAS RA, Yerevan 0014, Armenia; (L.G.); (G.K.); (T.S.); (N.M.); (R.Z.); (A.C.); (V.H.)
- Institute of Biomedicine and Pharmacy, Russian-Armenian University, Yerevan 0051, Armenia; (M.N.); (A.H.)
| | - Tamara Sirunyan
- Laboratory of Human Genomics, Institute of Molecular Biology NAS RA, Yerevan 0014, Armenia; (L.G.); (G.K.); (T.S.); (N.M.); (R.Z.); (A.C.); (V.H.)
- Institute of Biomedicine and Pharmacy, Russian-Armenian University, Yerevan 0051, Armenia; (M.N.); (A.H.)
| | - Nelli Muradyan
- Laboratory of Human Genomics, Institute of Molecular Biology NAS RA, Yerevan 0014, Armenia; (L.G.); (G.K.); (T.S.); (N.M.); (R.Z.); (A.C.); (V.H.)
| | - Roksana Zakharyan
- Laboratory of Human Genomics, Institute of Molecular Biology NAS RA, Yerevan 0014, Armenia; (L.G.); (G.K.); (T.S.); (N.M.); (R.Z.); (A.C.); (V.H.)
- Institute of Biomedicine and Pharmacy, Russian-Armenian University, Yerevan 0051, Armenia; (M.N.); (A.H.)
| | - Andranik Chavushyan
- Laboratory of Human Genomics, Institute of Molecular Biology NAS RA, Yerevan 0014, Armenia; (L.G.); (G.K.); (T.S.); (N.M.); (R.Z.); (A.C.); (V.H.)
- Davidyants Laboratories, Yerevan 0054, Armenia
| | - Varduhi Hayrapetyan
- Laboratory of Human Genomics, Institute of Molecular Biology NAS RA, Yerevan 0014, Armenia; (L.G.); (G.K.); (T.S.); (N.M.); (R.Z.); (A.C.); (V.H.)
- Institute of Biomedicine and Pharmacy, Russian-Armenian University, Yerevan 0051, Armenia; (M.N.); (A.H.)
| | - Anahit Hovhannisyan
- Institute of Biomedicine and Pharmacy, Russian-Armenian University, Yerevan 0051, Armenia; (M.N.); (A.H.)
- Laboratory of Evolutionary Genomics, Institute of Molecular Biology NAS RA, Yerevan 0014, Armenia
| | - Shah A. Mohamed Bakhash
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98102, USA; (S.A.M.B.); (K.R.J.); (P.R.); (A.L.G.)
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Keith R. Jerome
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98102, USA; (S.A.M.B.); (K.R.J.); (P.R.); (A.L.G.)
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98102, USA; (S.A.M.B.); (K.R.J.); (P.R.); (A.L.G.)
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98102, USA; (S.A.M.B.); (K.R.J.); (P.R.); (A.L.G.)
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Lyudmila Niazyan
- NORK Infection Clinical Hospital, MoH RA, Yerevan 0047, Armenia; (L.N.); (M.D.)
| | - Mher Davidyants
- NORK Infection Clinical Hospital, MoH RA, Yerevan 0047, Armenia; (L.N.); (M.D.)
| | - Gayane Melik-Andreasyan
- National Center of Disease Control and Prevention, Ministry of Health RA, Yerevan 0025, Armenia; (G.M.-A.); (S.S.)
| | - Shushan Sargsyan
- National Center of Disease Control and Prevention, Ministry of Health RA, Yerevan 0025, Armenia; (G.M.-A.); (S.S.)
| | - Lilit Nersisyan
- Armenian Bioinformatics Institute, Yerevan 0014, Armenia;
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Solna, Sweden
| | - Arsen Arakelyan
- Laboratory of Human Genomics, Institute of Molecular Biology NAS RA, Yerevan 0014, Armenia; (L.G.); (G.K.); (T.S.); (N.M.); (R.Z.); (A.C.); (V.H.)
- Institute of Biomedicine and Pharmacy, Russian-Armenian University, Yerevan 0051, Armenia; (M.N.); (A.H.)
- Bioinformatics Group, Institute of Molecular Biology NAS RA, Yerevan 0014, Armenia;
- Armenian Bioinformatics Institute, Yerevan 0014, Armenia;
- Correspondence: (D.A.); (A.A.)
| |
Collapse
|
8
|
Ecological and Anthropogenic Spatial Gradients Shape Patterns of Dispersal of Foot-and-Mouth Disease Virus in Uganda. Pathogens 2022; 11:pathogens11050524. [PMID: 35631045 PMCID: PMC9143568 DOI: 10.3390/pathogens11050524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 02/04/2023] Open
Abstract
Using georeferenced phylogenetic trees, phylogeography allows researchers to elucidate interactions between environmental heterogeneities and patterns of infectious disease spread. Concordant with the increasing availability of pathogen genetic sequence data, there is a growing need for tools to test epidemiological hypotheses in this field. In this study, we apply tools traditionally used in ecology to elucidate the epidemiology of foot-and-mouth disease virus (FMDV) in Uganda. We analyze FMDV serotype O genetic sequences and their corresponding spatiotemporal metadata from a cross-sectional study of cattle. We apply step selection function (SSF) models, typically used to study wildlife habitat selection, to viral phylogenies to show that FMDV is more likely to be found in areas of low rainfall. Next, we use a novel approach, a resource gradient function (RGF) model, to elucidate characteristics of viral source and sink areas. An RGF model applied to our data reveals that areas of high cattle density and areas near livestock markets may serve as sources of FMDV dissemination in Uganda, and areas of low rainfall serve as viral sinks that experience frequent reintroductions. Our results may help to inform risk-based FMDV control strategies in Uganda. More broadly, these tools advance the phylogenetic toolkit, as they may help to uncover patterns of spread of other organisms for which genetic sequences and corresponding spatiotemporal metadata exist.
Collapse
|
9
|
Nduva GM, Otieno F, Kimani J, McKinnon LR, Cholette F, Sandstrom P, Graham SM, Price MA, Smith AD, Bailey RC, Hassan AS, Esbjörnsson J, Sanders EJ. Phylogeographic Assessment Reveals Geographic Sources of HIV-1 Dissemination Among Men Who Have Sex With Men in Kenya. Front Microbiol 2022; 13:843330. [PMID: 35356525 PMCID: PMC8959701 DOI: 10.3389/fmicb.2022.843330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 01/19/2022] [Indexed: 12/14/2022] Open
Abstract
HIV-1 transmission dynamics involving men who have sex with men (MSM) in Africa are not well understood. We investigated the rates of HIV-1 transmission between MSM across three regions in Kenya: Coast, Nairobi, and Nyanza. We analyzed 372 HIV-1 partial pol sequences sampled during 2006-2019 from MSM in Coast (N = 178, 47.9%), Nairobi (N = 137, 36.8%), and Nyanza (N = 57, 15.3%) provinces in Kenya. Maximum-likelihood (ML) phylogenetics and Bayesian inference were used to determine HIV-1 clusters, evolutionary dynamics, and virus migration rates between geographic regions. HIV-1 sub-subtype A1 (72.0%) was most common followed by subtype D (11.0%), unique recombinant forms (8.9%), subtype C (5.9%), CRF 21A2D (0.8%), subtype G (0.8%), CRF 16A2D (0.3%), and subtype B (0.3%). Forty-six clusters (size range 2-20 sequences) were found-half (50.0%) of which had evidence of extensive HIV-1 mixing among different provinces. Data revealed an exponential increase in infections among MSM during the early-to-mid 2000s and stable or decreasing transmission dynamics in recent years (2017-2019). Phylogeographic inference showed significant (Bayes factor, BF > 3) HIV-1 dissemination from Coast to Nairobi and Nyanza provinces, and from Nairobi to Nyanza province. Strengthening HIV-1 prevention programs to MSM in geographic locations with higher HIV-1 prevalence among MSM (such as Coast and Nairobi) may reduce HIV-1 incidence among MSM in Kenya.
Collapse
Affiliation(s)
- George M. Nduva
- Department of Translational Medicine, Lund University, Lund, Sweden
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Joshua Kimani
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Lyle R. McKinnon
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Francois Cholette
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- National Microbiology Laboratory at the JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Paul Sandstrom
- National Microbiology Laboratory at the JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Susan M. Graham
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Epidemiology, University of Washington, Seattle, WA, United States
| | - Matt A. Price
- IAVI, San Francisco, CA, United States
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
| | - Adrian D. Smith
- Nuffield Department of Medicine, The University of Oxford, Oxford, United Kingdom
| | - Robert C. Bailey
- Nyanza Reproductive Health Society, Kisumu, Kenya
- Division of Epidemiology and Biostatistics, University of Illinois Chicago, Chicago, IL, United States
| | - Amin S. Hassan
- Department of Translational Medicine, Lund University, Lund, Sweden
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Joakim Esbjörnsson
- Department of Translational Medicine, Lund University, Lund, Sweden
- Nuffield Department of Medicine, The University of Oxford, Oxford, United Kingdom
| | - Eduard J. Sanders
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, The University of Oxford, Oxford, United Kingdom
| |
Collapse
|
10
|
Hindupur A, Menon T, Dhandapani P. Molecular investigation of human metapneumovirus in children with acute respiratory infections in Chennai, South India, from 2016-2018. Braz J Microbiol 2022; 53:655-661. [PMID: 35118597 PMCID: PMC9151977 DOI: 10.1007/s42770-022-00689-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 01/28/2022] [Indexed: 02/06/2023] Open
Abstract
Human metapneumovirus (hMPV) has emerged as a frequent cause of acute respiratory infections (ARI) among young children. The prevalence and genetic diversity of hMPV circulating in Chennai, Southern India, has not been studied yet. Hence, this study was aimed to investigate the prevalence, co-infection with other respiratory viruses like HRSV A and B, influenza A and B, hRV and HPIV 1-4 viruses, socio-demographic associations, and genotypes of hMPV among children in Chennai. A total of 350 nasal swab specimens were collected from children with ARI during April 2016 to August 2018 and tested for hMPV by real time PCR method. In this study, hMPV was detected in 4% (14/350) of the samples. One hMPV positive sample was found to be co-infected with influenza B virus. The mean and median ages of the children with hMPV infection were 61.5 months (5.1 years) and 83 months (6.9 years), respectively. Phylogenetic analysis of the partial F gene revealed the presence of A2c subcluster among the study strains as well as with B1 and B2 lineages. The prevalence data obtained in this study is important in evaluating the role of hMPV in childhood ARI and emphasizes the importance of routine viral diagnosis in hospitals. To the best of our knowledge, this is the first study to report the prevalence, seasonality, and genetic diversity of hMPV in Chennai as well as the first study to report A2c subcluster of hMPV among children in India.
Collapse
Affiliation(s)
- Anusha Hindupur
- grid.413015.20000 0004 0505 215XDepartment of Microbiology, Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Chennai, Tamil Nadu India
| | - Thangam Menon
- Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu India
| | - Prabu Dhandapani
- grid.413015.20000 0004 0505 215XDepartment of Microbiology, Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Chennai, Tamil Nadu India
| |
Collapse
|
11
|
Hunting alters viral transmission and evolution in a large carnivore. Nat Ecol Evol 2022; 6:174-182. [PMID: 35087217 PMCID: PMC10111630 DOI: 10.1038/s41559-021-01635-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 11/24/2021] [Indexed: 11/09/2022]
Abstract
Hunting can fundamentally alter wildlife population dynamics but the consequences of hunting on pathogen transmission and evolution remain poorly understood. Here, we present a study that leverages a unique landscape-scale quasi-experiment coupled with pathogen-transmission tracing, network simulation and phylodynamics to provide insights into how hunting shapes feline immunodeficiency virus (FIV) dynamics in puma (Puma concolor). We show that removing hunting pressure enhances the role of males in transmission, increases the viral population growth rate and increases the role of evolutionary forces on the pathogen compared to when hunting was reinstated. Changes in transmission observed with the removal of hunting could be linked to short-term social changes while the male puma population increased. These findings are supported through comparison with a region with stable hunting management over the same time period. This study shows that routine wildlife management can have impacts on pathogen transmission and evolution not previously considered.
