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Zecchin B, Fusaro A, Milani A, Schivo A, Ravagnan S, Ormelli S, Mavian C, Michelutti A, Toniolo F, Barzon L, Monne I, Capelli G. The central role of Italy in the spatial spread of USUTU virus in Europe. Virus Evol 2021; 7:veab048. [PMID: 34513027 PMCID: PMC8427344 DOI: 10.1093/ve/veab048] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
USUTU virus (USUV) is an arbovirus maintained in the environment through a bird-mosquito enzootic cycle. Previous surveillance plans highlighted the endemicity of USUV in North-eastern Italy. In this work, we sequenced 138 new USUV full genomes from mosquito pools (Culex pipiens) and wild birds collected in North-eastern Italy and we investigated the evolutionary processes (phylogenetic analysis, selection pressure and evolutionary time-scale analysis) and spatial spread of USUV strains circulating in the European context and in Italy, with a particular focus on North-eastern Italy. Our results confirmed the circulation of viruses belonging to four different lineages in Italy (EU1, EU2, EU3 and EU4), with the newly sequenced viruses from the North-eastern regions, Veneto and Friuli Venezia Giulia, belonging to the EU2 lineage and clustering into two different sub-lineages, EU2-A and EU2-B. Specific mutations characterize each European lineage and geographic location seem to have shaped their phylogenetic structure. By investigating the spatial spread in Europe, we were able to show that Italy acted mainly as donor of USUV to neighbouring countries. At a national level, we identified two geographical clusters mainly circulating in Northern and North-western Italy, spreading both northward and southward. Our analyses provide important information on the spatial and evolutionary dynamics of USUTU virus that can help to improve surveillance plans and control strategies for this virus of increasing concern for human health.
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Affiliation(s)
- B Zecchin
- Department of Research and Innovation, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - A Fusaro
- Department of Research and Innovation, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - A Milani
- Department of Research and Innovation, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - A Schivo
- Department of Research and Innovation, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - S Ravagnan
- National Reference Centre/OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - S Ormelli
- Department of Research and Innovation, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - C Mavian
- Emerging Pathogens Institute, Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - A Michelutti
- National Reference Centre/OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - F Toniolo
- National Reference Centre/OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - L Barzon
- Department of Molecular Medicine, University of Padua, Padova, Italy
| | - I Monne
- Department of Research and Innovation, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - G Capelli
- National Reference Centre/OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
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52
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Visseaux B, Bertine M, Le Hingrat Q, Ferré V, Charpentier C, Collin F, Damond F, Matheron S, Hué S, Descamps D. HIV-2 diversity displays two clades within group A with distinct geographical distribution and evolution. Virus Evol 2021; 7:veab024. [PMID: 34422316 PMCID: PMC8377049 DOI: 10.1093/ve/veab024] [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] [Indexed: 11/13/2022] Open
Abstract
Genetic diversity of HIV-2 groups A and B has not yet been fully described, especially in a few Western Africa countries such as Ivory-Coast or Mali. We collected 444 pol, 152 vif, 129 env, and 74 LTR sequences from patients of the French ANRS CO5 HIV-2 cohort completed by 221 pol, 18 vif, 377 env, and 63 LTR unique sequences from public databases. We performed phylogenetic reconstructions and revealed two distinct lineages within HIV-2 group A, herein called A1 and A2, presenting non-negligible genetic distances and distinct geographic distributions as A1 is related to coastal Western African countries and A2 to inland Western countries. Estimated early diversification times for groups A and B in human populations were 1940 [95% higher probability densitiy: 1935–53] and 1961 [1952–70]. A1 experienced an early diversification in 1942 [1937–58] with two distinct early epidemics in Guinea-Bissau or Senegal, raising the possibility of group A emergence in those countries from an initial introduction from Ivory-Coast to Senegal, two former French colonies. Changes in effective population sizes over time revealed that A1 exponentially grew concomitantly to Guinea-Bissau independence war, but both A2 and B lineages experienced a latter growth, starting during the 80s economic crisis. This large HIV-2 genetic analysis provides the existence of two distinct subtypes within group A and new data about HIV-2 early spreading patterns and recent epidemiologic evolution for which data are scarce outside Guinea-Bissau.
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Affiliation(s)
- Benoit Visseaux
- Université de Paris, IAME, UMR 1137, INSERM, Paris, France.,Assistance Publique - Hôpitaux de Paris, Hôpital Bichat, Department of Virology, Paris, France
| | - Mélanie Bertine
- Université de Paris, IAME, UMR 1137, INSERM, Paris, France.,Assistance Publique - Hôpitaux de Paris, Hôpital Bichat, Department of Virology, Paris, France
| | - Quentin Le Hingrat
- Université de Paris, IAME, UMR 1137, INSERM, Paris, France.,Assistance Publique - Hôpitaux de Paris, Hôpital Bichat, Department of Virology, Paris, France
| | - Valentine Ferré
- Université de Paris, IAME, UMR 1137, INSERM, Paris, France.,Assistance Publique - Hôpitaux de Paris, Hôpital Bichat, Department of Virology, Paris, France
| | - Charlotte Charpentier
- Université de Paris, IAME, UMR 1137, INSERM, Paris, France.,Assistance Publique - Hôpitaux de Paris, Hôpital Bichat, Department of Virology, Paris, France
| | - Fidéline Collin
- ISPED, UMR 897, INSERM, Université de Bordeaux, Epidémiologie-Biostatistique, Bordeaux, France
| | - Florence Damond
- Université de Paris, IAME, UMR 1137, INSERM, Paris, France.,Assistance Publique - Hôpitaux de Paris, Hôpital Bichat, Department of Virology, Paris, France
| | - Sophie Matheron
- Université de Paris, IAME, UMR 1137, INSERM, Paris, France.,Assistance Publique - Hôpitaux de Paris, Hôpital Bichat, Department of Infectious and Tropical Diseases, Paris, France
| | - Stéphane Hué
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Diane Descamps
- Université de Paris, IAME, UMR 1137, INSERM, Paris, France.,Assistance Publique - Hôpitaux de Paris, Hôpital Bichat, Department of Virology, Paris, France
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53
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Hoxie I, Dennehy JJ. Rotavirus A Genome Segments Show Distinct Segregation and Codon Usage Patterns. Viruses 2021; 13:v13081460. [PMID: 34452326 PMCID: PMC8402926 DOI: 10.3390/v13081460] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 12/29/2022] Open
Abstract
Reassortment of the Rotavirus A (RVA) 11-segment dsRNA genome may generate new genome constellations that allow RVA to expand its host range or evade immune responses. Reassortment may also produce phylogenetic incongruities and weakly linked evolutionary histories across the 11 segments, obscuring reassortment-specific epistasis and changes in substitution rates. To determine the co-segregation patterns of RVA segments, we generated time-scaled phylogenetic trees for each of the 11 segments of 789 complete RVA genomes isolated from mammalian hosts and compared the segments’ geodesic distances. We found that segments 4 (VP4) and 9 (VP7) occupied significantly different tree spaces from each other and from the rest of the genome. By contrast, segments 10 and 11 (NSP4 and NSP5/6) occupied nearly indistinguishable tree spaces, suggesting strong co-segregation. Host-species barriers appeared to vary by segment, with segment 9 (VP7) presenting the weakest association with host species. Bayesian Skyride plots were generated for each segment to compare relative genetic diversity among segments over time. All segments showed a dramatic decrease in diversity around 2007 coinciding with the introduction of RVA vaccines. To assess selection pressures, codon adaptation indices and relative codon deoptimization indices were calculated with respect to different host genomes. Codon usage varied by segment with segment 11 (NSP5) exhibiting significantly higher adaptation to host genomes. Furthermore, RVA codon usage patterns appeared optimized for expression in humans and birds relative to the other hosts examined, suggesting that translational efficiency is not a barrier in RVA zoonosis.
