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Athamneh RY, Abudalo R, Sallam M, Alqudah A, Alquran H, Amawi KF, Abu-Harirah HA. Sub-genotypes of hepatitis C virus in the Middle East and North Africa: Patterns of distribution and temporal changes. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 109:105412. [PMID: 36791585 DOI: 10.1016/j.meegid.2023.105412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/04/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023]
Abstract
Infection with the hepatitis C virus (HCV) remains a considerable public health concern in the Middle East and North Africa (MENA). The objectives of this study were to analyze the HCV genotype (GT) and sub-genotype (SGT) distribution in the MENA region and to assess the temporal change in the number of sequences within the MENA region. All HCV molecular sequences collected in the MENA region had been retrieved from GenBank as of 1 August 2022. The number of HCV sequences retrieved was 6740 representing sequences from a total of 17 MENA countries with a majority from Iran (n = 1969, 29.2%), Egypt (n = 1591, 23.6%), Tunisia (n = 1305, 19.4%) and Saudi Arabia (n = 1085, 16.1%). The determination of GT/SGT was based on the NCBI genotyping and Blast tool. Genotype 1 (GT1) dominated infections in the MENA (n = 2777, 41.2%), followed by GT4 (n = 2566, 39.0%). Additionally, SGT4a (1515/6393, 23.7%) was the most common SGT in the MENA, and SGT4a was dominant in Egypt and Saudi Arabia, followed by SGT1b (n = 1308, 20.5%), which was dominant in Morocco and Tunisia, while SGT1a (n = 1275, 19.9%) was common in Iran, Iraq and Palestine. Furthermore, significant temporal increase in the number of HCV MENA sequences was observed. On the SGT level, specific patterns of HCV genetic diversity were seen in the MENA region, with the most common SGT being 4a, in addition to increasing the availability of HCV sequences in the MENA region.
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Affiliation(s)
- Rabaa Y Athamneh
- Department of Medical Laboratories Sciences, Faculty of Allied Medical Sciences, Zarqa University, Zarqa, Jordan.
| | - Rawan Abudalo
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmaceutical Sciences, The Hashemite University, Zarqa, Jordan
| | - Malik Sallam
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman, Jordan; Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman, Jordan
| | - Abdelrahim Alqudah
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmaceutical Sciences, The Hashemite University, Zarqa, Jordan
| | - Hasan Alquran
- Department of Medical Laboratories Sciences, Faculty of Allied Medical Sciences, Zarqa University, Zarqa, Jordan
| | - Kawther Faisal Amawi
- Department of Medical Laboratories Sciences, Faculty of Allied Medical Sciences, Zarqa University, Zarqa, Jordan
| | - Hashem A Abu-Harirah
- Department of Medical Laboratories Sciences, Faculty of Allied Medical Sciences, Zarqa University, Zarqa, Jordan
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Lopez Luis BA, Rodríguez-Díaz R, Angulo-Medina L, Soto-Ramírez LE. The Emergence of Hepatitis C Virus Genotype 4d Among Human Immunodeficiency Virus-Infected Patients in Mexico City: A Molecular Epidemiological Study. Sex Transm Dis 2022; 49:e90-e94. [PMID: 35001015 DOI: 10.1097/olq.0000000000001596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
ABSTRACT The recent detection of hepatitis C virus genotype 4 infection in human immunodeficiency virus-infected patients prompted performing molecular characterization of these isolates. All the Mexican isolates belonged to a subcluster within the 4d group and shared a common ancestor with a French isolate. The estimated timing of introduction in Mexico City was as recent as December 2015.
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Affiliation(s)
- Bruno Ali Lopez Luis
- From the Laboratory of Molecular Virology, Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Avenida Vasco de Quiroga No. 15, Colonia Belisario Domínguez Sección XVI, Delegación Tlalpan, Mexico City, Mexico
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3
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Avila-Rios S, García-Morales C, Reyes-Terán G, González-Rodríguez A, Matías-Florentino M, Mehta SR, Chaillon A. Phylodynamics of HIV in the Mexico City Metropolitan Region. J Virol 2022; 96:e0070822. [PMID: 35762759 PMCID: PMC9327710 DOI: 10.1128/jvi.00708-22] [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: 05/04/2022] [Accepted: 06/06/2022] [Indexed: 12/30/2022] Open
Abstract
Evolutionary analyses of viral sequences can provide insights into transmission dynamics, which in turn can optimize prevention interventions. Here, we characterized the dynamics of HIV transmission within the Mexico City metropolitan area. HIV pol sequences from persons recently diagnosed at the largest HIV clinic in Mexico City (between 2016 and 2021) were annotated with demographic/geographic metadata. A multistep phylogenetic approach was applied to identify putative transmission clades. A data set of publicly available sequences was used to assess international introductions. Clades were analyzed with a discrete phylogeographic model to evaluate the timing and intensity of HIV introductions and transmission dynamics among municipalities in the region. A total of 6,802 sequences across 96 municipalities (5,192 from Mexico City and 1,610 from the neighboring State of Mexico) were included (93.6% cisgender men, 5.0% cisgender women, and 1.3% transgender women); 3,971 of these sequences formed 1,206 clusters, involving 78 municipalities, including 89 clusters of ≥10 sequences. Discrete phylogeographic analysis revealed (i) 1,032 viral introductions into the region, over one-half of which were from the United States, and (ii) 354 migration events between municipalities with high support (adjusted Bayes factor of ≥3). The most frequent viral migrations occurred between northern municipalities within Mexico City, i.e., Cuauhtémoc to Iztapalapa (5.2% of events), Iztapalapa to Gustavo A. Madero (5.4%), and Gustavo A. Madero to Cuauhtémoc (6.5%). Our analysis illustrates the complexity of HIV transmission within the Mexico City metropolitan area but also identifies a spatially active transmission area involving a few municipalities in the north of the city, where targeted interventions could have a more pronounced effect on the entire regional epidemic. IMPORTANCE Phylogeographic investigation of the Mexico City HIV epidemic illustrates the complexity of HIV transmission in the region. An active transmission area involving a few municipalities in the north of the city, with transmission links throughout the region, is identified and could be a location where targeted interventions could have a more pronounced effect on the entire regional epidemic, compared with those dispersed in other manners.