Collapse
|
12
|
Accounting for spatial sampling patterns in Bayesian phylogeography. Proc Natl Acad Sci U S A 2021; 118:2105273118. [PMID: 34930835 PMCID: PMC8719894 DOI: 10.1073/pnas.2105273118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2021] [Indexed: 12/13/2022] Open
Abstract
Statistical phylogeography has led to substantial progress in our understanding of the pace and means by which organisms colonize their habitats. Yet, inference from these models often relies on implicit assumptions pertaining to spatial sampling design, potentially leading to biased estimation of key biological parameters. While sampled locations sometimes convey signal about the processes that shape spatial biodiversity, they do not always do so. We present a statistical approach that permits accurate estimation of dispersal rates, even in cases where spatial sampling is driven by practical motivations unrelated to the outcome of the evolutionary process. The proposed framework paves the way to further developments in phylogeography with key applications, including the efficient monitoring of pandemics and invasive species during the course of their evolution. Statistical phylogeography provides useful tools to characterize and quantify the spread of organisms during the course of evolution. Analyzing georeferenced genetic data often relies on the assumption that samples are preferentially collected in densely populated areas of the habitat. Deviation from this assumption negatively impacts the inference of the spatial and demographic dynamics. This issue is pervasive in phylogeography. It affects analyses that approximate the habitat as a set of discrete demes as well as those that treat it as a continuum. The present study introduces a Bayesian modeling approach that explicitly accommodates for spatial sampling strategies. An original inference technique, based on recent advances in statistical computing, is then described that is most suited to modeling data where sequences are preferentially collected at certain locations, independently of the outcome of the evolutionary process. The analysis of georeferenced genetic sequences from the West Nile virus in North America along with simulated data shows how assumptions about spatial sampling may impact our understanding of the forces shaping biodiversity across time and space.
Collapse
|
13
|
Berry IM, Melendrez MC, Pollett S, Figueroa K, Buddhari D, Klungthong C, Nisalak A, Panciera M, Thaisomboonsuk B, Li T, Vallard TG, Macareo L, Yoon IK, Thomas SJ, Endy T, Jarman RG. Precision Tracing of Household Dengue Spread Using Inter- and Intra-Host Viral Variation Data, Kamphaeng Phet, Thailand. Emerg Infect Dis 2021; 27:1637-1644. [PMID: 34013878 PMCID: PMC8153871 DOI: 10.3201/eid2706.204323] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Dengue control approaches are best informed by granular spatial epidemiology of these viruses, yet reconstruction of inter- and intra-household transmissions is limited when analyzing case count, serologic, or genomic consensus sequence data. To determine viral spread on a finer spatial scale, we extended phylogenomic discrete trait analyses to reconstructions of house-to-house transmissions within a prospective cluster study in Kamphaeng Phet, Thailand. For additional resolution and transmission confirmation, we mapped dengue intra-host single nucleotide variants on the taxa of these time-scaled phylogenies. This approach confirmed 19 household transmissions and revealed that dengue disperses an average of 70 m per day between households in these communities. We describe an evolutionary biology framework for the resolution of dengue transmissions that cannot be differentiated based on epidemiologic and consensus genome data alone. This framework can be used as a public health tool to inform control approaches and enable precise tracing of dengue transmissions.
Collapse
|
14
|
Ficetola GF, Rubolini D. Containment measures limit environmental effects on COVID-19 early outbreak dynamics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 761:144432. [PMID: 33360124 PMCID: PMC7744010 DOI: 10.1016/j.scitotenv.2020.144432] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/07/2020] [Accepted: 12/07/2020] [Indexed: 04/13/2023]
Abstract
Environmental factors are well known to affect spatio-temporal patterns of infectious disease outbreaks, but whether the rapid spread of COVID-19 across the globe is related to local environmental conditions is highly debated. We assessed the impact of environmental factors (temperature, humidity and air pollution) on the global patterns of COVID-19 early outbreak dynamics during January-May 2020, controlling for several key socio-economic factors and airport connections. We showed that during the earliest phase of the global outbreak (January-March), COVID-19 growth rates were non-linearly related to climate, with fastest spread in regions with a mean temperature of ca. 5 °C, and in the most polluted regions. However, environmental effects faded almost completely when considering later outbreaks, in keeping with the progressive enforcement of containment actions. Accordingly, COVID-19 growth rates consistently decreased with stringent containment actions during both early and late outbreaks. Our findings indicate that environmental drivers may have played a role in explaining the early variation among regions in disease spread. With limited policy interventions, seasonal patterns of disease spread might emerge, with temperate regions of both hemispheres being most at risk of severe outbreaks during colder months. Nevertheless, containment measures play a much stronger role and overwhelm impacts of environmental variation, highlighting the key role for policy interventions in curbing COVID-19 diffusion within a given region. If the disease will become seasonal in the next years, information on environmental drivers of COVID-19 can be integrated with epidemiological models to inform forecasting of future outbreak risks and improve management plans.
Collapse
Affiliation(s)
- Gentile Francesco Ficetola
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, via Celoria 26, I-20133 Milano, Italy; Université Grenoble Alpes, CNRS, Université Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine, F-38000 Grenoble, France.
| | - Diego Rubolini
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, via Celoria 26, I-20133 Milano, Italy
| |
Collapse
|
15
|
Prasetyowati H, Dhewantara PW, Hendri J, Astuti EP, Gelaw YA, Harapan H, Ipa M, Widyastuti W, Handayani DOTL, Salama N, Picasso M. Geographical heterogeneity and socio-ecological risk profiles of dengue in Jakarta, Indonesia. GEOSPATIAL HEALTH 2021; 16. [PMID: 33733650 DOI: 10.4081/gh.2021.948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 01/26/2021] [Indexed: 06/12/2023]
Abstract
The aim of this study was to assess the role of climate variability on the incidence of dengue fever (DF), an endemic arboviral infection existing in Jakarta, Indonesia. The work carried out included analysis of the spatial distribution of confirmed DF cases from January 2007 to December 2018 characterising the sociodemographical and ecological factors in DF high-risk areas. Spearman's rank correlation was used to examine the relationship between DF incidence and climatic factors. Spatial clustering and hotspots of DF were examined using global Moran's I statistic and the local indicator for spatial association analysis. Classification and regression tree (CART) analysis was performed to compare and identify demographical and socio-ecological characteristics of the identified hotspots and low-risk clusters. The seasonality of DF incidence was correlated with precipitation (r=0.254, P<0.01), humidity (r=0.340, P<0.01), dipole mode index (r= -0.459, P<0.01) and Tmin (r= -0.181, P<0.05). DF incidence was spatially clustered at the village level (I=0.294, P<0.001) and 22 hotspots were identified with a concentration in the central and eastern parts of Jakarta. CART analysis showed that age and occupation were the most important factors explaining DF clustering. Areaspecific and population-targeted interventions are needed to improve the situation among those living in the identified DF high-risk areas in Jakarta.
Collapse
Affiliation(s)
- Heni Prasetyowati
- Pangandaran Unit for Health Research and Development, National Institute of Health Research and Development (NIHRD), Ministry of Health of Indonesia, Pangandaran.
| | - Pandji Wibawa Dhewantara
- Center for Research and Development of Public Health Effort, National Institute of Health Research and Development (NIHRD), Ministry of Health of Indonesia, Jakarta.
| | - Joni Hendri
- Pangandaran Unit for Health Research and Development, National Institute of Health Research and Development (NIHRD), Ministry of Health of Indonesia, Pangandaran.
| | - Endang Puji Astuti
- Pangandaran Unit for Health Research and Development, National Institute of Health Research and Development (NIHRD), Ministry of Health of Indonesia, Pangandaran.
| | - Yalemzewod Assefa Gelaw
- Population Child Health Research Group, School of Women's and Children's Health, UNSW, NSW Australia; Institute of Public Health, College of Medicine and Health Science, University of Gondar, Gondar.
| | - Harapan Harapan
- Medical Research Unit, School of Medicine, Syiah Kuala University, Banda Aceh, Aceh, Indonesia; Tropical Disease Centre, School of Medicine, Syiah Kuala University, Banda Aceh, Aceh, Indonesia; Department of Microbiology, School of Medicine, Syiah Kuala University, Banda Aceh, Aceh.
| | - Mara Ipa
- Pangandaran Unit for Health Research and Development, National Institute of Health Research and Development (NIHRD), Ministry of Health of Indonesia, Pangandaran.
| | | | | | | | | |
Collapse
|
16
|
Sallam M, Mahafzah A. Molecular Analysis of SARS-CoV-2 Genetic Lineages in Jordan: Tracking the Introduction and Spread of COVID-19 UK Variant of Concern at a Country Level. Pathogens 2021; 10:302. [PMID: 33807556 PMCID: PMC8000902 DOI: 10.3390/pathogens10030302] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/03/2021] [Accepted: 03/03/2021] [Indexed: 12/18/2022] Open
Abstract
The rapid evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is manifested by the emergence of an ever-growing pool of genetic lineages. The aim of this study was to analyze the genetic variability of SARS-CoV-2 in Jordan, with a special focus on the UK variant of concern. A total of 579 SARS-CoV-2 sequences collected in Jordan were subjected to maximum likelihood and Bayesian phylogenetic analysis. Genetic lineage assignment was undertaken using the Pango system. Amino acid substitutions were investigated using the Protein Variation Effect Analyzer (PROVEAN) tool. A total of 19 different SARS-CoV-2 genetic lineages were detected, with the most frequent being the first Jordan lineage (B.1.1.312), first detected in August 2020 (n = 424, 73.2%). This was followed by the second Jordan lineage (B.1.36.10), first detected in September 2020 (n = 62, 10.7%), and the UK variant of concern (B.1.1.7; n = 36, 6.2%). In the spike gene region, the molecular signature for B.1.1.312 was the non-synonymous mutation A24432T resulting in a deleterious amino acid substitution (Q957L), while the molecular signature for B.1.36.10 was the synonymous mutation C22444T. Bayesian analysis revealed that the UK variant of concern (B.1.1.7) was introduced into Jordan in late November 2020 (mean estimate); four weeks earlier than its official reporting in the country. In Jordan, an exponential increase in COVID-19 cases due to B.1.1.7 lineage coincided with the new year 2021. The highest proportion of phylogenetic clustering was detected for the B.1.1.7 lineage. The amino acid substitution D614G in the spike glycoprotein was exclusively present in the country from July 2020 onwards. Two Jordanian lineages dominated infections in the country, with continuous introduction/emergence of new lineages. In Jordan, the rapid spread of the UK variant of concern should be monitored closely. The spread of SARS-CoV-2 mutants appeared to be related to the founder effect; nevertheless, the biological impact of certain mutations should be further investigated.
Collapse
Affiliation(s)
- Malik Sallam
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan;
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman 11942, Jordan
| | - Azmi Mahafzah
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan;
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman 11942, Jordan
| |
Collapse
|
17
|
Serra A, Marzo N, Pons B, Maduell P, López M, Grancha S. Characterization of antibodies in human immunoglobulin products from different regions worldwide. Int J Infect Dis 2021; 104:610-616. [PMID: 33524620 PMCID: PMC7844383 DOI: 10.1016/j.ijid.2021.01.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/08/2021] [Accepted: 01/13/2021] [Indexed: 12/31/2022] Open
Abstract
AIM The antibody levels against a broad spectrum of pathogens were assessed in commercial intravenous immunoglobulin (IVIG) manufactured from pooled plasma obtained from different global regions. METHODS Twenty-four IVIG commercial lots from eight manufacturers corresponding to 12 brands were analyzed. The plasma was collected in 10 countries/regions. Depending on each pathogen, antibody levels were measured using specific commercial IgG-specific enzyme immunoassay kits or by cell culture neutralization test and guinea pig skin neutralization test. A principal component analysis was performed. RESULTS For polio and diphtheria (reference markers of the US authorities), all IVIGs had relevant titers in accordance with reference levels. IVIGs from Canada, Australia, and the USA were positive for titers against globally distributed pathogens or those under vaccination programs in the developed world (parainfluenza, Epstein-Barr, varicella-zoster, influenza B, parvovirus B19, and measles viruses). IVIG from Taiwan and Hong Kong showed low antibody titers for these pathogens but high titers for Pseudomonas aeruginosa. IVIG from India had high titers for pathogens frequently found in developing countries (West Nile, dengue, chikungunya, and hepatitis E viruses and Streptococcus pneumoniae). IVIGs from Argentina, Spain, Israel, and Czechia showed intermediate antibody concentrations. CONCLUSION The antibody profile in IVIG was greatly influenced by regional characteristics including climate, vaccination programs, and the prevalence of pathogens in the different countries and regions.