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Affiliation(s)
- Irene Hoxie
- Biology Department, The Graduate Center, The City University of New York, New York, NY 10016, USA;
- Biology Department, Queens College, The City University of New York, Flushing, New York, NY 11367, USA
- Correspondence:
| | - John J. Dennehy
- Biology Department, The Graduate Center, The City University of New York, New York, NY 10016, USA;
- Biology Department, Queens College, The City University of New York, Flushing, New York, NY 11367, USA
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Yu X, Zhu H, Bo Y, Li Y, Zhang J, Jiang L, Chen G, Zhang X, Wen Y. Molecular evolutionary analysis reveals Arctic-like rabies viruses evolved and dispersed independently in North and South Asia. J Vet Sci 2021; 22:e5. [PMID: 33522157 PMCID: PMC7850786 DOI: 10.4142/jvs.2021.22.e5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/06/2020] [Accepted: 10/28/2020] [Indexed: 02/05/2023] Open
Abstract
Background Arctic-like (AL) lineages of rabies viruses (RABVs) remains endemic in some Arctic and Asia countries. However, their evolutionary dynamics are largely unappreciated. Objectives We attempted to estimate the evolutionary history, geographic origin and spread of the Arctic-related RABVs. Methods Full length or partial sequences of the N and G genes were used to infer the evolutionary aspects of AL RABVs by Bayesian evolutionary analysis. Results The most recent common ancestor (tMRCA) of the current Arctic and AL RABVs emerged in the 1830s and evolved independently after diversification. Population demographic analysis indicated that the viruses experienced gradual growth followed by a sudden decrease in its population size from the mid-1980s to approximately 2000. Genetic flow patterns among the regions reveal a high geographic correlation in AL RABVs transmission. Discrete phylogeography suggests that the geographic origin of the AL RABVs was in east Russia in approximately the 1830s. The ancestral AL RABV then diversified and immigrated to the countries in Northeast Asia, while the viruses in South Asia were dispersed to the neighboring regions from India. The N and G genes of RABVs in both clades sustained high levels of purifying selection, and the positive selection sites were mainly found on the C-terminus of the G gene. Conclusions The current AL RABVs circulating in South and North Asia evolved and dispersed independently.
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Affiliation(s)
- Xin Yu
- School of Life Sciences, Ludong University, Yantai 264025, China.,Shandong Provincial Key Laboratory of Quality Safety Monitoring and Risk Assessment for Animal Products, Ji?nan 250022, China
| | - Hongwei Zhu
- School of Life Sciences, Ludong University, Yantai 264025, China.,Shandong Provincial Key Laboratory of Quality Safety Monitoring and Risk Assessment for Animal Products, Ji?nan 250022, China
| | - Yongheng Bo
- Shandong Provincial Key Laboratory of Quality Safety Monitoring and Risk Assessment for Animal Products, Ji?nan 250022, China
| | - Youzhi Li
- Shandong Provincial Key Laboratory of Quality Safety Monitoring and Risk Assessment for Animal Products, Ji?nan 250022, China
| | - Jianlong Zhang
- School of Life Sciences, Ludong University, Yantai 264025, China.,Yantai Key Laboratory of Animal Pathogenetic Microbiology and Immunology, Yantai 264025, China
| | - Linlin Jiang
- School of Life Sciences, Ludong University, Yantai 264025, China.,Yantai Key Laboratory of Animal Pathogenetic Microbiology and Immunology, Yantai 264025, China
| | - Guozhong Chen
- School of Life Sciences, Ludong University, Yantai 264025, China.,Yantai Key Laboratory of Animal Pathogenetic Microbiology and Immunology, Yantai 264025, China
| | - Xingxiao Zhang
- School of Life Sciences, Ludong University, Yantai 264025, China.,Yantai Key Laboratory of Animal Pathogenetic Microbiology and Immunology, Yantai 264025, China.
| | - Yongjun Wen
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010018, China.
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55
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McBroome J, Thornlow B, Hinrichs AS, De Maio N, Goldman N, Haussler D, Corbett-Detig R, Turakhia Y. A daily-updated database and tools for comprehensive SARS-CoV-2 mutation-annotated trees. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33821270 PMCID: PMC8020970 DOI: 10.1101/2021.04.03.438321] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The vast scale of SARS-CoV-2 sequencing data has made it increasingly challenging to comprehensively analyze all available data using existing tools and file formats. To address this, we present a database of SARS-CoV-2 phylogenetic trees inferred with unrestricted public sequences, which we update daily to incorporate new sequences. Our database uses the recently-proposed mutation-annotated tree (MAT) format to efficiently encode the tree with branches labeled with parsimony-inferred mutations as well as Nextstrain clade and Pango lineage labels at clade roots. As of June 9, 2021, our SARS-CoV-2 MAT consists of 834,521 sequences and provides a comprehensive view of the virus’ evolutionary history using public data. We also present matUtils – a command-line utility for rapidly querying, interpreting and manipulating the MATs. Our daily-updated SARS-CoV-2 MAT database and matUtils software are available at http://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/ and https://github.com/yatisht/usher, respectively.