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Affiliation(s)
- Santiago Avila-Rios
- Center for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Claudia García-Morales
- Center for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Gustavo Reyes-Terán
- Coordinating Commission of the National Institutes of Health and High Specialty Hospitals, Ministry of Health, Mexico City, Mexico
| | | | | | - Sanjay R. Mehta
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, San Diego, California, USA
- Veterans Affairs Health System, San Diego, California, USA
| | - Antoine Chaillon
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, San Diego, California, USA
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4
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Almosa FAM, Alnasser AHA, Al-Tawfiq JA. Distribution of hepatitis C virus (HCV) genotypes in a Saudi Arabian hospital during the 2015-2020 period. LE INFEZIONI IN MEDICINA 2021; 29:450-455. [PMID: 35146350 PMCID: PMC8805486 DOI: 10.53854/liim-2903-16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 07/15/2021] [Indexed: 06/14/2023]
Abstract
Hepatitis C virus (HCV) is the leading cause of chronic liver disease. HCV genotypes and subtypes are important predictors of disease progression and antiviral treatment response. To our knowledge, there had been limited studies of HCV genotypes in Qatif, Saudi Arabia. This study aims to assess the distribution of HCV genotypes in Qatif Central Hospital, Qatif, Saudi Arabia. This is a retrospective study of adult patients with HCV infection between January 2015 and December 2020. Only patients with documented HCV genotyping were included. A total of 356 HCVinfected patients fulfilled the inclusion criteria and were included in further analysis. Of those patients, 179 (50.3%) were males, and most were Saudi (N=347, 97.5%). The median age was 60 years, and 191 (53.7%) were 50-69 years of age. Genotype 2 was present in 118 (33.1%) of the patients, followed by genotype 4 in 92 (25.8%), genotype 1B in 62 (17.4%), and genotype 1A in 37 (10.4%). The study showed that HCV genotype 2 is the predominant variant among chronic HCV patients in the study population. Monitoring the epidemiology of HCV genotypes may provide guidance in treatment decisions.
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Affiliation(s)
- Fadel Ali M. Almosa
- Gastroenterology Unit, Department of Internal Medicine, Qatif Central Hospital, Ministry of Health, Qatif, Saudi Arabia
| | - Ali Hassan A. Alnasser
- Department of Laboratory, Dhahran Eye Specialist Hospital, Ministry of Health, Dhahran, Saudi Arabia
| | - Jaffar A. Al-Tawfiq
- Infectious Disease Unit, Specialty Internal Medicine, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
- Department of Medicine, School of Medicine, Indiana University, Indianapolis, IN, USA
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
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5
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Li N, Feng Y, Vrancken B, Chen Y, Dong L, Yang Q, Kraemer MU, Pybus OG, Zhang H, Brady OJ, Tian H. Assessing the impact of COVID-19 border restrictions on dengue transmission in Yunnan Province, China: an observational epidemiological and phylogenetic analysis. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2021; 14:100259. [PMID: 34528006 PMCID: PMC8387751 DOI: 10.1016/j.lanwpc.2021.100259] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 07/15/2021] [Accepted: 07/21/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND In response to the COVID-19 pandemic, China implemented strict restrictions on cross-border travel to prevent disease importation. Yunnan, a Chinese province that borders dengue-endemic countries in Southeast Asia, experienced unprecedented reduction in dengue, from 6840 recorded cases in 2019 to 260 in 2020. METHODS Using a combination of epidemiological and virus genomic data, collected from 2013 to 2020 in Yunnan and neighbouring countries, we conduct a series of analyses to characterise the role of virus importation in driving dengue dynamics in Yunnan and assess the association between recent international travel restrictions and the decline in dengue reported in Yunnan in 2020. FINDINGS We find strong evidence that dengue incidence between 2013-2019 in Yunnan was closely linked with international importation of cases. A 0-2 month lag in incidence not explained by seasonal differences, absence of local transmission in the winter, effective reproductive numbers < 1 (as estimated independently using genetic data) and diverse cosmopolitan dengue virus phylogenies all suggest dengue is non-endemic in Yunnan. Using a multivariate statistical model we show that the substantial decline in dengue incidence observed in Yunnan in 2020 but not in neighbouring countries is closely associated with the timing of international travel restrictions, even after accounting for other environmental drivers of dengue incidence. INTERPRETATION We conclude that Yunnan is a regional sink for DENV lineage movement and that border restrictions may have substantially reduced dengue burden in 2020, potentially averting thousands of cases. Targeted testing and surveillance of travelers returning from high-risk areas could help to inform public health strategies to minimise or even eliminate dengue outbreaks in non-endemic settings like southern China. FUNDING Funding for this study was provided by National Key Research and Development Program of China, Beijing Science and Technology Planning Project (Z201100005420010); Beijing Natural Science Foundation (JQ18025); Beijing Advanced Innovation Program for Land Surface Science; National Natural Science Foundation of China (82073616); Young Elite Scientist Sponsorship Program by CAST (YESS) (2018QNRC001); H.T., O.P.G. and M.U.G.K. acknowledge support from the Oxford Martin School. O.J.B was supported by a Wellcome Trust Sir Henry Wellcome Fellowship (206471/Z/17/Z). Chinese translation of the abstract (Appendix 2).