Collapse
Affiliation(s)
| | - Núria Marzo
- Grifols, Research and Development, Barcelona, Spain.
| | - Berta Pons
- Grifols, Research and Development, Barcelona, Spain
| | - Pau Maduell
- Grifols, Research and Development, Barcelona, Spain
| | - Maite López
- Grifols, Research and Development, Barcelona, Spain
| | | |
Collapse
|
18
|
Li SL, Messina JP, Pybus OG, Kraemer MUG, Gardner L. A review of models applied to the geographic spread of Zika virus. Trans R Soc Trop Med Hyg 2021; 115:956-964. [PMID: 33570155 PMCID: PMC8417088 DOI: 10.1093/trstmh/trab009] [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: 06/29/2020] [Revised: 12/13/2020] [Accepted: 01/08/2021] [Indexed: 11/13/2022] Open
Abstract
In recent years, Zika virus (ZIKV) has expanded its geographic range and in 2015–2016 caused a substantial epidemic linked to a surge in developmental and neurological complications in newborns. Mathematical models are powerful tools for assessing ZIKV spread and can reveal important information for preventing future outbreaks. We reviewed the literature and retrieved modelling studies that were developed to understand the spatial epidemiology of ZIKV spread and risk. We classified studies by type, scale, aim and applications and discussed their characteristics, strengths and limitations. We examined the main objectives of these models and evaluated the effectiveness of integrating epidemiological and phylogeographic data, along with socioenvironmental risk factors that are known to contribute to vector–human transmission. We also assessed the promising application of human mobility data as a real-time indicator of ZIKV spread. Lastly, we summarised model validation methods used in studies to ensure accuracy in models and modelled outcomes. Models are helpful for understanding ZIKV spread and their characteristics should be carefully considered when developing future modelling studies to improve arbovirus surveillance.
Collapse
Affiliation(s)
- Sabrina L Li
- School of Geography and the Environment, University of Oxford, South Parks Road, Oxford, OX1 3QY, UK
| | - Jane P Messina
- School of Geography and the Environment, University of Oxford, South Parks Road, Oxford, OX1 3QY, UK.,School of Global and Area Studies, University of Oxford, 12 Bevington Road, Oxford, OX2 6LH, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, 11a Mansfield Rd, Oxford, OX1 3SZ, UK
| | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, 11a Mansfield Rd, Oxford, OX1 3SZ, UK
| | - Lauren Gardner
- Department of Civil and Systems Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218-2682, USA.,Center for Systems Science and Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218-2682, USA
| |
Collapse
|
19
|
Maljkovic Berry I, Melendrez MC, Bishop-Lilly KA, Rutvisuttinunt W, Pollett S, Talundzic E, Morton L, Jarman RG. Next Generation Sequencing and Bioinformatics Methodologies for Infectious Disease Research and Public Health: Approaches, Applications, and Considerations for Development of Laboratory Capacity. J Infect Dis 2021; 221:S292-S307. [PMID: 31612214 DOI: 10.1093/infdis/jiz286] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Next generation sequencing (NGS) combined with bioinformatics has successfully been used in a vast array of analyses for infectious disease research of public health relevance. For instance, NGS and bioinformatics approaches have been used to identify outbreak origins, track transmissions, investigate epidemic dynamics, determine etiological agents of a disease, and discover novel human pathogens. However, implementation of high-quality NGS and bioinformatics in research and public health laboratories can be challenging. These challenges mainly include the choice of the sequencing platform and the sequencing approach, the choice of bioinformatics methodologies, access to the appropriate computation and information technology infrastructure, and recruiting and retaining personnel with the specialized skills and experience in this field. In this review, we summarize the most common NGS and bioinformatics workflows in the context of infectious disease genomic surveillance and pathogen discovery, and highlight the main challenges and considerations for setting up an NGS and bioinformatics-focused infectious disease research public health laboratory. We describe the most commonly used sequencing platforms and review their strengths and weaknesses. We review sequencing approaches that have been used for various pathogens and study questions, as well as the most common difficulties associated with these approaches that should be considered when implementing in a public health or research setting. In addition, we provide a review of some common bioinformatics tools and procedures used for pathogen discovery and genome assembly, along with the most common challenges and solutions. Finally, we summarize the bioinformatics of advanced viral, bacterial, and parasite pathogen characterization, including types of study questions that can be answered when utilizing NGS and bioinformatics.
Collapse
Affiliation(s)
- Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | | | - Kimberly A Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Maryland
| | - Wiriya Rutvisuttinunt
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Simon Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland.,Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Eldin Talundzic
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Lindsay Morton
- Global Emerging Infections Surveillance, Armed Forces Health Surveillance Branch, Silver Spring, Maryland
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| |
Collapse
|
20
|
Kim WK, Cho S, Lee SH, No JS, Lee GY, Park K, Lee D, Jeong ST, Song JW. Genomic Epidemiology and Active Surveillance to Investigate Outbreaks of Hantaviruses. Front Cell Infect Microbiol 2021; 10:532388. [PMID: 33489927 PMCID: PMC7819890 DOI: 10.3389/fcimb.2020.532388] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 11/19/2020] [Indexed: 12/11/2022] Open
Abstract
Emerging and re-emerging RNA viruses pose significant public health, economic, and societal burdens. Hantaviruses (genus Orthohantavirus, family Hantaviridae, order Bunyavirales) are enveloped, negative-sense, single-stranded, tripartite RNA viruses that are emerging zoonotic pathogens harbored by small mammals such as rodents, bats, moles, and shrews. Orthohantavirus infections cause hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome in humans (HCPS). Active targeted surveillance has elucidated high-resolution phylogeographic relationships between patient- and rodent-derived orthohantavirus genome sequences and identified the infection source by temporally and spatially tracking viral genomes. Active surveillance of patients with HFRS entails 1) recovering whole-genome sequences of Hantaan virus (HTNV) using amplicon (multiplex PCR-based) next-generation sequencing, 2) tracing the putative infection site of a patient by administering an epidemiological questionnaire, and 3) collecting HTNV-positive rodents using targeted rodent trapping. Moreover, viral genome tracking has been recently performed to rapidly and precisely characterize an outbreak from the emerging virus. Here, we reviewed genomic epidemiological and active surveillance data for determining the emergence of zoonotic RNA viruses based on viral genomic sequences obtained from patients and natural reservoirs. This review highlights the recent studies on tracking viral genomes for identifying and characterizing emerging viral outbreaks worldwide. We believe that active surveillance is an effective method for identifying rodent-borne orthohantavirus infection sites, and this report provides insights into disease mitigation and preparedness for managing emerging viral outbreaks.
Collapse
Affiliation(s)
- Won-Keun Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, South Korea.,Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, South Korea
| | - Seungchan Cho
- Department of Microbiology, Korea University College of Medicine, Seoul, South Korea
| | - Seung-Ho Lee
- Department of Microbiology, Korea University College of Medicine, Seoul, South Korea
| | - Jin Sun No
- Department of Microbiology, Korea University College of Medicine, Seoul, South Korea
| | - Geum-Young Lee
- Department of Microbiology, Korea University College of Medicine, Seoul, South Korea
| | - Kyungmin Park
- Department of Microbiology, Korea University College of Medicine, Seoul, South Korea.,BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, South Korea
| | - Daesang Lee
- 4th R&D Institute, Agency for Defense Development, Daejeon, South Korea
| | - Seong Tae Jeong
- 4th R&D Institute, Agency for Defense Development, Daejeon, South Korea
| | - Jin-Won Song
- Department of Microbiology, Korea University College of Medicine, Seoul, South Korea.,BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, South Korea
| |
Collapse
|
21
|
Harvey WT, Mulatti P, Fusaro A, Scolamacchia F, Zecchin B, Monne I, Marangon S. Spatiotemporal reconstruction and transmission dynamics during the 2016-17 H5N8 highly pathogenic avian influenza epidemic in Italy. Transbound Emerg Dis 2021; 68:37-50. [PMID: 31788978 PMCID: PMC8048528 DOI: 10.1111/tbed.13420] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 10/03/2019] [Accepted: 10/29/2019] [Indexed: 11/29/2022]
Abstract
Effective control of avian diseases in domestic populations requires understanding of the transmission dynamics facilitating viral emergence and spread. In 2016-17, Italy experienced a significant avian influenza epidemic caused by a highly pathogenic A(H5N8) virus, which affected domestic premises housing around 2.7 million birds, primarily in the north-eastern regions with the highest density of poultry farms (Lombardy, Emilia-Romagna and Veneto). We perform integrated analyses of genetic, spatiotemporal and host data within a Bayesian phylogenetic framework. Using continuous and discrete phylogeography, we estimate the locations of movements responsible for the spread and persistence of the epidemic. The information derived from these analyses on rates of transmission between regions through time can be used to assess the success of control measures. Using an approach based on phylogenetic-temporal distances between domestic cases, we infer the presence of cryptic wild bird-mediated transmission, information that can be used to complement existing epidemiological methods for distinguishing transmission within the domestic population from incursions across the wildlife-domestic interface, a common challenge in veterinary epidemiology. Spatiotemporal reconstruction of the epidemic reveals a highly skewed distribution of virus movements with a high proportion of shorter distance local movements interspersed with occasional long-distance dispersal events associated with wild birds. We also show how such inference be used to identify possible instances of human-mediated movements where distances between phylogenetically linked domestic cases are unusually high.
Collapse
Affiliation(s)
- William T. Harvey
- Boyd Orr Centre for Population and Ecosystem HealthInstitute of Biodiversity, Animal Health and Comparative MedicineCollege of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
| | - Paolo Mulatti
- Istituto Zooprofilattico Sperimentale delle VenezieLegnaro (Padua)Italy
| | - Alice Fusaro
- Istituto Zooprofilattico Sperimentale delle VenezieLegnaro (Padua)Italy
| | | | - Bianca Zecchin
- Istituto Zooprofilattico Sperimentale delle VenezieLegnaro (Padua)Italy
| | - Isabella Monne
- Istituto Zooprofilattico Sperimentale delle VenezieLegnaro (Padua)Italy
| | - Stefano Marangon
- Istituto Zooprofilattico Sperimentale delle VenezieLegnaro (Padua)Italy
| |
Collapse
|
22
|
Rasmussen DA, Grünwald NJ. Phylogeographic Approaches to Characterize the Emergence of Plant Pathogens. PHYTOPATHOLOGY 2021; 111:68-77. [PMID: 33021879 DOI: 10.1094/phyto-07-20-0319-fi] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Phylogeography combines geographic information with phylogenetic and population genomic approaches to infer the evolutionary history of a species or population in a geographic context. This approach has been instrumental in understanding the emergence, spread, and evolution of a range of plant pathogens. In particular, phylogeography can address questions about where a pathogen originated, whether it is native or introduced, and when and how often introductions occurred. We review the theory, methods, and approaches underpinning phylogeographic inference and highlight applications providing novel insights into the emergence and spread of select pathogens. We hope that this review will be useful in assessing the power, pitfalls, and opportunities presented by various phylogeographic approaches.
Collapse
Affiliation(s)
- David A Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC
| | - Niklaus J Grünwald
- Horticultural Crops Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Corvallis, OR
| |
Collapse
|
23
|
Kuno G. The Absence of Yellow Fever in Asia: History, Hypotheses, Vector Dispersal, Possibility of YF in Asia, and Other Enigmas. Viruses 2020; 12:E1349. [PMID: 33255615 PMCID: PMC7759908 DOI: 10.3390/v12121349] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/12/2020] [Accepted: 11/17/2020] [Indexed: 01/11/2023] Open
Abstract
Since the recent epidemics of yellow fever in Angola and Brazil as well as the importation of cases to China in 2016, there has been an increased interest in the century-old enigma, absence of yellow fever in Asia. Although this topic has been repeatedly reviewed before, the history of human intervention has never been considered a critical factor. A two-stage literature search online for this review, however, yielded a rich history indispensable for the debate over this medical enigma. As we combat the pandemic of COVID-19 coronavirus worldwide today, we can learn invaluable lessons from the historical events in Asia. In this review, I explore the history first and then critically examine in depth major hypotheses proposed in light of accumulated data, global dispersal of the principal vector, patterns of YF transmission, persistence of urban transmission, and the possibility of YF in Asia. Through this process of re-examination of the current knowledge, the subjects for research that should be conducted are identified. This review also reveals the importance of holistic approach incorporating ecological and human factors for many unresolved subjects, such as the enigma of YF absence in Asia, vector competence, vector dispersal, spillback, viral persistence and transmission mechanisms.