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Affiliation(s)
- Jakob McBroome
- Department of Biomolecular Engineering, University of California Santa Cruz. Santa Cruz, CA 95064, USA.,Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Bryan Thornlow
- Department of Biomolecular Engineering, University of California Santa Cruz. Santa Cruz, CA 95064, USA.,Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Angie S Hinrichs
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Nicola De Maio
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Nick Goldman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - David Haussler
- Department of Biomolecular Engineering, University of California Santa Cruz. Santa Cruz, CA 95064, USA.,Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz. Santa Cruz, CA 95064, USA.,Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Yatish Turakhia
- Department of Biomolecular Engineering, University of California Santa Cruz. Santa Cruz, CA 95064, USA.,Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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56
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The Molecular Epidemiology and Clinical Phylogenetics of Rhinoviruses Among Paediatric Cases in Sydney, Australia. Int J Infect Dis 2021; 110:69-74. [PMID: 34174431 PMCID: PMC10161873 DOI: 10.1016/j.ijid.2021.06.046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/29/2021] [Accepted: 06/20/2021] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVES Rhinoviruses (RV) represent the most common aetiological agent of all acute respiratory tract infections across all age groups and a significant burden of disease among children. Recent studies have shown that RV-A and RV-C species are associated with increased disease severity. In order to better understand the potential associations between RV species and clinical features among paediatric cases, this study aimed to integrate genetic and epidemiological data using Bayesian phylogenetic methods. METHODS Potential associations between RV species and subtypes, and clinical disease severity using a matched dataset of 52 RV isolates sampled from children (< 18 years) in Sydney, Australia, between 2006 and 2009 were uncovered using epidemiological and phylogenetic methods. RESULTS It was found that RV-C was significantly more likely to be isolated from paediatric cases aged < 2 years compared with RV-A, although no significant differences in recorded symptoms were observed. Significant phylogenetic-trait associations between age and the VP4/VP2 capsid protein phylogeny suggest that age-specific variations in infectivity among subtypes may may be possible. CONCLUSION This study adds to the growing body of epidemiological evidence concerning RV. Improving surveillance and testing for RV, including routine whole genome sequencing, may improve understanding of the varied disease outcomes of RV species and subtypes. Future studies could aim to identify specific genetic markers associated with age-specific infectivity of RV, which could inform treatment practices and public health surveillance of RV.
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57
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Catalano S, Léger E, Fall CB, Borlase A, Diop SD, Berger D, Webster BL, Faye B, Diouf ND, Rollinson D, Sène M, Bâ K, Webster JP. Multihost Transmission of Schistosoma mansoni in Senegal, 2015-2018. Emerg Infect Dis 2021; 26:1234-1242. [PMID: 32441625 PMCID: PMC7258455 DOI: 10.3201/eid2606.200107] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
In West Africa, Schistosoma spp. are capable of infecting multiple definitive hosts, a lifecycle feature that may complicate schistosomiasis control. We characterized the evolutionary relationships among multiple Schistosoma mansoni isolates collected from snails (intermediate hosts), humans (definitive hosts), and rodents (definitive hosts) in Senegal. On a local scale, diagnosis of S. mansoni infection ranged 3.8%-44.8% in school-aged children, 1.7%-52.6% in Mastomys huberti mice, and 1.8%-7.1% in Biomphalaria pfeifferi snails. Our phylogenetic framework confirmed the presence of multiple S. mansoni lineages that could infect both humans and rodents; divergence times of these lineages varied (0.13-0.02 million years ago). We propose that extensive movement of persons across West Africa might have contributed to the establishment of these various multihost S. mansoni clades. High S. mansoni prevalence in rodents at transmission sites frequented by humans further highlights the implications that alternative hosts could have on future public health interventions.
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58
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Genetic and phylogenetic characterization of polycistronic dsRNA segment-10 of bluetongue virus isolates from India between 1985 and 2011. Virus Genes 2021; 57:369-379. [PMID: 34120252 DOI: 10.1007/s11262-021-01855-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/08/2021] [Indexed: 01/07/2023]
Abstract
The smallest polycistronic dsRNA segment-10 (S10) of bluetongue virus (BTV) encodes NS3/3A and putative NS5. The S10 sequence data of 46 Indian BTV field isolates obtained between 1985 and 2011 were determined and compared with the cognate sequences of global BTV strains. The largest ORF on S10 encodes NS3 (229 aa) and an amino-terminal truncated form of the protein (NS3A) and a putative NS5 (50-59 aa) due to alternate translation initiation site. The overall mean distance of the global NS3 was 0.1106 and 0.0269 at nt and deduced aa sequence, respectively. The global BTV strains formed four major clusters. The major cluster of Indian BTV strains was closely related to the viruses reported from Australia and China. A minor sub-cluster of Indian BTV strains were closely related to the USA strains and a few of the Indian strains were similar to the South African reference and vaccine strains. The global trait association of phylogenetic structure indicates the evolution of the global BTV S10 was not homogenous but rather represents a moderate level of geographical divergence. There was no evidence of an association between the virus and the host species, suggesting a random spread of the viruses. Conflicting selection pressure on the alternate coding sequences of the S10 was evident where NS3/3A might have evolved through strong purifying (negative) selection and NS5 through a positive selection. The presence of multiple positively selected codons on the putative NS5 may be advantageous for adaptation of the virus though their precise role is unknown.
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59
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Ridenour CL, Cocking J, Poidmore S, Erickson D, Brock B, Valentine M, Roe CC, Young SJ, Henke JA, Hung KY, Wittie J, Stefanakos E, Sumner C, Ruedas M, Raman V, Seaton N, Bendik W, Hornstra O’Neill HM, Sheridan K, Centner H, Lemmer D, Fofanov V, Smith K, Will J, Townsend J, Foster JT, Keim PS, Engelthaler DM, Hepp CM. St. Louis Encephalitis Virus in the Southwestern United States: A Phylogeographic Case for a Multi-Variant Introduction Event. Front Genet 2021; 12:667895. [PMID: 34168675 PMCID: PMC8217752 DOI: 10.3389/fgene.2021.667895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/28/2021] [Indexed: 11/14/2022] Open
Abstract
Since the reemergence of St. Louis Encephalitis (SLE) Virus (SLEV) in the Southwest United States, identified during the 2015 outbreak in Arizona, SLEV has been seasonally detected within Culex spp. populations throughout the Southwest United States. Previous work revealed the 2015 outbreak was caused by an importation of SLEV genotype III, which had only been detected previously in Argentina. However, little is known about when the importation occurred or the transmission and genetic dynamics since its arrival into the Southwest. In this study, we sought to determine whether the annual detection of SLEV in the Southwest is due to enzootic cycling or new importations. To address this question, we analyzed 174 SLEV genomes (142 sequenced as part of this study) using Bayesian phylogenetic analyses to estimate the date of arrival into the American Southwest and characterize the underlying population structure of SLEV. Phylogenetic clustering showed that SLEV variants circulating in Maricopa and Riverside counties form two distinct populations with little evidence of inter-county transmission since the onset of the outbreak. Alternatively, it appears that in 2019, Yuma and Clark counties experienced annual importations of SLEV that originated in Riverside and Maricopa counties. Finally, the earliest representatives of SLEV genotype III in the Southwest form a polytomy that includes both California and Arizona samples. We propose that the initial outbreak most likely resulted from the importation of a population of SLEV genotype III variants, perhaps in multiple birds, possibly multiple species, migrating north in 2013, rather than a single variant introduced by one bird.