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Affiliation(s)
- Naizhe Li
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China,College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yun Feng
- Yunnan Institute of Endemic Diseases Control and Prevention, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, China
| | - Bram Vrancken
- Department of Microbiology and Immunology, Rega Institute, Laboratory of Evolutionary and Computational Virology, KU Leuven, Leuven, Belgium
| | - Yuyang Chen
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China,College of Life Sciences, Beijing Normal University, Beijing, China
| | - Lu Dong
- College of Life Sciences, Beijing Normal University, Beijing, China
| | - Qiqi Yang
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Moritz U.G. Kraemer
- Department of Zoology, University of Oxford, Oxford, UK,Harvard Medical School, Harvard University, Boston, MA, USA,Boston Children's Hospital, Boston, MA, USA
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, Oxford, UK,Department of Pathobiology and Population Science, The Royal Veterinary College, London, UK
| | - Hailin Zhang
- Yunnan Institute of Endemic Diseases Control and Prevention, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, China,Corresponding author
| | - Oliver J. Brady
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK,Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK,Corresponding author
| | - Huaiyu Tian
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China,College of Life Sciences, Beijing Normal University, Beijing, China,Corresponding author
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6
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Shah R, Ahovegbe L, Niebel M, Shepherd J, Thomson EC. Non-epidemic HCV genotypes in low- and middle-income countries and the risk of resistance to current direct-acting antiviral regimens. J Hepatol 2021; 75:462-473. [PMID: 33974951 PMCID: PMC8310923 DOI: 10.1016/j.jhep.2021.04.045] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 03/12/2021] [Accepted: 04/21/2021] [Indexed: 02/06/2023]
Abstract
The hepatitis C virus (HCV) is an extremely diverse virus, subtypes of which are distributed variably around the world. Viral genotypes may be divided into epidemic subtypes; those that have become prevalent globally, and endemic subtypes that have a more limited distribution, mainly in Africa and Asia. The high variability of endemic strains reflects evolutionary origins in the locations where they are found. This increased genetic diversity raises the possibility of resistance to pan-genotypic direct-acting antiviral regimens. While many endemic subtypes respond well to direct-acting antiviral therapies, others, for example genotypes 1l, 3b and 4r, do not respond as well as predicted. Many genotypes that are rare in high-income countries but common in other parts of the world have not yet been fully assessed in clinical trials. Further sequencing and clinical studies in sub-Saharan Africa and Asia are indicated to monitor response to treatment and to facilitate the World Health Organization's 2030 elimination strategy.
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Affiliation(s)
- Rajiv Shah
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Lucrece Ahovegbe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; Mbarara University of Science and Technology, Mbarara, Uganda
| | - Marc Niebel
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - James Shepherd
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; London School of Hygiene and Tropical Medicine, London, UK.
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7
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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.
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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
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8
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Gill MS, Lemey P, Suchard MA, Rambaut A, Baele G. Online Bayesian Phylodynamic Inference in BEAST with Application to Epidemic Reconstruction. Mol Biol Evol 2020; 37:1832-1842. [PMID: 32101295 PMCID: PMC7253210 DOI: 10.1093/molbev/msaa047] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Reconstructing pathogen dynamics from genetic data as they become available during an outbreak or epidemic represents an important statistical scenario in which observations arrive sequentially in time and one is interested in performing inference in an "online" fashion. Widely used Bayesian phylogenetic inference packages are not set up for this purpose, generally requiring one to recompute trees and evolutionary model parameters de novo when new data arrive. To accommodate increasing data flow in a Bayesian phylogenetic framework, we introduce a methodology to efficiently update the posterior distribution with newly available genetic data. Our procedure is implemented in the BEAST 1.10 software package, and relies on a distance-based measure to insert new taxa into the current estimate of the phylogeny and imputes plausible values for new model parameters to accommodate growing dimensionality. This augmentation creates informed starting values and re-uses optimally tuned transition kernels for posterior exploration of growing data sets, reducing the time necessary to converge to target posterior distributions. We apply our framework to data from the recent West African Ebola virus epidemic and demonstrate a considerable reduction in time required to obtain posterior estimates at different time points of the outbreak. Beyond epidemic monitoring, this framework easily finds other applications within the phylogenetics community, where changes in the data-in terms of alignment changes, sequence addition or removal-present common scenarios that can benefit from online inference.