Collapse
Affiliation(s)
- Goro Kuno
- Centers for Disease Control and Prevention, Formerly Division of Vector-Borne Infectious Diseases, Fort Collins, CO 80521, USA
| |
Collapse
|
24
|
Vrancken B, Zhao B, Li X, Han X, Liu H, Zhao J, Zhong P, Lin Y, Zai J, Liu M, Smith DM, Dellicour S, Chaillon A. Comparative Circulation Dynamics of the Five Main HIV Types in China. J Virol 2020; 94:e00683-20. [PMID: 32938762 PMCID: PMC7654276 DOI: 10.1128/jvi.00683-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/02/2020] [Indexed: 01/17/2023] Open
Abstract
The HIV epidemic in China accounts for 3% of the global HIV incidence. We compared the patterns and determinants of interprovincial spread of the five most prevalent circulating types. HIV pol sequences sampled across China were used to identify relevant transmission networks of the five most relevant HIV-1 types (B and circulating recombinant forms [CRFs] CRF01_AE, CRF07_BC, CRF08_BC, and CRF55_01B) in China. From these, the dispersal history across provinces was inferred. A generalized linear model (GLM) was used to test the association between migration rates among provinces and several measures of human mobility. A total of 10,707 sequences were collected between 2004 and 2017 across 26 provinces, among which 1,962 are newly reported here. A mean of 18 (minimum and maximum, 1 and 54) independent transmission networks involving up to 17 provinces were identified. Discrete phylogeographic analysis largely recapitulates the documented spread of the HIV types, which in turn, mirrors within-China population migration flows to a large extent. In line with the different spatiotemporal spread dynamics, the identified drivers thereof were also heterogeneous but are consistent with a central role of human mobility. The comparative analysis of the dispersal dynamics of the five main HIV types circulating in China suggests a key role of large population centers and developed transportation infrastructures as hubs of HIV dispersal. This advocates for coordinated public health efforts in addition to local targeted interventions.IMPORTANCE While traditional epidemiological studies are of great interest in describing the dynamics of epidemics, they struggle to fully capture the geospatial dynamics and factors driving the dispersal of pathogens like HIV as they have difficulties capturing linkages between infections. To overcome this, we used a discrete phylogeographic approach coupled to a generalized linear model extension to characterize the dynamics and drivers of the across-province spread of the five main HIV types circulating in China. Our results indicate that large urbanized areas with dense populations and developed transportation infrastructures are facilitators of HIV dispersal throughout China and highlight the need to consider harmonized country-wide public policies to control local HIV epidemics.
Collapse
Affiliation(s)
- Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Computational and Evolutionary Virology, KU Leuven, Leuven, Belgium
| | - Bin Zhao
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xingguang Li
- Department of Hospital Office, The First People's Hospital of Fangchenggang, Fangchenggang, China
| | - Xiaoxu Han
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Haizhou Liu
- Centre for Emerging Infectious Diseases, The State Key Laboratory of Virology, Wuhan Institute of Virology, University of Chinese Academy of Sciences, Wuhan, China
| | - Jin Zhao
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Ping Zhong
- Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Yi Lin
- Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Junjie Zai
- Immunology innovation Team, School of Medicine, Ningbo University, Ningbo, Zhejiang China
| | - Mingchen Liu
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Davey M Smith
- Division of Infectious Diseases and Global Public Health, University of California San Diego, California, USA
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Computational and Evolutionary Virology, KU Leuven, Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium
| | - Antoine Chaillon
- Division of Infectious Diseases and Global Public Health, University of California San Diego, California, USA
| |
Collapse
|
25
|
Ji X, Zhang Z, Holbrook A, Nishimura A, Baele G, Rambaut A, Lemey P, Suchard MA. Gradients Do Grow on Trees: A Linear-Time O(N)-Dimensional Gradient for Statistical Phylogenetics. Mol Biol Evol 2020; 37:3047-3060. [PMID: 32458974 PMCID: PMC7530611 DOI: 10.1093/molbev/msaa130] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Calculation of the log-likelihood stands as the computational bottleneck for many statistical phylogenetic algorithms. Even worse is its gradient evaluation, often used to target regions of high probability. Order O(N)-dimensional gradient calculations based on the standard pruning algorithm require O(N2) operations, where N is the number of sampled molecular sequences. With the advent of high-throughput sequencing, recent phylogenetic studies have analyzed hundreds to thousands of sequences, with an apparent trend toward even larger data sets as a result of advancing technology. Such large-scale analyses challenge phylogenetic reconstruction by requiring inference on larger sets of process parameters to model the increasing data heterogeneity. To make these analyses tractable, we present a linear-time algorithm for O(N)-dimensional gradient evaluation and apply it to general continuous-time Markov processes of sequence substitution on a phylogenetic tree without a need to assume either stationarity or reversibility. We apply this approach to learn the branch-specific evolutionary rates of three pathogenic viruses: West Nile virus, Dengue virus, and Lassa virus. Our proposed algorithm significantly improves inference efficiency with a 126- to 234-fold increase in maximum-likelihood optimization and a 16- to 33-fold computational performance increase in a Bayesian framework.
Collapse
Affiliation(s)
- Xiang Ji
- Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
- Department of Mathematics, School of Science & Engineering, Tulane University, New Orleans, LA
| | - Zhenyu Zhang
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA
| | - Andrew Holbrook
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA
| | - Akihiko Nishimura
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Andrew Rambaut
- Institute of Evolutionary Biology, Centre for Immunology, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| |
Collapse
|
26
|
Coelho MTP, Rodrigues JFM, Medina AM, Scalco P, Terribile LC, Vilela B, Diniz-Filho JAF, Dobrovolski R. Global expansion of COVID-19 pandemic is driven by population size and airport connections. PeerJ 2020. [DOI: 10.7717/peerj.9708] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The pandemic state of COVID-19 caused by the SARS CoV-2 put the world in quarantine, led to hundreds of thousands of deaths and is causing an unprecedented economic crisis. However, COVID-19 is spreading in different rates at different countries. Here, we tested the effect of three classes of predictors, i.e., socioeconomic, climatic and transport, on the rate of daily increase of COVID-19 on its exponential phase. We found that population size and global connections, represented by countries’ importance in the global air transportation network, are the main explanations for the early growth rate of COVID-19 in different countries. Climate and socioeconomics had no significant effect in this big picture analysis. Our results indicate that the current claims that the growth rate of COVID-19 may be lower in warmer and humid countries should be taken very carefully, risking to disturb well-established and effective policy of social isolation that may help to avoid higher mortality rates due to the collapse of national health systems.
Collapse
Affiliation(s)
| | | | | | - Paulo Scalco
- Faculdade de Administração, Economia, Ciências Contábeis (FACE), Universidade Federal de Goiás, Goiânia, GO, Brazil
| | | | - Bruno Vilela
- Instituto de Biologia, Universidade Federal da Bahia, Salvador, BA, Brazil
| | | | | |
Collapse
|
27
|
da Silva W, Kutnjak D, Xu Y, Xu Y, Giovannoni J, Elena SF, Gray S. Transmission modes affect the population structure of potato virus Y in potato. PLoS Pathog 2020; 16:e1008608. [PMID: 32574227 PMCID: PMC7347233 DOI: 10.1371/journal.ppat.1008608] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 07/09/2020] [Accepted: 05/06/2020] [Indexed: 01/13/2023] Open
Abstract
Transmission is a crucial part of a viral life cycle and transmission mode can have an important impact on virus biology. It was demonstrated that transmission mode can influence the virulence and evolution of a virus; however, few empirical data are available to describe the direct underlying changes in virus population structure dynamics within the host. Potato virus Y (PVY) is an RNA virus and one of the most damaging pathogens of potato. It comprises several genetically variable strains that are transmitted between plants via different transmission modes. To investigate how transmission modes affect the within-plant viral population structure, we have used a deep sequencing approach to examine the changes in the genetic structure of populations (in leaves and tubers) of three PVY strains after successive passages by horizontal (aphid and mechanical) and vertical (via tubers) transmission modes. Nucleotide diversities of viral populations were significantly influenced by transmission modes; lineages transmitted by aphids were the least diverse, whereas lineages transmitted by tubers were the most diverse. Differences in nucleotide diversities of viral populations between leaves and tubers were transmission mode-dependent, with higher diversities in tubers than in leaves for aphid and mechanically transmitted lineages. Furthermore, aphid and tuber transmissions were shown to impose stronger genetic bottlenecks than mechanical transmission. To better understand the structure of virus populations within the host, transmission mode, movement of the virus within the host, and the number of replication cycles after transmission event need to be considered. Collectively, our results suggest a significant impact of virus transmission modes on the within-plant diversity of virus populations and provide quantitative fundamental data for understanding how transmission can shape virus diversity in the natural ecosystems, where different transmission modes are expected to affect virus population structure and consequently its evolution.
Collapse
Affiliation(s)
- Washington da Silva
- Department of Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, Connecticut, United States of America
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, New York, United States of America
- * E-mail: (WdS); (DK)
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, Paterna, València, Spain
- * E-mail: (WdS); (DK)
| | - Yi Xu
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, New York, United States of America
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Yimin Xu
- Boyce Thompson Institute, Cornell University, Ithaca, New York, United States of America
- Emerging Pests & Pathogens Research Unit, USDA, ARS, Ithaca, New York, United States of America
| | - James Giovannoni
- Boyce Thompson Institute, Cornell University, Ithaca, New York, United States of America
- Emerging Pests & Pathogens Research Unit, USDA, ARS, Ithaca, New York, United States of America
| | - Santiago F. Elena
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, Paterna, València, Spain
- The Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Stewart Gray
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, New York, United States of America
- Emerging Pests & Pathogens Research Unit, USDA, ARS, Ithaca, New York, United States of America
| |
Collapse
|
28
|
Albery GF, Eskew EA, Ross N, Olival KJ. Predicting the global mammalian viral sharing network using phylogeography. Nat Commun 2020; 11:2260. [PMID: 32385239 PMCID: PMC7210981 DOI: 10.1038/s41467-020-16153-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/15/2020] [Indexed: 02/08/2023] Open
Abstract
Understanding interspecific viral transmission is key to understanding viral ecology and evolution, disease spillover into humans, and the consequences of global change. Prior studies have uncovered macroecological drivers of viral sharing, but analyses have never attempted to predict viral sharing in a pan-mammalian context. Using a conservative modelling framework, we confirm that host phylogenetic similarity and geographic range overlap are strong, nonlinear predictors of viral sharing among species across the entire mammal class. Using these traits, we predict global viral sharing patterns of 4196 mammal species and show that our simulated network successfully predicts viral sharing and reservoir host status using internal validation and an external dataset. We predict high rates of mammalian viral sharing in the tropics, particularly among rodents and bats, and within- and between-order sharing differed geographically and taxonomically. Our results emphasize the importance of ecological and phylogenetic factors in shaping mammalian viral communities, and provide a robust, general model to predict viral host range and guide pathogen surveillance and conservation efforts. Prior studies have investigated macroecological patterns of host sharing among viruses, although certain mammal clades have not been represented in these analyses, and the findings have not been used to predict the true network. Here the authors model the species level traits that predict viral sharing across all mammal clades and validate their predictions using an independent dataset.
Collapse
Affiliation(s)
- Gregory F Albery
- EcoHealth Alliance, New York, NY, USA. .,Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, Scotland. .,Department of Biology, Georgetown University, Washington, DC, USA.
| | | | - Noam Ross
- EcoHealth Alliance, New York, NY, USA
| | | |
Collapse
|
29
|
Chaters GL, Johnson PCD, Cleaveland S, Crispell J, de Glanville WA, Doherty T, Matthews L, Mohr S, Nyasebwa OM, Rossi G, Salvador LCM, Swai E, Kao RR. Analysing livestock network data for infectious disease control: an argument for routine data collection in emerging economies. Philos Trans R Soc Lond B Biol Sci 2020; 374:20180264. [PMID: 31104601 DOI: 10.1098/rstb.2018.0264] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Livestock movements are an important mechanism of infectious disease transmission. Where these are well recorded, network analysis tools have been used to successfully identify system properties, highlight vulnerabilities to transmission, and inform targeted surveillance and control. Here we highlight the main uses of network properties in understanding livestock disease epidemiology and discuss statistical approaches to infer network characteristics from biased or fragmented datasets. We use a 'hurdle model' approach that predicts (i) the probability of movement and (ii) the number of livestock moved to generate synthetic 'complete' networks of movements between administrative wards, exploiting routinely collected government movement permit data from northern Tanzania. We demonstrate that this model captures a significant amount of the observed variation. Combining the cattle movement network with a spatial between-ward contact layer, we create a multiplex, over which we simulated the spread of 'fast' ( R0 = 3) and 'slow' ( R0 = 1.5) pathogens, and assess the effects of random versus targeted disease control interventions (vaccination and movement ban). The targeted interventions substantially outperform those randomly implemented for both fast and slow pathogens. Our findings provide motivation to encourage routine collection and centralization of movement data to construct representative networks. This article is part of the theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control'. This theme issue is linked with the earlier issue 'Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes'.