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Affiliation(s)
- Chase L. Ridenour
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Jill Cocking
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Samuel Poidmore
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Daryn Erickson
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Breezy Brock
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Michael Valentine
- Translational Genomics Research Institute, Flagstaff, AZ, United States
| | - Chandler C. Roe
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Steven J. Young
- Vector Control Division, Maricopa County Environmental Services Department, Phoenix, AZ, United States
| | - Jennifer A. Henke
- Coachella Valley Mosquito and Vector Control District, Indio, CA, United States
| | - Kim Y. Hung
- Coachella Valley Mosquito and Vector Control District, Indio, CA, United States
| | - Jeremy Wittie
- Coachella Valley Mosquito and Vector Control District, Indio, CA, United States
| | | | - Chris Sumner
- Yuma County Pest Abatement District, Yuma, AZ, United States
| | - Martha Ruedas
- Yuma County Pest Abatement District, Yuma, AZ, United States
| | - Vivek Raman
- Southern Nevada Health District, Las Vegas, NV, United States
| | - Nicole Seaton
- Southern Nevada Health District, Las Vegas, NV, United States
| | - William Bendik
- Southern Nevada Health District, Las Vegas, NV, United States
| | | | - Krystal Sheridan
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
- Translational Genomics Research Institute, Flagstaff, AZ, United States
| | - Heather Centner
- Translational Genomics Research Institute, Flagstaff, AZ, United States
| | - Darrin Lemmer
- Translational Genomics Research Institute, Flagstaff, AZ, United States
| | - Viacheslav Fofanov
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Kirk Smith
- Vector Control Division, Maricopa County Environmental Services Department, Phoenix, AZ, United States
| | - James Will
- Vector Control Division, Maricopa County Environmental Services Department, Phoenix, AZ, United States
| | - John Townsend
- Vector Control Division, Maricopa County Environmental Services Department, Phoenix, AZ, United States
| | - Jeffrey T. Foster
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Paul S. Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
- Translational Genomics Research Institute, Flagstaff, AZ, United States
| | | | - Crystal M. Hepp
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
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Shen HX, Li X, Yang DQ, Ju HB, Ge FF, Wang J, Zhao HJ. Phylogenetic analysis and evolutionary dynamics of H3N2 canine and feline influenza virus strains from 2006 to 2019. J Med Virol 2021; 93:3496-3507. [PMID: 33386745 DOI: 10.1002/jmv.26767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/20/2020] [Accepted: 12/23/2020] [Indexed: 02/01/2023]
Abstract
H3N2 feline influenza virus (FIV) and canine influenza virus (CIV) are very common in cats and dogs. Due to the ability of the influenza virus to spread across hosts and frequent contact between pets and people, there exist huge public health problems. In this study, we collected H3N2 CIV and FIV genomes from 2006 to 2019 from NCBI and analyzed the evolutionary dynamics and molecular variation using a series of phylogenetic analysis methods. Results indicated that H3N2 FIVs were closely related to CIVs with high posterior probability and CIVs and FIVs have certain regional characteristics. However, compared with previous studies, the significance of geographical structure correlation decreased. Furthermore, we also found that the intrasubtypic reassortment between FIVs and CIVs were common during epidemics. The integrated analysis was also performed for different selection pressure acting on HA (566 codons), NA (469 codons), M1 (252 codons), and M2 (97 codons) proteins. One HA, two NA, three M1, and two M2 sites were found under positive selection. We subsequently performed the evolutionary dynamics of H3N2 CIV. The results indicated that the time of the most recent common ancestor of CIV H3N2 may have occurred earlier than indicated in a previous study. The Bayesian skyline plot analysis in this study showed the period of divergence of major H3N2 CIVs segments occurred between 2008 and 2010. Notably, according to our research, the PB1 has experienced two divergence periods (2006-2008 and 2009-2011).
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Affiliation(s)
- Hai-Xiao Shen
- Shanghai Animal Disease Control Center, Shanghai, People's Republic of China
| | - Xin Li
- Shanghai Animal Disease Control Center, Shanghai, People's Republic of China
| | - De-Quan Yang
- Shanghai Animal Disease Control Center, Shanghai, People's Republic of China
| | - Hou-Bin Ju
- Shanghai Animal Disease Control Center, Shanghai, People's Republic of China
| | - Fei-Fei Ge
- Shanghai Animal Disease Control Center, Shanghai, People's Republic of China
| | - Jian Wang
- Shanghai Animal Disease Control Center, Shanghai, People's Republic of China
| | - Hong-Jin Zhao
- Shanghai Animal Disease Control Center, Shanghai, People's Republic of China
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61
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Simmonds P, Ansari MA. Extensive C->U transition biases in the genomes of a wide range of mammalian RNA viruses; potential associations with transcriptional mutations, damage- or host-mediated editing of viral RNA. PLoS Pathog 2021; 17:e1009596. [PMID: 34061905 PMCID: PMC8195396 DOI: 10.1371/journal.ppat.1009596] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/11/2021] [Accepted: 04/29/2021] [Indexed: 11/18/2022] Open
Abstract
The rapid evolution of RNA viruses has been long considered to result from a combination of high copying error frequencies during RNA replication, short generation times and the consequent extensive fixation of neutral or adaptive changes over short periods. While both the identities and sites of mutations are typically modelled as being random, recent investigations of sequence diversity of SARS coronavirus 2 (SARS-CoV-2) have identified a preponderance of C->U transitions, proposed to be driven by an APOBEC-like RNA editing process. The current study investigated whether this phenomenon could be observed in datasets of other RNA viruses. Using a 5% divergence filter to infer directionality, 18 from 36 datasets of aligned coding region sequences from a diverse range of mammalian RNA viruses (including Picornaviridae, Flaviviridae, Matonaviridae, Caliciviridae and Coronaviridae) showed a >2-fold base composition normalised excess of C->U transitions compared to U->C (range 2.1x-7.5x), with a consistently observed favoured 5' U upstream context. The presence of genome scale RNA secondary structure (GORS) was the only other genomic or structural parameter significantly associated with C->U/U->C transition asymmetries by multivariable analysis (ANOVA), potentially reflecting RNA structure dependence of sites targeted for C->U mutations. Using the association index metric, C->U changes were specifically over-represented at phylogenetically uninformative sites, potentially paralleling extensive homoplasy of this transition reported in SARS-CoV-2. Although mechanisms remain to be functionally characterised, excess C->U substitutions accounted for 11-14% of standing sequence variability of structured viruses and may therefore represent a potent driver of their sequence diversification and longer-term evolution.