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Affiliation(s)
- Mandev S Gill
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Marc A Suchard
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA
- Department of Biostatistics, School of Public Health, University of California, Los Angeles, CA
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, United Kingdom
- Fogarty International Center, National Institutes of Health, Bethesda, MD
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
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9
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Hong SL, Dellicour S, Vrancken B, Suchard MA, Pyne MT, Hillyard DR, Lemey P, Baele G. In Search of Covariates of HIV-1 Subtype B Spread in the United States-A Cautionary Tale of Large-Scale Bayesian Phylogeography. Viruses 2020; 12:v12020182. [PMID: 32033422 PMCID: PMC7077180 DOI: 10.3390/v12020182] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/24/2020] [Accepted: 01/28/2020] [Indexed: 12/21/2022] Open
Abstract
Infections with HIV-1 group M subtype B viruses account for the majority of the HIV epidemic in the Western world. Phylogeographic studies have placed the introduction of subtype B in the United States in New York around 1970, where it grew into a major source of spread. Currently, it is estimated that over one million people are living with HIV in the US and that most are infected with subtype B variants. Here, we aim to identify the drivers of HIV-1 subtype B dispersal in the United States by analyzing a collection of 23,588 pol sequences, collected for drug resistance testing from 45 states during 2004-2011. To this end, we introduce a workflow to reduce this large collection of data to more computationally-manageable sample sizes and apply the BEAST framework to test which covariates associate with the spread of HIV-1 across state borders. Our results show that we are able to consistently identify certain predictors of spread under reasonable run times across datasets of up to 10,000 sequences. However, the general lack of phylogenetic structure and the high uncertainty associated with HIV trees make it difficult to interpret the epidemiological relevance of the drivers of spread we are able to identify. While the workflow we present here could be applied to other virus datasets of a similar scale, the characteristic star-like shape of HIV-1 phylogenies poses a serious obstacle to reconstructing a detailed evolutionary and spatial history for HIV-1 subtype B in the US.
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Affiliation(s)
- Samuel L. Hong
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (S.D.); (B.V.); (P.L.); (G.B.)
- Correspondence:
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (S.D.); (B.V.); (P.L.); (G.B.)
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (S.D.); (B.V.); (P.L.); (G.B.)
| | - Marc A. Suchard
- 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
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA 90095, USA
| | - Michael T. Pyne
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT 84108, USA;
| | - David R. Hillyard
- Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA;
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (S.D.); (B.V.); (P.L.); (G.B.)
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (S.D.); (B.V.); (P.L.); (G.B.)
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10
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Vrancken B, Cuypers L, Pérez AB, Chueca N, Anton-Basantas J, de la Iglesia A, Fuentes J, Pineda JA, Téllez F, Bernal E, Rincón P, Von Wichman MA, Fuentes A, Vera F, Rivero-Juárez A, Jiménez M, Vandamme AM, García F. Cross-country migration linked to people who inject drugs challenges the long-term impact of national HCV elimination programmes. J Hepatol 2019; 71:1270-1272. [PMID: 31585736 DOI: 10.1016/j.jhep.2019.08.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/26/2019] [Accepted: 08/07/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Bram Vrancken
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium.
| | - Lize Cuypers
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium.
| | - Ana Belen Pérez
- Clinical Microbiology, University Hospital San Cecilio, Research Institute Ibs, Granada, Spain
| | - Natalia Chueca
- Clinical Microbiology, University Hospital San Cecilio, Research Institute Ibs, Granada, Spain
| | | | | | - Javier Fuentes
- Hepatology Unit, Hospital Miguel Servet, Zaragoza, Spain
| | | | - Francisco Téllez
- Infectious Diseases Unit, University Hospital of Puerto Real, Cádiz, Spain
| | - Enrique Bernal
- Infectious Diseases, University Hospital Reina Sofía, Murcia, Spain
| | - Pilar Rincón
- Infectious Diseases Unit, University Hospital of Valme, Sevilla, Spain
| | | | - Ana Fuentes
- Clinical Microbiology, University Hospital San Cecilio, Research Institute Ibs, Granada, Spain
| | - Francisco Vera
- Infectious Disease Unit, University Hospital Santa Lucía, Cartagena, Murcia, Spain
| | | | | | - Anne-Mieke Vandamme
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium; Center for Global Health and Tropical Medicine, Microbiology Unit, Institute of Hygiene and Tropical Medicine, University Nova Lisbon, Lisbon, Portugal
| | - Federico García
- Clinical Microbiology, University Hospital San Cecilio, Research Institute Ibs, Granada, Spain
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11
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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.