Collapse
Affiliation(s)
- G L Chaters
- 1 Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow , Glasgow G12 8QQ , UK
| | - P C D Johnson
- 1 Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow , Glasgow G12 8QQ , UK
| | - S Cleaveland
- 1 Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow , Glasgow G12 8QQ , UK
| | - J Crispell
- 2 School of Veterinary Medicine, University College Dublin , Dublin , Ireland
| | - W A de Glanville
- 1 Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow , Glasgow G12 8QQ , UK
| | - T Doherty
- 3 Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh , Easter Bush Campus, Midlothian EH25 9RG , UK
| | - L Matthews
- 1 Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow , Glasgow G12 8QQ , UK
| | - S Mohr
- 1 Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow , Glasgow G12 8QQ , UK
| | - O M Nyasebwa
- 6 Department of Veterinary Services, Ministry of Livestock and Fisheries, Nelson Mandela Road , Dar Es Salaam , Tanzania
| | - G Rossi
- 3 Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh , Easter Bush Campus, Midlothian EH25 9RG , UK
| | - L C M Salvador
- 3 Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh , Easter Bush Campus, Midlothian EH25 9RG , UK.,4 Department of Infectious Diseases, University of Georgia , Athens, GA 30602 , USA.,5 Institute of Bioinformatics, University of Georgia , Athens, GA 30602 , USA
| | - E Swai
- 6 Department of Veterinary Services, Ministry of Livestock and Fisheries, Nelson Mandela Road , Dar Es Salaam , Tanzania
| | - R R Kao
- 3 Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh , Easter Bush Campus, Midlothian EH25 9RG , UK
| |
Collapse
|
30
|
Nduva GM, Hassan AS, Nazziwa J, Graham SM, Esbjörnsson J, Sanders EJ. HIV-1 Transmission Patterns Within and Between Risk Groups in Coastal Kenya. Sci Rep 2020; 10:6775. [PMID: 32317722 PMCID: PMC7174422 DOI: 10.1038/s41598-020-63731-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/30/2020] [Indexed: 11/09/2022] Open
Abstract
HIV-1 transmission patterns within and between populations at different risk of HIV-1 acquisition in Kenya are not well understood. We investigated HIV-1 transmission networks in men who have sex with men (MSM), injecting drug users (IDU), female sex workers (FSW) and heterosexuals (HET) in coastal Kenya. We used maximum-likelihood and Bayesian phylogenetics to analyse new (N = 163) and previously published (N = 495) HIV-1 polymerase sequences collected during 2005-2019. Of the 658 sequences, 131 (20%) were from MSM, 58 (9%) IDU, 109 (17%) FSW, and 360 (55%) HET. Overall, 206 (31%) sequences formed 61 clusters. Most clusters (85%) consisted of sequences from the same risk group, suggesting frequent within-group transmission. The remaining clusters were mixed between HET/MSM (7%), HET/FSW (5%), and MSM/FSW (3%) sequences. One large IDU-exclusive cluster was found, indicating an independent sub-epidemic among this group. Phylodynamic analysis of this cluster revealed a steady increase in HIV-1 infections among IDU since the estimated origin of the cluster in 1987. Our results suggest mixing between high-risk groups and heterosexual populations and could be relevant for the development of targeted HIV-1 prevention programmes in coastal Kenya.
Collapse
Affiliation(s)
- George M Nduva
- Lund University, Lund, Sweden
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
| | - Amin S Hassan
- Lund University, Lund, Sweden
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Susan M Graham
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- University of Washington, Seattle, WA, USA
| | - Joakim Esbjörnsson
- Lund University, Lund, Sweden.
- The University of Oxford, Oxford, United Kingdom.
| | - Eduard J Sanders
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- The University of Oxford, Oxford, United Kingdom
| |
Collapse
|
31
|
Rüdiger S, Plietzsch A, Sagués F, Sokolov IM, Kurths J. Epidemics with mutating infectivity on small-world networks. Sci Rep 2020; 10:5919. [PMID: 32246023 PMCID: PMC7125191 DOI: 10.1038/s41598-020-62597-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 03/10/2020] [Indexed: 01/24/2023] Open
Abstract
Epidemics and evolution of many pathogens occur on similar timescales so that their dynamics are often entangled. Here, in a first step to study this problem theoretically, we analyze mutating pathogens spreading on simple SIR networks with grid-like connectivity. We have in mind the spatial aspect of epidemics, which often advance on transport links between hosts or groups of hosts such as cities or countries. We focus on the case of mutations that enhance an agent’s infection rate. We uncover that the small-world property, i.e., the presence of long-range connections, makes the network very vulnerable, supporting frequent supercritical mutations and bringing the network from disease extinction to full blown epidemic. For very large numbers of long-range links, however, the effect reverses and we find a reduced chance for large outbreaks. We study two cases, one with discrete number of mutational steps and one with a continuous genetic variable, and we analyze various scaling regimes. For the continuous case we derive a Fokker-Planck-like equation for the probability density and solve it for small numbers of shortcuts using the WKB approximation. Our analysis supports the claims that a potentiating mutation in the transmissibility might occur during an epidemic wave and not necessarily before its initiation.
Collapse
Affiliation(s)
- Sten Rüdiger
- Department of Physics, Humboldt-Universität zu Berlin, 12489, Berlin, Germany.
| | - Anton Plietzsch
- Department of Physics, Humboldt-Universität zu Berlin, 12489, Berlin, Germany.,Potsdam Institute for Climate Impact Research (PIK), 14473, Potsdam, Germany
| | - Francesc Sagués
- Departament de Química Física, Universitat de Barcelona, 08028, Barcelona, Spain
| | - Igor M Sokolov
- Department of Physics, Humboldt-Universität zu Berlin, 12489, Berlin, Germany.,IRIS Adlershof, Zum Großen Windkanal 6, 12489, Berlin, Germany
| | - Jürgen Kurths
- Department of Physics, Humboldt-Universität zu Berlin, 12489, Berlin, Germany.,Potsdam Institute for Climate Impact Research (PIK), 14473, Potsdam, Germany.,Saratov State University, 83, Astrakhanskaya Str., 410012, Saratov, Russia
| |
Collapse
|
32
|
Pollett S, Fauver JR, Berry IM, Melendrez M, Morrison A, Gillis LD, Johansson MA, Jarman RG, Grubaugh ND. Genomic Epidemiology as a Public Health Tool to Combat Mosquito-Borne Virus Outbreaks. J Infect Dis 2020; 221:S308-S318. [PMID: 31711190 PMCID: PMC11095994 DOI: 10.1093/infdis/jiz302] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Next-generation sequencing technologies, exponential increases in the availability of virus genomic data, and ongoing advances in phylogenomic methods have made genomic epidemiology an increasingly powerful tool for public health response to a range of mosquito-borne virus outbreaks. In this review, we offer a brief primer on the scope and methods of phylogenomic analyses that can answer key epidemiological questions during mosquito-borne virus public health emergencies. We then focus on case examples of outbreaks, including those caused by dengue, Zika, yellow fever, West Nile, and chikungunya viruses, to demonstrate the utility of genomic epidemiology to support the prevention and control of mosquito-borne virus threats. We extend these case studies with operational perspectives on how to best incorporate genomic epidemiology into structured surveillance and response programs for mosquito-borne virus control. Many tools for genomic epidemiology already exist, but so do technical and nontechnical challenges to advancing their use. Frameworks to support the rapid sharing of multidimensional data and increased cross-sector partnerships, networks, and collaborations can support advancement on all scales, from research and development to implementation by public health agencies.
Collapse
Affiliation(s)
- S. Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Department of Preventive Medicine and Biostatistics, Uniformed Services University, Bethesda, Maryland
- Marie Bashir Institute, University of Sydney, Camperdown, New South Wales, Australia
| | - J. R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | | | | | - L. D. Gillis
- Bureau of Public Health Laboratories–Miami, Florida Department of Health
| | - M. A. Johansson
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - R. G. Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - N. D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut
| |
Collapse
|
33
|
Pérez-Losada M, Arenas M, Galán JC, Bracho MA, Hillung J, García-González N, González-Candelas F. High-throughput sequencing (HTS) for the analysis of viral populations. INFECTION GENETICS AND EVOLUTION 2020; 80:104208. [PMID: 32001386 DOI: 10.1016/j.meegid.2020.104208] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/21/2020] [Accepted: 01/24/2020] [Indexed: 12/12/2022]
Abstract
The development of High-Throughput Sequencing (HTS) technologies is having a major impact on the genomic analysis of viral populations. Current HTS platforms can capture nucleic acid variation across millions of genes for both selected amplicons and full viral genomes. HTS has already facilitated the discovery of new viruses, hinted new taxonomic classifications and provided a deeper and broader understanding of their diversity, population and genetic structure. Hence, HTS has already replaced standard Sanger sequencing in basic and applied research fields, but the next step is its implementation as a routine technology for the analysis of viruses in clinical settings. The most likely application of this implementation will be the analysis of viral genomics, because the huge population sizes, high mutation rates and very fast replacement of viral populations have demonstrated the limited information obtained with Sanger technology. In this review, we describe new technologies and provide guidelines for the high-throughput sequencing and genetic and evolutionary analyses of viral populations and metaviromes, including software applications. With the development of new HTS technologies, new and refurbished molecular and bioinformatic tools are also constantly being developed to process and integrate HTS data. These allow assembling viral genomes and inferring viral population diversity and dynamics. Finally, we also present several applications of these approaches to the analysis of viral clinical samples including transmission clusters and outbreak characterization.
Collapse
Affiliation(s)
- Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, USA; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain; Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain.
| | - Juan Carlos Galán
- Microbiology Service, Hospital Ramón y Cajal, Madrid, Spain; CIBER in Epidemiology and Public Health, Spain.
| | - Mª Alma Bracho
- CIBER in Epidemiology and Public Health, Spain; Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain.
| | - Julia Hillung
- Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain; Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, Valencia, Spain.
| | - Neris García-González
- Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain; Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, Valencia, Spain.
| | - Fernando González-Candelas
- CIBER in Epidemiology and Public Health, Spain; Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain; Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, Valencia, Spain.
| |
Collapse
|
34
|
The Impact of Human Mobility on Regional and Global Efforts to Control HIV Transmission. Viruses 2020; 12:v12010067. [PMID: 31935811 PMCID: PMC7019949 DOI: 10.3390/v12010067] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/30/2019] [Accepted: 01/02/2020] [Indexed: 12/30/2022] Open
Abstract
HIV prevention and control methods are implemented on different scales to reduce the spread of the virus amongst populations. However, despite such efforts, HIV continues to persist in populations with a global incidence rate of 1.8 million in 2017 alone. The introduction of new infections into susceptible regional populations promotes the spread of HIV, indicating a crucial need to study the impact of migration and mobility on regional and global efforts to prevent HIV transmission. Here we reviewed studies that assess the impact of human mobility on HIV transmission and spread. We found an important role for both travel and migration in driving the spread of HIV across regional and national borders. Combined, our results indicate that even in the presence of control and preventive efforts, if migration and travel are occurring, public health efforts will need to remain persistent to ensure that new infections do not grow into outbreaks.