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Affiliation(s)
- Peter Simmonds
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - M. Azim Ansari
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
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62
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Bacus MG, Buenaventura SGC, Mamites AMC, Elizagaque HG, Labrador CC, Delfin FC, Eng MNJ, Lagare AP, Marquez GN, Murao LAE. Genome-based local dynamics of canine rabies virus epidemiology, transmission, and evolution in Davao City, Philippines, 2018-2019. INFECTION GENETICS AND EVOLUTION 2021; 92:104868. [PMID: 33878454 DOI: 10.1016/j.meegid.2021.104868] [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: 10/27/2020] [Revised: 04/01/2021] [Accepted: 04/13/2021] [Indexed: 11/19/2022]
Abstract
Rabies is a fatal zoonotic and neglected tropical disease caused by the rabies virus (RABV) and is associated with neuronal dysfunction and death, with dogs as the predominant carrier. The Philippines plans to eradicate rabies by 2022, but this is challenged with sub-optimal coverage of vaccination programs coupled with sustained transmission chains, making it unable to eradicate the disease. We investigated the dynamics of canine rabies in the highly urbanized Davao City of the Philippines and its neighboring localities by assessing genetic relationships, transmission patterns, selection pressure, and recombination events using the whole genome sequence of 49 RABV cases from June 2018 to May 2019, majority of which (46%) were from the district of Talomo, Davao City. Although phylogeographic clustering was observed, local variants also exhibited genetic sub-lineages. Phylogenetic and spatial transmission analysis provided evidence for intra- and inter-city transmission predominantly through the Talomo district of Davao City. Around 84% of the cases were owned dogs, but the genetic similiarity of RABVs from stray and owned dogs further alluded to the role of the former as transmission vectors. The high rate of improper vaccination among the affected dogs (80%) was also a likely contributor to transmission. The RABV population under Investigation is generally under strong purifying selection with no evidence of vaccine evasion due to the genetic homogeneity of viruses from vaccinated and improperly vaccinated dogs. However, some homologous recombination (HR) events were identified along the G and L genes, also predominantly associated with viruses from Talomo. The complementary findings on epidemiology, transmission, and recombination for Talomo suggest that high incidence areas can be seeds for virus dispersal and evolution. We recommend further Investigations on the possibility of HR in future large-scale genome studies. Finally, districts associated with these phenomena can be targeted for evidence-based local strategies that can help break RABV transmission chains and prevent emergence of novel strains in Davao City.
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Affiliation(s)
- Michael G Bacus
- Philippine Genome Center Mindanao, University of the Philippines Mindanao, Tugbok District, Mintal, Davao City, Philippines
| | - Sheryl Grace C Buenaventura
- Department of Biological Sciences and Environmental Studies, University of the Philippines Mindanao, Tugbok District, Mintal, Davao City, Philippines
| | - Allan Michael C Mamites
- Department of Biological Sciences and Environmental Studies, University of the Philippines Mindanao, Tugbok District, Mintal, Davao City, Philippines
| | - Hannah G Elizagaque
- Department of Biological Sciences and Environmental Studies, University of the Philippines Mindanao, Tugbok District, Mintal, Davao City, Philippines
| | - Christian C Labrador
- Philippine Genome Center Mindanao, University of the Philippines Mindanao, Tugbok District, Mintal, Davao City, Philippines
| | - Frederick C Delfin
- DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Quezon City, Philippines
| | - Ma Noreen J Eng
- Davao City Veterinary Office, Pichon St., Davao City, Philippines
| | - Arlene P Lagare
- Davao City Veterinary Office, Pichon St., Davao City, Philippines
| | - Gloria N Marquez
- Davao City Veterinary Office, Pichon St., Davao City, Philippines
| | - Lyre Anni E Murao
- Department of Biological Sciences and Environmental Studies, University of the Philippines Mindanao, Tugbok District, Mintal, Davao City, Philippines; Philippine Genome Center Mindanao, University of the Philippines Mindanao, Tugbok District, Mintal, Davao City, Philippines.
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63
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Ntumvi NF, Diffo JLD, Tamoufe U, Ndze VN, Takuo JM, Mouiche MMM, Nwobegahay J, LeBreton M, Gillis A, Rimoin AW, Schneider BS, Monagin C, McIver DJ, Joly DO, Wolfe ND, Rubin EM, Lange CE. Evaluation of bat adenoviruses suggests co-evolution and host roosting behaviour as drivers for diversity. Microb Genom 2021; 7:000561. [PMID: 33871330 PMCID: PMC8208681 DOI: 10.1099/mgen.0.000561] [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: 02/07/2020] [Accepted: 03/15/2021] [Indexed: 11/19/2022] Open
Abstract
Adenoviruses (AdVs) are diverse pathogens of humans and animals, with several dozen bat AdVs already identified. Considering that over 100 human AdVs are known, and the huge diversity of bat species, many bat AdVs likely remain undiscovered. To learn more about AdV prevalence, diversity and evolution, we sampled and tested bats in Cameroon using several PCR assays for viral and host DNA. AdV DNA was detected in 14 % of the 671 sampled animals belonging to 37 different bat species. There was a correlation between species roosting in larger groups and AdV DNA detection. The detected AdV DNA belonged to between 28 and 44 different, mostly previously unknown, mastadenovirus species. The novel isolates are phylogenetically diverse and while some cluster with known viruses, others appear to form divergent new clusters. The phylogenetic tree of novel and previously known bat AdVs does not mirror that of the various host species, but does contain structures consistent with a degree of virus-host co-evolution. Given that closely related isolates were found in different host species, it seems likely that at least some bat AdVs have jumped species barriers, probably in the more recent past; however, the tree is also consistent with such events having taken place throughout bat AdV evolution. AdV diversity was highest in bat species roosting in large groups. The study significantly increased the diversity of AdVs known to be harboured by bats, and suggests that host behaviours, such as roosting size, may be what limits some AdVs to one species rather than an inability of AdVs to infect other related hosts.
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Affiliation(s)
- Nkom F. Ntumvi
- Metabiota Cameroon Ltd, Yaoundé, Centre Region, Cameroon
| | | | - Ubald Tamoufe
- Metabiota Cameroon Ltd, Yaoundé, Centre Region, Cameroon
| | - Valantine Ngum Ndze
- Metabiota Cameroon Ltd, Yaoundé, Centre Region, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé, Yaoundé, Centre Region, Cameroon
| | | | | | | | | | | | | | - Bradley S. Schneider
- Metabiota Inc., San Francisco, CA, USA
- Etiologic, Oakland, CA, USA
- Pinpoint Science, San Francisco, CA, USA
| | - Corina Monagin
- Metabiota Inc., San Francisco, CA, USA
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA, USA
| | | | - Damien O. Joly
- Metabiota Inc, Nanaimo, British Columbia, Canada
- British Columbia Ministry of Environment and Climate Change Strategy, Victoria, British Columbia, Canada
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64
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McKee CD, Bai Y, Webb CT, Kosoy MY. Bats are key hosts in the radiation of mammal-associated Bartonella bacteria. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 89:104719. [PMID: 33444855 PMCID: PMC10915969 DOI: 10.1016/j.meegid.2021.104719] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 12/25/2022]
Abstract
Bats are notorious reservoirs of several zoonotic diseases and may be uniquely tolerant of infection among mammals. Broad sampling has revealed the importance of bats in the diversification and spread of viruses and eukaryotes to other animal hosts. Vector-borne bacteria of the genus Bartonella are prevalent and diverse in mammals globally and recent surveys have revealed numerous Bartonella lineages in bats. We assembled a sequence database of Bartonella strains, consisting of nine genetic loci from 209 previously characterized Bartonella lineages and 121 new cultured isolates from bats, and used these data to perform a comprehensive phylogenetic analysis of the Bartonella genus. This analysis included estimation of divergence dates using a molecular clock and ancestral reconstruction of host associations and geography. We estimate that Bartonella began infecting mammals 62 million years ago near the Cretaceous-Paleogene boundary. Additionally, the radiation of particular Bartonella clades correlate strongly to the timing of diversification and biogeography of mammalian hosts. Bats were inferred to be the ancestral hosts of all mammal-associated Bartonella and appear to be responsible for the early geographic expansion of the genus. We conclude that bats have had a deep influence on the evolutionary radiation of Bartonella bacteria and their spread to other mammalian orders. These results support a 'bat seeding' hypothesis that could explain similar evolutionary patterns in other mammalian parasite taxa. Application of such phylogenetic tools as we have used to other taxa may reveal the general importance of bats in the ancient diversification of mammalian parasites.