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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
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12
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Khedhiri M, Ghedira K, Chouikha A, Touzi H, Sadraoui A, Hammemi W, Triki H. Tracing the epidemic history of hepatitis C virus genotype 1b in Tunisia and in the world, using a Bayesian coalescent approach. INFECTION GENETICS AND EVOLUTION 2019; 75:103944. [PMID: 31260787 DOI: 10.1016/j.meegid.2019.103944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 06/25/2019] [Accepted: 06/27/2019] [Indexed: 01/10/2023]
Affiliation(s)
- Marwa Khedhiri
- Laboratory of Clinical Virology, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia; Research Laboratory: "Transmission Controle et Immunobiologie des Infections" (LR11-IPT02), Pasteur Institute of Tunis, Tunisia; Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia; Faculty of Sciences of Tunis, University Tunis El Manar, Tunis, Tunisia.
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics - LR16IPT09, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia.
| | - Anissa Chouikha
- Laboratory of Clinical Virology, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia; Research Laboratory: "Transmission Controle et Immunobiologie des Infections" (LR11-IPT02), Pasteur Institute of Tunis, Tunisia; Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia.
| | - Henda Touzi
- Laboratory of Clinical Virology, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia; Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Amel Sadraoui
- Laboratory of Clinical Virology, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia; Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Walid Hammemi
- Laboratory of Clinical Virology, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia; Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Henda Triki
- Laboratory of Clinical Virology, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia; Research Laboratory: "Transmission Controle et Immunobiologie des Infections" (LR11-IPT02), Pasteur Institute of Tunis, Tunisia; Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia; Faculty of Medicine of Tunis, University Tunis El Manar, Tunis, Tunisia.
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13
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Clinical, Virological Characteristics, and Outcomes of Treatment with Sofosbuvir/Ledipasvir in Two Pediatric Patients Infected by HCV Genotype 4. Cells 2019; 8:cells8050416. [PMID: 31060315 PMCID: PMC6562692 DOI: 10.3390/cells8050416] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 04/27/2019] [Accepted: 05/03/2019] [Indexed: 02/06/2023] Open
Abstract
Direct-acting antiviral drugs to cure infections with Hepatitis C virus (HCV) achieve a sustained virological response (SVR) in more than 90% of adult patients. At present, clinical trials are ongoing and real-life data are still limited in children. Herein, we report two cases of pediatric patients treated with fixed-dose combination of sofosbuvir/ledipasvir, already approved to treat HCV4 genotype. Both young girls achieved SVR even though HCV4 isolates carried L28M and M31L NS5A resistance-associated substitutions (RASs). Therefore, possible effects of these RASs merit further study, especially in children.
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14
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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.
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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
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15
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Baele G, Dellicour S, Suchard MA, Lemey P, Vrancken B. Recent advances in computational phylodynamics. Curr Opin Virol 2018; 31:24-32. [PMID: 30248578 DOI: 10.1016/j.coviro.2018.08.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 08/16/2018] [Accepted: 08/20/2018] [Indexed: 01/02/2023]
Abstract
Time-stamped, trait-annotated phylogenetic trees built from virus genome data are increasingly used for outbreak investigation and monitoring ongoing epidemics. This routinely involves reconstructing the spatial and demographic processes from large data sets to help unveil the patterns and drivers of virus spread. Such phylodynamic inferences can however become quite time-consuming as the dimensions of the data increase, which has led to a myriad of approaches that aim to tackle this complexity. To elucidate the current state of the art in the field of phylodynamics, we discuss recent developments in Bayesian inference and accompanying software, highlight methods for improving computational efficiency and relevant visualisation tools. As an alternative to fully Bayesian approaches, we touch upon conditional software pipelines that compromise between statistical coherence and turn-around-time, and we highlight the available software packages. Finally, we outline future directions that may facilitate the large-scale tracking of epidemics in near real time.
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Affiliation(s)
- Guy Baele
- KU Leuven Department of Microbiology and Immunology, Rega Institute, Laboratory of Evolutionary and Computational Virology, Leuven, Belgium.
| | - Simon Dellicour
- KU Leuven Department of Microbiology and Immunology, Rega Institute, Laboratory of Evolutionary and Computational Virology, Leuven, Belgium; Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Philippe Lemey
- KU Leuven Department of Microbiology and Immunology, Rega Institute, Laboratory of Evolutionary and Computational Virology, Leuven, Belgium
| | - Bram Vrancken
- KU Leuven Department of Microbiology and Immunology, Rega Institute, Laboratory of Evolutionary and Computational Virology, Leuven, Belgium
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16
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Palladino C, Ezeonwumelu IJ, Marcelino R, Briz V, Moranguinho I, Serejo F, Velosa JF, Marinho RT, Borrego P, Taveira N. Epidemic history of hepatitis C virus genotypes and subtypes in Portugal. Sci Rep 2018; 8:12266. [PMID: 30116054 PMCID: PMC6095915 DOI: 10.1038/s41598-018-30528-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/27/2018] [Indexed: 12/15/2022] Open
Abstract
Any successful strategy to prevent and control HCV infection requires an understanding of the epidemic behaviour among the different genotypes. Here, we performed the first characterization of the epidemic history and transmission dynamics of HCV subtypes in Portugal. Direct sequencing of NS5B was performed on 230 direct-acting antiviral drugs (DAA)-treatment naïve patients in Lisbon. Phylogenetic analysis was used for subtyping and transmission cluster identification. Bayesian methods were used to reconstruct the epidemic history of HCV subtypes. Sequences were analysed for resistance-associated substitutions (RAS). The majority of strains were HCV-GT1 (62.6%), GT3 (18.3%, all subtype 3a) and GT4 (16.1%). Among GT1, the most frequent were subtypes 1a (75.5%) and 1b (24.5%). Polyphyletic patterns were found in all but 12 lineages suggesting multiple introductions of the different subtypes in this population. Five distinct epidemics were identified. The first significant HCV epidemic in Portugal occurred between 1930s and 1960s, was caused almost exclusively by GT1b and was likely associated with blood transfusions. Rapid expansion of GT3a occurred in the 1960s and GT1a in the 1980s, associated with intravenous drug use. The most recent epidemics were caused by GT4a and GT4d and seem to be associated with the resurgence of opioid use. The C316N substitution was found in 31.4% of GT1b-patients. Close surveillance of patients bearing this mutation and undergoing dasabuvir-based regimens will be important to determine its impact on treatment outcome.