Collapse
|
35
|
Hietanen E, Susi P. Recombination Events and Conserved Nature of Receptor Binding Motifs in Coxsackievirus A9 Isolates. Viruses 2020; 12:E68. [PMID: 31935831 PMCID: PMC7019539 DOI: 10.3390/v12010068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/31/2019] [Accepted: 01/01/2020] [Indexed: 01/11/2023] Open
Abstract
Coxsackievirus A9 (CVA9) is an enterically transmitted enterovirus and one of the most pathogenic type among human enteroviruses. CVA9 isolates use a distinctive RGD (Arg-Gly-Asp) motif within VP1 capsid protein that defines its ability to bind to integrin receptor(s) for cellular entry. To investigate CVA9 evolution and pathogenicity, genetic relationships and recombination events were analyzed between 54 novel clinical isolates of CVA9, as well as 21 previously published full length CVA9 sequences from GenBank. Samples were investigated by partial sequencing of the novel VP1 and 3Dpol genes, as well as including the corresponding areas from GenBank sequences. Phylogenetic analyses were combined with clinical data in a further attempt to analyze whether sequence evolution reflects CVA9 pathogenicity in the phylogenies. Furthermore, VP1 gene was also analyzed for receptor binding sites including the RGD motif and the putative heparan sulfate (HS) site. Analysis of the 559-nucleotide-long VP1 sequences identified six clades. Although most of the strains within each clade showed geographical clustering, the grouping pattern of the isolates in the analysis of the VP1 gene was strikingly different from grouping of 3Dpol, which suggests that recombination events may have occurred in the region encoding the nonstructural proteins. Inclusion of clinical data did not provide any evidence of symptom based phylogenetic clustering of CVA9 isolates. Amino acid sequence analysis of the VP1 polypeptide demonstrated that the RGD motif was fully conserved among the isolates while the putative HS binding site was only found in one isolate. These data suggest that integrin binding is essential for virus tropism, but do not explain the symptom repertoire.
Collapse
Affiliation(s)
| | - Petri Susi
- Institute of Biomedicine, University of Turku, 20520 Turku, Finland;
| |
Collapse
|
36
|
Serdari D, Kostaki EG, Paraskevis D, Stamatakis A, Kapli P. Automated, phylogeny-based genotype delimitation of the Hepatitis Viruses HBV and HCV. PeerJ 2019; 7:e7754. [PMID: 31667012 PMCID: PMC6816385 DOI: 10.7717/peerj.7754] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/26/2019] [Indexed: 12/15/2022] Open
Abstract
Background The classification of hepatitis viruses still predominantly relies on ad hoc criteria, i.e., phenotypic traits and arbitrary genetic distance thresholds. Given the subjectivity of such practices coupled with the constant sequencing of samples and discovery of new strains, this manual approach to virus classification becomes cumbersome and impossible to generalize. Methods Using two well-studied hepatitis virus datasets, HBV and HCV, we assess if computational methods for molecular species delimitation that are typically applied to barcoding biodiversity studies can also be successfully deployed for hepatitis virus classification. For comparison, we also used ABGD, a tool that in contrast to other distance methods attempts to automatically identify the barcoding gap using pairwise genetic distances for a set of aligned input sequences. Results—Discussion We found that the mPTP species delimitation tool identified even without adapting its default parameters taxonomic clusters that either correspond to the currently acknowledged genotypes or to known subdivision of genotypes (subtypes or subgenotypes). In the cases where the delimited cluster corresponded to subtype or subgenotype, there were previous concerns that their status may be underestimated. The clusters obtained from the ABGD analysis differed depending on the parameters used. However, under certain values the results were very similar to the taxonomy and mPTP which indicates the usefulness of distance based methods in virus taxonomy under appropriate parameter settings. The overlap of predicted clusters with taxonomically acknowledged genotypes implies that virus classification can be successfully automated.
Collapse
Affiliation(s)
- Dora Serdari
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Evangelia-Georgia Kostaki
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Alexandros Stamatakis
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.,Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Paschalia Kapli
- Centre for Life's Origins and Evolution, Department of Genetics Evolution and Environment, University College London, University of London, London, United Kingdom
| |
Collapse
|
37
|
Hostager R, Ragonnet-Cronin M, Murrell B, Hedskog C, Osinusi A, Susser S, Sarrazin C, Svarovskaia E, Wertheim JO. Hepatitis C virus genotype 1 and 2 recombinant genomes and the phylogeographic history of the 2k/1b lineage. Virus Evol 2019; 5:vez041. [PMID: 31616569 PMCID: PMC6785677 DOI: 10.1093/ve/vez041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Recombination is an important driver of genetic diversity, though it is relatively uncommon in hepatitis C virus (HCV). Recent investigation of sequence data acquired from HCV clinical trials produced twenty-one full-genome recombinant viruses belonging to three putative inter-subtype forms 2b/1a, 2b/1b, and 2k/1b. The 2k/1b chimera is the only known HCV circulating recombinant form (CRF), provoking interest in its genetic structure and origin. Discovered in Russia in 1999, 2k/1b cases have since been detected throughout the former Soviet Union, Western Europe, and North America. Although 2k/1b prevalence is highest in the Caucasus mountain region (i.e., Armenia, Azerbaijan, and Georgia), the origin and migration patterns of CRF 2k/1b have remained obscure due to a paucity of available sequences. We assembled an alignment which spans the entire coding region of the HCV genome containing all available 2k/1b sequences (>500 nucleotides; n = 109) sampled in ninteen countries from public databases (102 individuals), additional newly sequenced genomic regions (from 48 of these 102 individuals), unpublished isolates with newly sequenced regions (5 additional individuals), and novel complete genomes (2 additional individuals) generated in this study. Analysis of this expanded dataset reconfirmed the monophyletic origin of 2k/1b with a recombination breakpoint at position 3,187 (95% confidence interval: 3,172–3,202; HCV GT1a reference strain H77). Phylogeography is a valuable tool used to reveal viral migration dynamics. Inference of the timed history of spread in a Bayesian framework identified Russia as the ancestral source of the CRF 2k/1b clade. Further, we found evidence for migration routes leading out of Russia to other former Soviet Republics or countries under the Soviet sphere of influence. These findings suggest an interplay between geopolitics and the historical spread of CRF 2k/1b.
Collapse
Affiliation(s)
- Reilly Hostager
- Department of Medicine, University of California, San Diego, CA, USA
| | | | - Ben Murrell
- Department of Medicine, University of California, San Diego, CA, USA
| | | | | | - Simone Susser
- Goethe-University Hospital, Medical Clinic, Frankfurt, Germany
| | - Christoph Sarrazin
- Gilead Sciences, Foster City, CA, USA.,St. Josefs-Hospital, Medical Clinic 2, Wiesbaden, Germany
| | | | - Joel O Wertheim
- Department of Medicine, University of California, San Diego, CA, USA
| |
Collapse
|
38
|
Dellicour S, Troupin C, Jahanbakhsh F, Salama A, Massoudi S, Moghaddam MK, Baele G, Lemey P, Gholami A, Bourhy H. Using phylogeographic approaches to analyse the dispersal history, velocity and direction of viral lineages - Application to rabies virus spread in Iran. Mol Ecol 2019; 28:4335-4350. [PMID: 31535448 DOI: 10.1111/mec.15222] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 08/04/2019] [Accepted: 08/05/2019] [Indexed: 12/26/2022]
Abstract
Recent years have seen the extensive use of phylogeographic approaches to unveil the dispersal history of virus epidemics. Spatially explicit reconstructions of viral spread represent valuable sources of lineage movement data that can be exploited to investigate the impact of underlying environmental layers on the dispersal of pathogens. Here, we performed phylogeographic inference and applied different post hoc approaches to analyse a new and comprehensive data set of viral genomes to elucidate the dispersal history and dynamics of rabies virus (RABV) in Iran, which have remained largely unknown. We first analysed the association between environmental factors and variations in dispersal velocity among lineages. Second, we present, test and apply a new approach to study the link between environmental conditions and the dispersal direction of lineages. The statistical performance (power of detection, false-positive rate) of this new method was assessed using simulations. We performed phylogeographic analyses of RABV genomes, allowing us to describe the large diversity of RABV in Iran and to confirm the cocirculation of several clades in the country. Overall, we estimate a relatively high lineage dispersal velocity, similar to previous estimates for dog rabies virus spread in northern Africa. Finally, we highlight a tendency for RABV lineages to spread in accessible areas associated with high human population density. Our analytical workflow illustrates how phylogeographic approaches can be used to investigate the impact of environmental factors on several aspects of viral dispersal dynamics.
Collapse
Affiliation(s)
- Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium.,Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
| | - Cécile Troupin
- Unit Lyssavirus Epidemiology and Neuropathology, WHO Collaborating Centre for Reference and Research on Rabies, Institut Pasteur, Paris, France
| | - Fatemeh Jahanbakhsh
- WHO Collaborating Centre for Reference and Research on Rabies, Pasteur Institute of Iran, Tehran, Iran
| | - Akram Salama
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
| | - Siamak Massoudi
- Department of Environment, Wildlife Diseases Group, Wildlife Bureau, Tehran, Iran
| | - Madjid K Moghaddam
- Department of Environment, Wildlife Diseases Group, Wildlife Bureau, Tehran, Iran
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Alireza Gholami
- WHO Collaborating Centre for Reference and Research on Rabies, Pasteur Institute of Iran, Tehran, Iran
| | - Hervé Bourhy
- Unit Lyssavirus Epidemiology and Neuropathology, WHO Collaborating Centre for Reference and Research on Rabies, Institut Pasteur, Paris, France
| |
Collapse
|
39
|
Abstract
Pandemic influenza remains the single greatest threat to global heath security. Efforts to increase our preparedness, by improving predictions of viral emergence, spread and disease severity, by targeting reduced transmission and improved vaccination and by mitigating health impacts in low- and middle-income countries, should receive renewed urgency.
Collapse
|
40
|
Galbreath KE, Hoberg EP, Cook JA, Armién B, Bell KC, Campbell ML, Dunnum JL, Dursahinhan AT, Eckerlin RP, Gardner SL, Greiman SE, Henttonen H, Jiménez FA, Koehler AVA, Nyamsuren B, Tkach VV, Torres-Pérez F, Tsvetkova A, Hope AG. Building an integrated infrastructure for exploring biodiversity: field collections and archives of mammals and parasites. J Mammal 2019; 100:382-393. [PMID: 31043762 PMCID: PMC6479512 DOI: 10.1093/jmammal/gyz048] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 02/22/2019] [Indexed: 02/07/2023] Open
Abstract
Museum specimens play an increasingly important role in predicting the outcomes and revealing the consequences of anthropogenically driven disruption of the biosphere. As ecological communities respond to ongoing environmental change, host-parasite interactions are also altered. This shifting landscape of host-parasite associations creates opportunities for colonization of different hosts and emergence of new pathogens, with implications for wildlife conservation and management, public health, and other societal concerns. Integrated archives that document and preserve mammal specimens along with their communities of associated parasites and ancillary data provide a powerful resource for investigating, anticipating, and mitigating the epidemiological, ecological, and evolutionary impacts of environmental perturbation. Mammalogists who collect and archive mammal specimens have a unique opportunity to expand the scope and impact of their field work by collecting the parasites that are associated with their study organisms. We encourage mammalogists to embrace an integrated and holistic sampling paradigm and advocate for this to become standard practice for museum-based collecting. To this end, we provide a detailed, field-tested protocol to give mammalogists the tools to collect and preserve host and parasite materials that are of high quality and suitable for a range of potential downstream analyses (e.g., genetic, morphological). Finally, we also encourage increased global cooperation across taxonomic disciplines to build an integrated series of baselines and snapshots of the changing biosphere. Los especímenes de museo desempeñan un papel cada vez más importante tanto en la descripción de los resultados de la alteración antropogénica de la biosfera como en la predicción de sus consecuencias. Dado que las comunidades ecológicas responden al cambio ambiental, también se alteran las interacciones hospedador-parásito. Este panorama cambiante de asociaciones hospedador-parásito crea oportunidades para la colonización de diferentes hospedadores y para la aparición de nuevos patógenos, con implicancias en la conservación y manejo de la vida silvestre, la salud pública y otras preocupaciones de importancia para la sociedad. Archivos integrados que documentan y preservan especímenes de mamíferos junto con sus comunidades de parásitos y datos asociados, proporcionan un fuerte recurso para investigar, anticipar y mitigar los impactos epidemiológicos, ecológicos y evolutivos de las perturbaciones ambientales. Los mastozoólogos que recolectan y archivan muestras de mamíferos, tienen una oportunidad única de ampliar el alcance e impacto de su trabajo de campo mediante la recolección de los parásitos que están asociados con los organismos que estudian. Alentamos a los mastozoólogos a adoptar un paradigma de muestreo integrado y holístico y abogamos para que esto se convierta en una práctica estándarizada de la obtención de muestras para museos. Con este objetivo, proporcionamos un protocolo detallado y probado en el campo para brindar a los mastozoólogos las herramientas para recolectar y preservar materiales de parásitos y hospedadores de alta calidad y adecuados para una gran variedad de análisis subsecuentes (e.g., genéticos, morfológicos, etc.). Finalmente, también abogamos por una mayor cooperación global entre las diversas disciplinas taxonómicas para construir una serie integrada de líneas de base y registros actuales de nuestra cambiante biosfera.