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Affiliation(s)
- Clifton D McKee
- Graduate Degree Program in Ecology, Colorado State University, 1021 Campus Delivery, Fort Collins, CO 80523, USA; Department of Biology, Colorado State University, 1878 Campus Delivery, Fort Collins, CO 80523, USA; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA.
| | - Ying Bai
- Bacterial Diseases Branch, Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, 3156 Rampart Road, Fort Collins, CO 80521, USA
| | - Colleen T Webb
- Graduate Degree Program in Ecology, Colorado State University, 1021 Campus Delivery, Fort Collins, CO 80523, USA; Department of Biology, Colorado State University, 1878 Campus Delivery, Fort Collins, CO 80523, USA
| | - Michael Y Kosoy
- KB One Health, LLC, 3244 Reedgrass Court, Fort Collins, CO 80521, USA
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65
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Pisano MB, Culasso ACA, Altabert N, Martínez Wassaf MG, Nates SV, González J, Contigiani MS, Campos R, Ré VE. Phylogeography and evolutionary history of hepatitis E virus genotype 3 in Argentina. Trans R Soc Trop Med Hyg 2021; 116:34-42. [PMID: 33739412 DOI: 10.1093/trstmh/trab044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/15/2021] [Accepted: 02/22/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Few studies about the evolutionary history of the hepatitis E virus (HEV) have been conducted. The aim of our work was to investigate and make inferences about the origin and routes of dispersion of HEV-3 in Argentina. METHODS Phylogenetic, coalescent and phylogeographic analyses were performed using a 322-bp ORF2 genomic fragment of all HEV-3 sequences with known date and place of isolation published at GenBank until May 2018 (n=926), including 16 Argentinian sequences (isolated from pigs, water and humans). RESULTS Phylogenetic analysis revealed two clades within HEV-3: abchij and efg. All Argentinian samples were grouped intermingled within clade 3abchij. The coalescent analysis showed that the most recent common ancestor for the clade 3abchij would have existed around the year 1967 (95% highest posterior density (HPD): 1963-1970). The estimated substitution rate was 1.01×10-2 (95%HPD: 9.3×10-3-1.09×10-2) substitutions/site/y, comparable with the rate previously described. The phylogeographic approach revealed a correspondence between phylogeny and place of origin for Argentinian samples, suggesting many HEV introductions in the country, probably from Europe and Japan. CONCLUSIONS This is the first evolutionary inference of HEV-3 that includes Argentinian strains, showing the circulation of many HEV-3 subtypes, obtained from different sources and places, with recent diversification processes. ACCESSION NUMBERS [KX812460], [KX812461], [KX812462], [KX812465], [KX812466], [KX812467], [KX812468], [KX812469].
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Affiliation(s)
- María B Pisano
- Instituto de Virología 'Dr J. M. Vanella', Facultad de Ciencias Médicas, Universidad Nacional de Córdoba. Enfermera Gordillo Gómez s/n. CP: 5016. Córdoba, Argentina
- Consejo Nacional de Investigaciones en Ciencia y Técnica (CONICET), Argentina
| | - Andrés C A Culasso
- Consejo Nacional de Investigaciones en Ciencia y Técnica (CONICET), Argentina
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires. Junín 954. CP: C1113 AAD. Ciudad Autónoma de Buenos Aires, Argentina
| | - Nancy Altabert
- Servicio de Hepatitis y Gastroenteritis, Departamento Virología, Laboratorio Nacional de Referencia INEI-ANLIS "Dr Carlos G. Malbrán". Vélez Sársfield 563. Buenos Aires, Argentina
| | - Maribel G Martínez Wassaf
- Laboratorio de Virología y Biología Molecular, LACE Laboratorios. Vélez Sársfield 528. CP: 5000. Córdoba, Argentina
| | - Silvia V Nates
- Instituto de Virología 'Dr J. M. Vanella', Facultad de Ciencias Médicas, Universidad Nacional de Córdoba. Enfermera Gordillo Gómez s/n. CP: 5016. Córdoba, Argentina
| | - Jorge González
- Servicio de Hepatitis y Gastroenteritis, Departamento Virología, Laboratorio Nacional de Referencia INEI-ANLIS "Dr Carlos G. Malbrán". Vélez Sársfield 563. Buenos Aires, Argentina
| | - Marta S Contigiani
- Instituto de Virología 'Dr J. M. Vanella', Facultad de Ciencias Médicas, Universidad Nacional de Córdoba. Enfermera Gordillo Gómez s/n. CP: 5016. Córdoba, Argentina
| | - Rodolfo Campos
- Consejo Nacional de Investigaciones en Ciencia y Técnica (CONICET), Argentina
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires. Junín 954. CP: C1113 AAD. Ciudad Autónoma de Buenos Aires, Argentina
| | - Viviana E Ré
- Instituto de Virología 'Dr J. M. Vanella', Facultad de Ciencias Médicas, Universidad Nacional de Córdoba. Enfermera Gordillo Gómez s/n. CP: 5016. Córdoba, Argentina
- Consejo Nacional de Investigaciones en Ciencia y Técnica (CONICET), Argentina
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66
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Montoya V, McLaughlin A, Mordecai GJ, Miller RL, Joy JB. Variable routes to genomic and host adaptation among coronaviruses. J Evol Biol 2021; 34:924-936. [PMID: 33751699 PMCID: PMC8242483 DOI: 10.1111/jeb.13771] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/19/2021] [Accepted: 01/25/2021] [Indexed: 12/19/2022]
Abstract
Natural selection operating on the genomes of viral pathogens in different host species strongly contributes to adaptation facilitating host colonization. Here, we analyse, quantify and compare viral adaptation in genomic sequence data derived from seven zoonotic events in the Coronaviridae family among primary, intermediate and human hosts. Rates of nonsynonymous (dN) and synonymous (dS) changes on specific amino acid positions were quantified for each open reading frame (ORF). Purifying selection accounted for 77% of all sites under selection. Diversifying selection was most frequently observed in viruses infecting the primary hosts of each virus and predominantly occurred in the orf1ab genomic region. Within all four intermediate hosts, diversifying selection on the spike gene was observed either solitarily or in combination with orf1ab and other genes. Consistent with previous evidence, pervasive diversifying selection on coronavirus spike genes corroborates the role this protein plays in host cellular entry, adaptation to new hosts and evasion of host cellular immune responses. Structural modelling of spike proteins identified a significantly higher proportion of sites for SARS‐CoV‐2 under positive selection in close proximity to sites of glycosylation relative to the other coronaviruses. Among human coronaviruses, there was a significant inverse correlation between the number of sites under positive selection and the estimated years since the virus was introduced into the human population. Abundant diversifying selection observed in SARS‐CoV‐2 suggests the virus remains in the adaptive phase of the host switch, typical of recent host switches. A mechanistic understanding of where, when and how genomic adaptation occurs in coronaviruses following a host shift is crucial for vaccine design, public health responses and predicting future pandemics.