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Affiliation(s)
- Claudia Palladino
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal.
| | - Ifeanyi Jude Ezeonwumelu
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Rute Marcelino
- Global Health and Tropical Medicine (GHTM), Unit of Medical Microbiology, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa, Lisbon, Portugal
| | - Verónica Briz
- Laboratory of Viral Hepatitis, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, Madrid, Spain
| | - Inês Moranguinho
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Fátima Serejo
- Department of Gastroenterology and Hepatology, Santa Maria Hospital, Universidade de Lisboa, Lisbon, Portugal
| | - José Fernando Velosa
- Department of Gastroenterology and Hepatology, Santa Maria Hospital, Universidade de Lisboa, Lisbon, Portugal
| | - Rui Tato Marinho
- Department of Gastroenterology and Hepatology, Santa Maria Hospital, Universidade de Lisboa, Lisbon, Portugal
| | - Pedro Borrego
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
- Centro de Administração e Políticas Públicas (CAPP), Instituto Superior de Ciências Sociais e Políticas, Universidade de Lisboa, Lisbon, Portugal
| | - Nuno Taveira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal.
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Universitário Egas Moniz, Caparica, Portugal.
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17
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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.
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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
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18
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Cuypers L, Pérez AB, Chueca N, Aldamiz-Echevarría T, Alados JC, Martínez-Sapiña AM, Merino D, Pineda JA, Téllez F, Espinosa N, Salméron J, Rivero-Juarez A, Vivancos MJ, Hontañón V, Vandamme AM, García F. Relapse or reinfection after failing hepatitis C direct acting antiviral treatment: Unravelled by phylogenetic analysis. PLoS One 2018; 13:e0201268. [PMID: 30044871 PMCID: PMC6059487 DOI: 10.1371/journal.pone.0201268] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 07/11/2018] [Indexed: 12/14/2022] Open
Abstract
Despite high response rates associated to hepatitis C virus (HCV) treatment, no protective immunity is acquired, allowing for reinfection and continued infectiousness. Distinguishing between relapse and reinfection is crucial for patient counselling and to choose the most appropriate retreatment. Here, refined phylogenetic analysis using multiple genes served to assess genotype and reinfection for 53 patients for whom the virus was sampled before start of therapy and at time of sustained virological response evaluation at week 12. At baseline, genotypes were determined as HCV1a (41.5%), HCV1b (24.5%), HCV4 (18.9%) and HCV3a (15.1%), while six cases revealed to be discordantly assigned by phylogeny and commercial assays. Overall, 60.4% was co-infected with HIV. The large majority was classified as people who inject drugs (78.6%), often co-infected with HIV. Transmission was sexual in seven cases, of which five in HIV-positive men-who-have-sex-with-men. Overall, relapse was defined for 44 patients, while no conclusion was drawn for four patients. Five patients were reinfected with a different HCV strain, of which three with a different genotype, showing that phylogeny is needed not only to determine the genotype, but also to distinguish between relapse and intra-subtype reinfection. Of note, phylogenies are more reliable when longer fragments of the viral genome are being sequenced.