Collapse
Affiliation(s)
- Kurt E Galbreath
- Department of Biology, Northern Michigan University, Marquette, MI, USA
| | - Eric P Hoberg
- Biology Department and Museum of Southwestern Biology, University of New Mexico, CERIA Building, Albuquerque, NM, USA
| | - Joseph A Cook
- Biology Department and Museum of Southwestern Biology, University of New Mexico, CERIA Building, Albuquerque, NM, USA
| | - Blas Armién
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panama
| | - Kayce C Bell
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Mariel L Campbell
- Biology Department and Museum of Southwestern Biology, University of New Mexico, CERIA Building, Albuquerque, NM, USA
| | - Jonathan L Dunnum
- Biology Department and Museum of Southwestern Biology, University of New Mexico, CERIA Building, Albuquerque, NM, USA
| | - Altangerel T Dursahinhan
- Harold W. Manter Laboratory of Parasitology, Division of Parasitology, University of Nebraska State Museum, W Nebraska Hall University of Nebraska–Lincoln, Lincoln, NE, USA
| | - Ralph P Eckerlin
- Mathematics, Science and Engineering Division, Northern Virginia Community College, Annandale, VA, USA
| | - Scott L Gardner
- Harold W. Manter Laboratory of Parasitology, Division of Parasitology, University of Nebraska State Museum, W Nebraska Hall University of Nebraska–Lincoln, Lincoln, NE, USA
| | - Stephen E Greiman
- Biology Department, Georgia Southern University, Statesboro, GA, USA
| | | | - F Agustín Jiménez
- Department of Zoology, Southern Illinois University, Carbondale, IL, USA
| | - Anson V A Koehler
- Department of Veterinary Biosciences, The University of Melbourne, Cnr Flemington Road and Park Drive, Parkville, Victoria, Australia
| | | | - Vasyl V Tkach
- Biology Department, University of North Dakota, Grand Forks, ND, USA
| | - Fernando Torres-Pérez
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Albina Tsvetkova
- Institute of Ecology and Evolution A.N. Severtsov RAS, Saratov Branch, Saratov, Russia
| | - Andrew G Hope
- Division of Biology, Kansas State University, Manhattan, KS, USA
| |
Collapse
|
41
|
Laenen L, Vergote V, Vanmechelen B, Tersago K, Baele G, Lemey P, Leirs H, Dellicour S, Vrancken B, Maes P. Identifying the patterns and drivers of Puumala hantavirus enzootic dynamics using reservoir sampling. Virus Evol 2019; 5:vez009. [PMID: 31024739 PMCID: PMC6476162 DOI: 10.1093/ve/vez009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Hantaviruses are zoonotic hemorrhagic fever viruses for which prevention of human spillover remains the first priority in disease management. Tailored intervention measures require an understanding of the drivers of enzootic dynamics, commonly inferred from distorted human incidence data. Here, we use longitudinal sampling of approximately three decades of Puumala orthohantavirus (PUUV) evolution in isolated reservoir populations to estimate PUUV evolutionary rates, and apply these to study the impact of environmental factors on viral spread. We find that PUUV accumulates genetic changes at a rate of ∼10−4 substitutions per site per year and that land cover type defines the dispersal dynamics of PUUV, with forests facilitating and croplands impeding virus spread. By providing reliable short-term PUUV evolutionary rate estimates, this work facilitates the evaluation of spatial risk heterogeneity starting from timed phylogeographic reconstructions based on virus sampling in its animal reservoir, thereby side-stepping the need for difficult-to-collect human disease incidence data.
Collapse
Affiliation(s)
- Lies Laenen
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Division of Clinical and Epidemiological Virology, Herestraat 49, 3000 Leuven, Belgium
| | - Valentijn Vergote
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Division of Clinical and Epidemiological Virology, Herestraat 49, 3000 Leuven, Belgium
| | - Bert Vanmechelen
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Division of Clinical and Epidemiological Virology, Herestraat 49, 3000 Leuven, Belgium
| | - Katrien Tersago
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium.,Epidemiology of Infectious Diseases, Belgian Institute of Health, Sciensano, Brussels, Belgium
| | - Guy Baele
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Division of Clinical and Epidemiological Virology, Herestraat 49, 3000 Leuven, Belgium
| | - Philippe Lemey
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Division of Clinical and Epidemiological Virology, Herestraat 49, 3000 Leuven, Belgium
| | - Herwig Leirs
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Simon Dellicour
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Division of Clinical and Epidemiological Virology, Herestraat 49, 3000 Leuven, Belgium.,Spatial Epidemiology Lab (spELL), Université Libre de Bruxelles, Bruxelles, Belgium
| | - Bram Vrancken
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Division of Clinical and Epidemiological Virology, Herestraat 49, 3000 Leuven, Belgium
| | - Piet Maes
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Division of Clinical and Epidemiological Virology, Herestraat 49, 3000 Leuven, Belgium
| |
Collapse
|
42
|
Kraemer MUG, Golding N, Bisanzio D, Bhatt S, Pigott DM, Ray SE, Brady OJ, Brownstein JS, Faria NR, Cummings DAT, Pybus OG, Smith DL, Tatem AJ, Hay SI, Reiner RC. Utilizing general human movement models to predict the spread of emerging infectious diseases in resource poor settings. Sci Rep 2019; 9:5151. [PMID: 30914669 PMCID: PMC6435716 DOI: 10.1038/s41598-019-41192-3] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 03/03/2019] [Indexed: 12/03/2022] Open
Abstract
Human mobility is an important driver of geographic spread of infectious pathogens. Detailed information about human movements during outbreaks are, however, difficult to obtain and may not be available during future epidemics. The Ebola virus disease (EVD) outbreak in West Africa between 2014–16 demonstrated how quickly pathogens can spread to large urban centers following one cross-species transmission event. Here we describe a flexible transmission model to test the utility of generalised human movement models in estimating EVD cases and spatial spread over the course of the outbreak. A transmission model that includes a general model of human mobility significantly improves prediction of EVD’s incidence compared to models without this component. Human movement plays an important role not only to ignite the epidemic in locations previously disease free, but over the course of the entire epidemic. We also demonstrate important differences between countries in population mixing and the improved prediction attributable to movement metrics. Given their relative rareness, locally derived mobility data are unlikely to exist in advance of future epidemics or pandemics. Our findings show that transmission patterns derived from general human movement models can improve forecasts of spatio-temporal transmission patterns in places where local mobility data is unavailable.
Collapse
Affiliation(s)
- M U G Kraemer
- Department of Zoology, University of Oxford, Oxford, UK. .,Harvard Medical School, Boston, MA, USA. .,Computational Epidemiology Lab, Boston Children's Hospital, Boston, MA, USA.
| | - N Golding
- Department of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - D Bisanzio
- RTI International, Washington, D.C., USA.,Epidemiology and Public Health Division, School of Medicine, University of Nottingham, Nottingham, UK
| | - S Bhatt
- Imperial College London, London, United Kingdom
| | - D M Pigott
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA
| | - S E Ray
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA
| | - O J Brady
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - J S Brownstein
- Harvard Medical School, Boston, MA, USA.,Computational Epidemiology Lab, Boston Children's Hospital, Boston, MA, USA
| | - N R Faria
- Department of Zoology, University of Oxford, Oxford, UK
| | - D A T Cummings
- Department of Biology, University of Florida, Gainesville, FL, USA.,Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - O G Pybus
- Department of Zoology, University of Oxford, Oxford, UK
| | - D L Smith
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA.,Sanaria Institute for Global Health and Tropical Medicine, Rockville, USA
| | - A J Tatem
- WorldPop, Department of Geography and Environmental Sciences, University of Southampton, Southampton, UK.,Flowminder Foundation, Stockholm, Sweden
| | - S I Hay
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA.
| | - R C Reiner
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA.
| |
Collapse
|
43
|
Pérez AB, Vrancken B, Chueca N, Aguilera A, Reina G, García-del Toro M, Vera F, Von Wichman MA, Arenas JI, Téllez F, Pineda JA, Omar M, Bernal E, Rivero-Juárez A, Fernández-Fuertes E, de la Iglesia A, Pascasio JM, Lemey P, Garcia F, Cuypers L. Increasing importance of European lineages in seeding the hepatitis C virus subtype 1a epidemic in Spain. Euro Surveill 2019; 24:1800227. [PMID: 30862327 PMCID: PMC6402173 DOI: 10.2807/1560-7917.es.2019.24.9.1800227] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
BackgroundReducing the burden of the hepatitis C virus (HCV) requires large-scale deployment of intervention programmes, which can be informed by the dynamic pattern of HCV spread. In Spain, ongoing transmission of HCV is mostly fuelled by people who inject drugs (PWID) infected with subtype 1a (HCV1a).AimOur aim was to map how infections spread within and between populations, which could help formulate more effective intervention programmes to halt the HCV1a epidemic in Spain.MethodsEpidemiological links between HCV1a viruses from a convenience sample of 283 patients in Spain, mostly PWID, collected between 2014 and 2016, and 1,317, 1,291 and 1,009 samples collected abroad between 1989 and 2016 were reconstructed using sequences covering the NS3, NS5A and NS5B genes. To efficiently do so, fast maximum likelihood-based tree estimation was coupled to a flexible Bayesian discrete phylogeographic inference method.ResultsThe transmission network structure of the Spanish HCV1a epidemic was shaped by continuous seeding of HCV1a into Spain, almost exclusively from North America and European countries. The latter became increasingly relevant and have dominated in recent times. Export from Spain to other countries in Europe was also strongly supported, although Spain was a net sink for European HCV1a lineages. Spatial reconstructions showed that the epidemic in Spain is diffuse, without large, dominant within-country networks.ConclusionTo boost the effectiveness of local intervention efforts, concerted supra-national strategies to control HCV1a transmission are needed, with a strong focus on the most important drivers of ongoing transmission, i.e. PWID and other high-risk populations.