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Affiliation(s)
- Vincent Montoya
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Angela McLaughlin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Bioinformatics Programme, University of British Columbia, Vancouver, BC, Canada
| | - Gideon J Mordecai
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Rachel L Miller
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Bioinformatics Programme, University of British Columbia, Vancouver, BC, Canada
| | - Jeffrey B Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Bioinformatics Programme, University of British Columbia, Vancouver, BC, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC, Canada
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67
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Resende PC, Delatorre E, Gräf T, Mir D, Motta FC, Appolinario LR, da Paixão ACD, Mendonça ACDF, Ogrzewalska M, Caetano B, Wallau GL, Docena C, dos Santos MC, de Almeida Ferreira J, Sousa Junior EC, da Silva SP, Fernandes SB, Vianna LA, Souza LDC, Ferro JFG, Nardy VB, Santos CA, Riediger I, do Carmo Debur M, Croda J, Oliveira WK, Abreu A, Bello G, Siqueira MM. Evolutionary Dynamics and Dissemination Pattern of the SARS-CoV-2 Lineage B.1.1.33 During the Early Pandemic Phase in Brazil. Front Microbiol 2021; 11:615280. [PMID: 33679622 PMCID: PMC7925893 DOI: 10.3389/fmicb.2020.615280] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/21/2020] [Indexed: 12/13/2022] Open
Abstract
A previous study demonstrates that most of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Brazilian strains fell in three local clades that were introduced from Europe around late February 2020. Here we investigated in more detail the origin of the major and most widely disseminated SARS-CoV-2 Brazilian lineage B.1.1.33. We recovered 190 whole viral genomes collected from 13 Brazilian states from February 29 to April 31, 2020 and combined them with other B.1.1 genomes collected globally. Our genomic survey confirms that lineage B.1.1.33 is responsible for a variable fraction of the community viral transmissions in Brazilian states, ranging from 2% of all SARS-CoV-2 genomes from Pernambuco to 80% of those from Rio de Janeiro. We detected a moderate prevalence (5-18%) of lineage B.1.1.33 in some South American countries and a very low prevalence (<1%) in North America, Europe, and Oceania. Our study reveals that lineage B.1.1.33 evolved from an ancestral clade, here designated B.1.1.33-like, that carries one of the two B.1.1.33 synapomorphic mutations. The B.1.1.33-like lineage may have been introduced from Europe or arose in Brazil in early February 2020 and a few weeks later gave origin to the lineage B.1.1.33. These SARS-CoV-2 lineages probably circulated during February 2020 and reached all Brazilian regions and multiple countries around the world by mid-March, before the implementation of air travel restrictions in Brazil. Our phylodynamic analysis also indicates that public health interventions were partially effective to control the expansion of lineage B.1.1.33 in Rio de Janeiro because its median effective reproductive number (R e ) was drastically reduced by about 66% during March 2020, but failed to bring it to below one. Continuous genomic surveillance of lineage B.1.1.33 might provide valuable information about epidemic dynamics and the effectiveness of public health interventions in some Brazilian states.
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Affiliation(s)
- Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Edson Delatorre
- Departamento de Biologia, Centro de Ciencias Exatas, Naturais e da Saude, Universidade Federal do Espirito Santo, Alegre, Brazil
| | - Tiago Gräf
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Daiana Mir
- Unidad de Genomica y Bioinformatica, Centro Universitario Regional del Litoral Norte, Universidad de la Republica, Salto, Uruguay
| | - Fernando Couto Motta
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Luciana Reis Appolinario
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Anna Carolina Dias da Paixão
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Ana Carolina da Fonseca Mendonça
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Maria Ogrzewalska
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | - Braulia Caetano
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
| | | | - Cássia Docena
- Instituto Aggeu Magalhaes, Fundação Oswaldo Cruz, Recife, Brazil
| | | | | | | | | | | | - Lucas Alves Vianna
- Laboratorio Central de Saude Publica do Estado Espirito Santo (LACEN-ES), Vitoria, Brazil
| | | | - Jean F. G. Ferro
- Laboratorio Central de Saude Publica de Alagoas (LACEN-AL), Maceio, Brazil
| | - Vanessa B. Nardy
- Laboratorio Central de Saude Publica da Bahia (LACEN-BA), Salvador, Brazil
| | - Cliomar A. Santos
- Laboratorio Central de Saude Publica de Sergipe (LACEN-SE), Aracaju, Brazil
| | - Irina Riediger
- Laboratorio Central de Saude Publica de Parana (LACEN-PR), Curitiba, Brazil
| | | | - Júlio Croda
- Fiocruz Mato Grosso do Sul, Campo Grande, Brazil
- Universidade Federal de Mato Grosso do Sul – UFMS, Campo Grande, Brazil
| | | | - André Abreu
- Coordenadoria Geral de Laboratorios – Ministério da Saude, Brazilia, Brazil
| | - Gonzalo Bello
- Laboratorio de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Marilda M. Siqueira
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), SARS-CoV-2 National Reference Laboratory for the Brazilian Ministry of Health (MoH) and Regional Reference Laboratory in Americas for the Pan-American Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
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68
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Bergner LM, Orton RJ, Broos A, Tello C, Becker DJ, Carrera JE, Patel AH, Biek R, Streicker DG. Diversification of mammalian deltaviruses by host shifting. Proc Natl Acad Sci U S A 2021; 118:e2019907118. [PMID: 33397804 PMCID: PMC7826387 DOI: 10.1073/pnas.2019907118] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Hepatitis delta virus (HDV) is an unusual RNA agent that replicates using host machinery but exploits hepatitis B virus (HBV) to mobilize its spread within and between hosts. In doing so, HDV enhances the virulence of HBV. How this seemingly improbable hyperparasitic lifestyle emerged is unknown, but it underpins the likelihood that HDV and related deltaviruses may alter other host-virus interactions. Here, we show that deltaviruses diversify by transmitting between mammalian species. Among 96,695 RNA sequence datasets, deltaviruses infected bats, rodents, and an artiodactyl from the Americas but were absent from geographically overrepresented Old World representatives of each mammalian order, suggesting a relatively recent diversification within the Americas. Consistent with diversification by host shifting, both bat and rodent-infecting deltaviruses were paraphyletic, and coevolutionary modeling rejected cospeciation with mammalian hosts. In addition, a 2-y field study showed common vampire bats in Peru were infected by two divergent deltaviruses, indicating multiple introductions to a single host species. One vampire bat-associated deltavirus was detected in the saliva of up to 35% of individuals, formed phylogeographically compartmentalized clades, and infected a sympatric bat, illustrating horizontal transmission within and between species on ecological timescales. Consistent absence of HBV-like viruses in two deltavirus-infected bat species indicated acquisitions of novel viral associations during the divergence of bat and human-infecting deltaviruses. Our analyses support an American zoonotic origin of HDV and reveal prospects for future cross-species emergence of deltaviruses. Given their peculiar life history, deltavirus host shifts will have different constraints and disease outcomes compared to ordinary animal pathogens.