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Affiliation(s)
- Lize Cuypers
- KU Leuven–University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ana Belén Pérez
- Clinical Microbiology Department, University Hospital San Cecilio Granada, Instituto de Investigación Ibs. Granada, Spain
| | - Natalia Chueca
- Clinical Microbiology Department, University Hospital San Cecilio Granada, Instituto de Investigación Ibs. Granada, Spain
| | | | | | | | - Dolores Merino
- Clinical Microbiology, Hospital Infanta Elena, Huelva, Spain
| | | | - Francisco Téllez
- UGC Enfermedades Infecciosas y Microbiología, Hospital La Línea, AGS Campo de Gibraltar, Cadiz, Spain
| | - Nuria Espinosa
- Clinical Microbiology, Hospital Virgen del Rocío, Sevilla, Spain
| | - Javier Salméron
- Hepatology Unit, University Hospital San Cecilio Granada, Instituto de Investigación Ibs. CIBERehd, Granada, Spain
| | - Antonio Rivero-Juarez
- Infectious Diseases Unit. Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC). Hospital Universitario Reina Sofía de Córdoba. Universidad de Córdoba, Córdoba, Spain
| | | | - Víctor Hontañón
- Clinical Microbiology, University Hospital La Paz, Madrid, Spain
| | - Anne-Mieke Vandamme
- KU Leuven–University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium
- Center for Global Health and Tropical Medicine, Microbiology Unit, Institute for Hygiene and Tropical Medicine, University Nova de Lisboa, Lisbon, Portugal
| | - Féderico García
- Clinical Microbiology Department, University Hospital San Cecilio Granada, Instituto de Investigación Ibs. Granada, Spain
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19
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Magee D, Scotch M. The effects of random taxa sampling schemes in Bayesian virus phylogeography. INFECTION GENETICS AND EVOLUTION 2018; 64:225-230. [PMID: 29991455 DOI: 10.1016/j.meegid.2018.07.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 06/07/2018] [Accepted: 07/02/2018] [Indexed: 11/30/2022]
Abstract
Public health researchers are often tasked with accurately and quickly identifying the location and time when an epidemic originated from a representative sample of nucleotide sequences. In this paper, we investigate multiple approaches to subsampling the sequence set when employing a Bayesian phylogeographic generalized linear model. Our results indicate that near-categorical posterior MCC estimates on the root can be obtained with replicate runs using 25-50% of the sequence data, and that including 90% of sequences does not necessarily entail more accurate inferences. We present the first analysis of predictor signal suppression and show how the ability to detect the influence of predictor variables is limited when sample size predictors are included in the models.
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Affiliation(s)
- Daniel Magee
- Department of Biomedical Informatics, Arizona State University, 13212 E. Shea Blvd., Scottsdale 85259, AZ, USA; Biodesign Center for Environmental Health Engineering, Arizona State University, 1001 S. McAllister Ave, Tempe 85281, AZ, USA
| | - Matthew Scotch
- Department of Biomedical Informatics, Arizona State University, 13212 E. Shea Blvd., Scottsdale 85259, AZ, USA; Biodesign Center for Environmental Health Engineering, Arizona State University, 1001 S. McAllister Ave, Tempe 85281, AZ, USA.
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20
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Bawazir A, AlGusheri F, Jradi H, AlBalwi M, Abdel-Gader AG. Hepatitis C virus genotypes in Saudi Arabia: a future prediction and laboratory profile. Virol J 2017; 14:208. [PMID: 29096662 PMCID: PMC5667522 DOI: 10.1186/s12985-017-0873-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 10/18/2017] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Hepatitis C virus (HCV) genotypes and subtypes are considered an important tool for epidemiological and clinical studies and valuable markers for disease progression and response to antiviral therapy. The aim of this study was to identify the prevalence of HCV genotypes and their relation to socio-demographic factors particularly age and sex, various biochemical profiles and viral load. METHODS The records (630) of Saudi patients positive for HCV (2007-2011) reported in the system of the Molecular Pathology Laboratory at a tertiary reference hospital in Riyadh, Saudi Arabia were analyzed. Socio-demographic characteristics, liver biochemical profile, viral load and co-infection with HBV and HIV were retrieved from the hospital database. The associations of continuous and categorical variables with genotypes were analyzed. RESULT The overall mean age of the surveyed patients was 59 years ±0.5 years (21% were <50 years (p = 0.02). The rate of infection is lower in males than in females (47.6% vs. 52.4%). HCV genotype 4 was the most prevalent (60.7%), followed by genotype 1 (24.8%). However, genotype 1 and 3 were found more in males (29.7% vs. 20.3% and 6% vs. 2.1%, respectively, p = 0.001), while genotype 2 and 4 were more among females (4.8% vs. 2% and 68.5% vs. 52.3%, respectively). In addition, genotype 1 was found dominant in younger males (33.8%). Biochemical parameters across gender showed significant variation in particular for the ALT (p = 0.007). The mean viral load was significantly higher in genotype 1 than genotype 4 (4,757,532 vs. 1,435,012, p = <001). There is a very low overall percentage of co-infection of HBV or HIV in this study (around 2% for each). CONCLUSION Although HCV genotype 4 shows an overall high prevalence in this study, a clear decline in the rate of this genotype was also demonstrated in particular among the younger age group who displayed increasing trends toward the global trend of genotype 1, rather than genotype 4. This finding would be of clinical interest in relation to future planning of the therapy for HCV infected patient.