Collapse
Affiliation(s)
- Ana Belen Pérez
- Department of Microbiology, Institute of Bio Sanitary Research (IBIS), AIDS Research Network, University Hospital of Granada, Granada, Spain,These authors contributed equally to the article
| | - Bram Vrancken
- These authors contributed equally to the article,KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Evolutionary and Computational Virology, Leuven, Belgium
| | - Natalia Chueca
- Department of Microbiology, Institute of Bio Sanitary Research (IBIS), AIDS Research Network, University Hospital of Granada, Granada, Spain
| | - Antonio Aguilera
- Department of Microbiology, University Hospital of Santiago, Santiago de Compostela, Spain
| | - Gabriel Reina
- Department of Microbiology, University Hospital of Navarra, Institute for Health Research (IdisNA), Pamplona, Spain
| | | | - Francisco Vera
- Unit of Infectious Diseases, Internal Medicine, General Hospital of Rosell, Cartagena, Murcia, Spain
| | | | - Juan Ignacio Arenas
- Unit of Infectious Diseases, Hospital Universitario de San Sebastian, San Sebastian, Spain
| | - Francisco Téllez
- Unit of Infectious Diseases and Microbiology, University Hospital of Puerto Real, Cádiz, Spain
| | - Juan A Pineda
- Unit of Infectious Diseases, University Hospital of Valme, Sevilla, Spain (J.A. Pineda)
| | | | - Enrique Bernal
- Unit of Infectious Diseases, General University Hospital, Murcia, Spain
| | - Antonio Rivero-Juárez
- Unit of Infectious Diseases, University Hospital Reina Sofía of Córdoba, Maimonides Institute of Biomedical Research of Córdoba, University of Córdoba, Córdoba, Spain
| | | | | | - Juan Manuel Pascasio
- Clinical Management Unit of Digestive Diseases, University Hospital of Virgen del Rocío, Sevilla, Spain
| | - Philippe Lemey
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Evolutionary and Computational Virology, Leuven, Belgium
| | - Féderico Garcia
- Department of Microbiology, Institute of Bio Sanitary Research (IBIS), AIDS Research Network, University Hospital of Granada, Granada, Spain,These authors contributed equally to the article
| | - Lize Cuypers
- These authors contributed equally to the article,KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| |
Collapse
|
44
|
Ogden KM, Tan Y, Akopov A, Stewart LS, McHenry R, Fonnesbeck CJ, Piya B, Carter MH, Fedorova NB, Halpin RA, Shilts MH, Edwards KM, Payne DC, Esona MD, Mijatovic-Rustempasic S, Chappell JD, Patton JT, Halasa NB, Das SR. Multiple Introductions and Antigenic Mismatch with Vaccines May Contribute to Increased Predominance of G12P[8] Rotaviruses in the United States. J Virol 2019; 93:e01476-18. [PMID: 30333170 PMCID: PMC6288334 DOI: 10.1128/jvi.01476-18] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/09/2018] [Indexed: 01/19/2023] Open
Abstract
Rotavirus is the leading global cause of diarrheal mortality for unvaccinated children under 5 years of age. The outer capsid of rotavirus virions consists of VP7 and VP4 proteins, which determine viral G and P types, respectively, and are primary targets of neutralizing antibodies. Successful vaccination depends upon generating broadly protective immune responses following exposure to rotaviruses presenting a limited number of G- and P-type antigens. Vaccine introduction resulted in decreased rotavirus disease burden but also coincided with the emergence of uncommon G and P genotypes, including G12. To gain insight into the recent predominance of G12P[8] rotaviruses in the United States, we evaluated 142 complete rotavirus genome sequences and metadata from 151 clinical specimens collected in Nashville, TN, from 2011 to 2013 through the New Vaccine Surveillance Network. Circulating G12P[8] strains were found to share many segments with other locally circulating strains but to have distinct constellations. Phylogenetic analyses of G12 sequences and their geographic sources provided evidence for multiple separate introductions of G12 segments into Nashville, TN. Antigenic epitopes of VP7 proteins of G12P[8] strains circulating in Nashville, TN, differ markedly from those of vaccine strains. Fully vaccinated children were found to be infected with G12P[8] strains more frequently than with other rotavirus genotypes. Multiple introductions and significant antigenic mismatch may in part explain the recent predominance of G12P[8] strains in the United States and emphasize the need for continued monitoring of rotavirus vaccine efficacy against emerging rotavirus genotypes.IMPORTANCE Rotavirus is an important cause of childhood diarrheal disease worldwide. Two immunodominant proteins of rotavirus, VP7 and VP4, determine G and P genotypes, respectively. Recently, G12P[8] rotaviruses have become increasingly predominant. By analyzing rotavirus genome sequences from stool specimens obtained in Nashville, TN, from 2011 to 2013 and globally circulating rotaviruses, we found evidence of multiple introductions of G12 genes into the area. Based on sequence polymorphisms, VP7 proteins of these viruses are predicted to present themselves to the immune system very differently than those of vaccine strains. Many of the sick children with G12P[8] rotavirus in their diarrheal stools also were fully vaccinated. Our findings emphasize the need for continued monitoring of circulating rotaviruses and the effectiveness of the vaccines against strains with emerging G and P genotypes.
Collapse
Affiliation(s)
- Kristen M Ogden
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Yi Tan
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- J. Craig Venter Institute, Rockville, Maryland, USA
| | - Asmik Akopov
- J. Craig Venter Institute, Rockville, Maryland, USA
| | - Laura S Stewart
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Rendie McHenry
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - Bhinnata Piya
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Maximilian H Carter
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | | | - Meghan H Shilts
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kathryn M Edwards
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Daniel C Payne
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Mathew D Esona
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - James D Chappell
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - John T Patton
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Natasha B Halasa
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Suman R Das
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- J. Craig Venter Institute, Rockville, Maryland, USA
| |
Collapse
|
45
|
Abstract
RNA viruses are diverse, abundant, and rapidly evolving. Genetic data have been generated from virus populations since the late 1970s and used to understand their evolution, emergence, and spread, culminating in the generation and analysis of many thousands of viral genome sequences. Despite this wealth of data, evolutionary genetics has played a surprisingly small role in our understanding of virus evolution. Instead, studies of RNA virus evolution have been dominated by two very different perspectives, the experimental and the comparative, that have largely been conducted independently and sometimes antagonistically. Here, we review the insights that these two approaches have provided over the last 40 years. We show that experimental approaches using in vitro and in vivo laboratory models are largely focused on short-term intrahost evolutionary mechanisms, and may not always be relevant to natural systems. In contrast, the comparative approach relies on the phylogenetic analysis of natural virus populations, usually considering data collected over multiple cycles of virus-host transmission, but is divorced from the causative evolutionary processes. To truly understand RNA virus evolution it is necessary to meld experimental and comparative approaches within a single evolutionary genetic framework, and to link viral evolution at the intrahost scale with that which occurs over both epidemiological and geological timescales. We suggest that the impetus for this new synthesis may come from methodological advances in next-generation sequencing and metagenomics.
Collapse
Affiliation(s)
- Jemma L Geoghegan
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, New South Wales 2006, Australia
- Charles Perkins Centre, The University of Sydney, New South Wales 2006, Australia
- School of Life and Environmental Sciences, The University of Sydney, New South Wales 2006, Australia
- Sydney Medical School, The University of Sydney, New South Wales 2006, Australia
| |
Collapse
|
46
|
Abstract
A growing number of infectious pathogens are spreading among geographic regions. Some pathogens that were previously not considered to pose a general threat to human health have emerged at regional and global scales, such as Zika and Ebola Virus Disease. Other pathogens, such as yellow fever virus, were previously thought to be under control but have recently re-emerged, causing new challenges to public health organisations. A wide array of new modelling techniques, aided by increased computing capabilities, novel diagnostic tools, and the increased speed and availability of genomic sequencing allow researchers to identify new pathogens more rapidly, assess the likelihood of geographic spread, and quantify the speed of human-to-human transmission. Despite some initial successes in predicting the spread of acute viral infections, the practicalities and sustainability of such approaches will need to be evaluated in the context of public health responses.
Collapse
|
47
|
Cuypers L, Libin PJK, Simmonds P, Nowé A, Muñoz-Jordán J, Alcantara LCJ, Vandamme AM, Santiago GA, Theys K. Time to Harmonize Dengue Nomenclature and Classification. Viruses 2018; 10:E569. [PMID: 30340326 PMCID: PMC6213058 DOI: 10.3390/v10100569] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/05/2018] [Accepted: 10/15/2018] [Indexed: 12/22/2022] Open
Abstract
Dengue virus (DENV) is estimated to cause 390 million infections per year worldwide. A quarter of these infections manifest clinically and are associated with a morbidity and mortality that put a significant burden on the affected regions. Reports of increased frequency, intensity, and extended geographical range of outbreaks highlight the virus's ongoing global spread. Persistent transmission in endemic areas and the emergence in territories formerly devoid of transmission have shaped DENV's current genetic diversity and divergence. This genetic layout is hierarchically organized in serotypes, genotypes, and sub-genotypic clades. While serotypes are well defined, the genotype nomenclature and classification system lack consistency, which complicates a broader analysis of their clinical and epidemiological characteristics. We identify five key challenges: (1) Currently, there is no formal definition of a DENV genotype; (2) Two different nomenclature systems are used in parallel, which causes significant confusion; (3) A standardized classification procedure is lacking so far; (4) No formal definition of sub-genotypic clades is in place; (5) There is no consensus on how to report antigenic diversity. Therefore, we believe that the time is right to re-evaluate DENV genetic diversity in an essential effort to provide harmonization across DENV studies.
Collapse
Affiliation(s)
- Lize Cuypers
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium.
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, UK.
| | - Pieter J K Libin
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium.
- Artificial Intelligence Lab, Department of Computer Science, Vrije Universiteit Brussel, 1050 Brussels, Belgium.
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, UK.
| | - Ann Nowé
- Artificial Intelligence Lab, Department of Computer Science, Vrije Universiteit Brussel, 1050 Brussels, Belgium.
| | - Jorge Muñoz-Jordán
- Division of Vector-Borne Diseases, Dengue Branch, Centers for Disease Control and Prevention, San Juan, PR 00920, USA.
| | | | - Anne-Mieke Vandamme
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium.
- Global Health and Tropical Medicine, Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, 1349-008 Lisbon, Portugal.
| | - Gilberto A Santiago
- Division of Vector-Borne Diseases, Dengue Branch, Centers for Disease Control and Prevention, San Juan, PR 00920, USA.
| | - Kristof Theys
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium.
| |
Collapse
|
48
|
Kobayashi N. Impact of Emerging, Re-Emerging and Zoonotic Viral Infectious Diseases, in a Virologist's Perspective. Open Virol J 2018; 12:131-133. [PMID: 30288201 PMCID: PMC6142664 DOI: 10.2174/1874357901812010131] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 03/14/2018] [Accepted: 05/16/2018] [Indexed: 11/22/2022] Open
|
49
|
Dellicour S, Vrancken B, Trovão NS, Fargette D, Lemey P. On the importance of negative controls in viral landscape phylogeography. Virus Evol 2018; 4:vey023. [PMID: 30151241 PMCID: PMC6101606 DOI: 10.1093/ve/vey023] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Phylogeographic reconstructions are becoming an established procedure to evaluate the factors that could impact virus spread. While a discrete phylogeographic approach can be used to test predictors of transition rates among discrete locations, alternative continuous phylogeographic reconstructions can also be exploited to investigate the impact of underlying environmental layers on the dispersal velocity of a virus. The two approaches are complementary tools for studying pathogens' spread, but in both cases, care must be taken to avoid misinterpretations. Here, we analyse rice yellow mottle virus (RYMV) sequence data from West and East Africa to illustrate how both approaches can be used to study the impact of environmental factors on the virus’ dispersal frequency and velocity. While it was previously reported that host connectivity was a major determinant of RYMV spread, we show that this was a false positive result due to the lack of appropriate negative controls. We also discuss and compare the phylodynamic tools currently available for investigating the impact of environmental factors on virus spread.
Collapse
Affiliation(s)
- Simon Dellicour
- Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium.,Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP160/12 50, av. FD Roosevelt, 1050 Bruxelles, Belgium
| | - Bram Vrancken
- Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Nídia S Trovão
- Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Denis Fargette
- Institut de Recherche pour le Développement (IRD), UMR IPME (IRD, CIRAD, Université de Montpellier), BP 64051 34394 Montpellier cedex 5, France
| | - Philippe Lemey
- Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
| |
Collapse
|
50
|
Dellicour S, Baele G, Dudas G, Faria NR, Pybus OG, Suchard MA, Rambaut A, Lemey P. Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak. Nat Commun 2018; 9:2222. [PMID: 29884821 PMCID: PMC5993714 DOI: 10.1038/s41467-018-03763-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/12/2018] [Indexed: 01/25/2023] Open
Abstract
Genetic analyses have provided important insights into Ebola virus spread during the recent West African outbreak, but their implications for specific intervention scenarios remain unclear. Here, we address this issue using a collection of phylodynamic approaches. We show that long-distance dispersal events were not crucial for epidemic expansion and that preventing viral lineage movement to any given administrative area would, in most cases, have had little impact. However, major urban areas were critical in attracting and disseminating the virus: preventing viral lineage movement to all three capitals simultaneously would have contained epidemic size to one-third. We also show that announcements of border closures were followed by a significant but transient effect on international virus dispersal. By quantifying the hypothetical impact of different intervention strategies, as well as the impact of barriers on dispersal frequency, our study illustrates how phylodynamic analyses can help to address specific epidemiological and outbreak control questions. During the last Ebola virus outbreak in West Africa, a large amount of viral genomic data was obtained. Here, Dellicour et al. use phylodynamic approaches to assess effect of intervention strategies such as border closures.
Collapse
Affiliation(s)
- Simon Dellicour
- Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Herestraat 49, 3000, Leuven, Belgium.
| | - Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Gytis Dudas
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, 98109, Seattle, WA, USA
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, United Kingdom
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, United Kingdom
| | - Marc A Suchard
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA, 90095, USA.,Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, 90095, USA.,Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, 90095, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, Edinburgh, EH9 3FL, UK.,Fogarty International Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Herestraat 49, 3000, Leuven, Belgium
| |
Collapse
|