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Affiliation(s)
- Amen Bawazir
- The King Abdullah International Medical Research Center (KAIMRC), Community and environmental Health,College of Public Health & Health Informatics. King Saud Bin Abdulaziz University for Health Sciences, Riyadh, 11481 Saudi Arabia
| | - Fahad AlGusheri
- Division of Molecular Pathology and Genetics, Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Hoda Jradi
- The King Abdullah International Medical Research Center (KAIMRC), Community and environmental Health,College of Public Health & Health Informatics. King Saud Bin Abdulaziz University for Health Sciences, Riyadh, 11481 Saudi Arabia
| | - Mohammed AlBalwi
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, 3660, Riyadh, 11481 Saudi Arabia
| | - Abdel-Galil Abdel-Gader
- Department of Basic Medical Sciences, College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
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21
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Vrancken B, Suchard MA, Lemey P. Accurate quantification of within- and between-host HBV evolutionary rates requires explicit transmission chain modelling. Virus Evol 2017; 3:vex028. [PMID: 29026650 PMCID: PMC5632516 DOI: 10.1093/ve/vex028] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Analyses of virus evolution in known transmission chains have the potential to elucidate the impact of transmission dynamics on the viral evolutionary rate and its difference within and between hosts. Lin et al. (2015, Journal of Virology, 89/7: 3512–22) recently investigated the evolutionary history of hepatitis B virus in a transmission chain and postulated that the ‘colonization–adaptation–transmission’ model can explain the differential impact of transmission on synonymous and non-synonymous substitution rates. Here, we revisit this dataset using a full probabilistic Bayesian phylogenetic framework that adequately accounts for the non-independence of sequence data when estimating evolutionary parameters. Examination of the transmission chain data under a flexible coalescent prior reveals a general inconsistency between the estimated timings and clustering patterns and the known transmission history, highlighting the need to incorporate host transmission information in the analysis. Using an explicit genealogical transmission chain model, we find strong support for a transmission-associated decrease of the overall evolutionary rate. However, in contrast to the initially reported larger transmission effect on non-synonymous substitution rate, we find a similar decrease in both non-synonymous and synonymous substitution rates that cannot be adequately explained by the colonization-adaptation-transmission model. An alternative explanation may involve a transmission/establishment advantage of hepatitis B virus variants that have accumulated fewer within-host substitutions, perhaps by spending more time in the covalently closed circular DNA state between each round of viral replication. More generally, this study illustrates that ignoring phylogenetic relationships can lead to misleading evolutionary estimates.
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Affiliation(s)
- Bram Vrancken
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, B-3000 Leuven, Belgium
| | - Marc A Suchard
- Department of Biomathematics, 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.,Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA 90095, USA
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, B-3000 Leuven, Belgium
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22
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Zhang Y, Vrancken B, Feng Y, Dellicour S, Yang Q, Yang W, Zhang Y, Dong L, Pybus OG, Zhang H, Tian H. Cross-border spread, lineage displacement and evolutionary rate estimation of rabies virus in Yunnan Province, China. Virol J 2017; 14:102. [PMID: 28578663 PMCID: PMC5457581 DOI: 10.1186/s12985-017-0769-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 05/25/2017] [Indexed: 12/12/2022] Open
Abstract
Background Rabies is an important but underestimated threat to public health, with most cases reported in Asia. Since 2000, a new epidemic wave of rabies has emerged in Yunnan Province, southwestern China, which borders three countries in Southeast Asia. Method We estimated gene-specific evolutionary rates for rabies virus using available data in GenBank, then used this information to calibrate the timescale of rabies virus (RABV) spread in Asia. We used 452 publicly available geo-referenced complete nucleoprotein (N) gene sequences, including 52 RABV sequences that were recently generated from samples collected in Yunnan between 2008 and 2012. Results The RABV N gene evolutionary rate was estimated to be 1.88 × 10−4 (1.37–2.41 × 10−4, 95% Bayesian credible interval, BCI) substitutions per site per year. Phylogenetic reconstructions show that the currently circulating RABV lineages in Yunnan result from at least seven independent introductions (95% BCI: 6–9 introductions) and represent each of the three main Asian RABV lineages, SEA-1, -2 and -3. We find that Yunnan is a sink location for the domestic spread of RABV and connects RABV epidemics in North China, South China, and Southeast Asia. Cross-border spread from southeast Asia (SEA) into South China, and intermixing of the North and South China epidemics is also well supported. The influx of RABV into Yunnan from SEA was not well-supported, likely due to the poor sampling of SEA RABV diversity. We found evidence for a lineage displacement of the Yunnan SEA-2 and -3 lineages by Yunnan SEA-1 strains, and considered whether this could be attributed to fitness differences. Conclusion Overall, our study contributes to a better understanding of the spread of RABV that could facilitate future rabies virus control and prevention efforts. Electronic supplementary material The online version of this article (doi:10.1186/s12985-017-0769-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuzhen Zhang
- Yunnan Institute of Endemic Diseases Control and Prevention, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, China
| | - Bram Vrancken
- Department of Microbiology and Immunology, Division of Clinical and Epidemiological Virology, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
| | - Yun Feng
- Yunnan Institute of Endemic Diseases Control and Prevention, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, China
| | - Simon Dellicour
- Department of Microbiology and Immunology, Division of Clinical and Epidemiological Virology, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
| | - Qiqi Yang
- State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
| | - Weihong Yang
- Yunnan Institute of Endemic Diseases Control and Prevention, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, China
| | - Yunzhi Zhang
- Yunnan Institute of Endemic Diseases Control and Prevention, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, China
| | - Lu Dong
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | | | - Hailin Zhang
- Yunnan Institute of Endemic Diseases Control and Prevention, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, China.
| | - Huaiyu Tian
- State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China.
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