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Affiliation(s)
- Laura M Bergner
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland;
- Medical Research Center-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland
| | - Richard J Orton
- Medical Research Center-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland
| | - Alice Broos
- Medical Research Center-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland
| | - Carlos Tello
- Association for the Conservation and Development of Natural Resources, 15037 Lima, Perú
- Yunkawasi, 15049 Lima, Perú
| | - Daniel J Becker
- Department of Biology, University of Oklahoma, Norman, OK 73019
| | - Jorge E Carrera
- Departamento de Mastozoología, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Lima 15081, Perú
- Programa de Conservación de Murciélagos de Perú, Piura 20001, Perú
| | - Arvind H Patel
- Medical Research Center-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland
| | - Roman Biek
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland
| | - Daniel G Streicker
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland;
- Medical Research Center-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland
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Deng Q, Shi M, Li Q, Wang P, Li M, Wang W, Gao Y, Li H, Lin L, Huang T, Wei P. Analysis of the evolution and transmission dynamics of the field MDV in China during the years 1995-2020, indicating the emergence of a unique cluster with the molecular characteristics of vv+ MDV that has become endemic in southern China. Transbound Emerg Dis 2020; 68:3574-3587. [PMID: 33354907 DOI: 10.1111/tbed.13965] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/19/2020] [Accepted: 12/20/2020] [Indexed: 01/23/2023]
Abstract
Marek's disease (MD) continues to threaten the sustainability of the world poultry industry. In this study, the sequences of the meq gene of 220 MDV strains isolated during the years 1964-2020 were analysed, including 50 from our group plus 170 isolates from the GenBank. Analyses, using phylogenetic trees, amino acid (aa)-mutation screening, evolutionary studies and transmission dynamics were all performed. All strains were divided into two clusters (Clusters 1 and 2), and Cluster 1 includes the mild strains, the vaccine strains and the foreign virulent strains, while Cluster 2 was dominated by the Chinese field strains. Our study identified that the Chinese field strains in Cluster 2 during the years 1995-2020 likely originated in the 1980s from abroad, and the estimated genetic diversity of these strains experienced two growth phases in the years 2005-2007.5 and 2015-2017. Viral phylogeography identified 3 major geographic provincial regions for the Chinese field strains of Cluster 2: the Northeastern Region (Jilin, Liaoning and Heilongjiang), the East-central Region (Henan, Shandong and Jiangsu) and the Southern Region (Guangxi, Guangdong and Yunnan). The spread of Northeastern strains to East-central chicken flocks and the further spread from Guangxi to Guangdong are strongly indicated. The emergence of the mutations A88T and Q93R together in the Southern strains during the years 2017-2020 with molecular characteristics of vv+ MDV were also found later than those in the Northern strains. Overall, the Chinese field strains in Cluster 2 in southern China in recent years have been rapidly evolving. Guangxi Province has become an epicentre for these viruses and the chicken flocks in the Southern region have been facing the adverse effects of the emerging vv+ MDV.
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Affiliation(s)
- Qiaomu Deng
- Institute for Poultry Science and Health, Guangxi University, Nanning, China
| | - Mengya Shi
- Institute for Poultry Science and Health, Guangxi University, Nanning, China
| | - Qiuhong Li
- Institute for Poultry Science and Health, Guangxi University, Nanning, China
| | - Peikun Wang
- Institute of Microbe and Host Health, Linyi University, Linyi, China
| | - Min Li
- Institute for Poultry Science and Health, Guangxi University, Nanning, China
| | - Weiwei Wang
- Institute for Poultry Science and Health, Guangxi University, Nanning, China
| | - Yanli Gao
- Institute for Poultry Science and Health, Guangxi University, Nanning, China
| | - Haijuan Li
- Institute for Poultry Science and Health, Guangxi University, Nanning, China
| | - Lulu Lin
- Institute for Poultry Science and Health, Guangxi University, Nanning, China
| | - Teng Huang
- Institute for Poultry Science and Health, Guangxi University, Nanning, China
| | - Ping Wei
- Institute for Poultry Science and Health, Guangxi University, Nanning, China
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70
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Dahiya SS, Subramaniam S, Biswal JK, Das B, Prusty BR, Ali SZ, Khulape SA, Mohapatra JK, Singh RK. Genetic characterization of foot-and-mouth disease virus serotype O isolates collected during 2014-2018 revealed dominance of O/ME-SA/Ind2001e and the emergence of a novel lineage in India. Transbound Emerg Dis 2020; 68:3498-3508. [PMID: 33305514 DOI: 10.1111/tbed.13954] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/30/2020] [Accepted: 12/08/2020] [Indexed: 11/30/2022]
Abstract
Foot-and-mouth disease (FMD) is endemic in India with a preponderance of outbreaks caused by FMD virus (FMDV) serotype O. Out of the 11 global topotypes of serotype O, only ME-SA topotype has been reported in the country so far. Lineage O/ME-SA/Ind2001 and O/ME-SA/PanAsia are documented as the most dominant ones in terms of the number of outbreaks caused by them. To understand the distribution of topotype/lineages in India and their antigenic behaviour during the year 2014-2018, a total of 286 FMDV serotype O viral isolates were sequence determined at the VP1 region, and 109 isolates were characterized antigenically. All the isolates grouped in the ME-SA topotype, being distributed in lineage O/ME-SA/Ind2001 (within sub-lineages O/ME-SA/Ind2001d and O/ME-SA/Ind2001e), and a new group designated here as O/ME-SA/2018 cluster. The sub-lineage O/ME-SA/Ind2001e reported for the first time in India during the year 2015, replaced sub-lineage O/ME-SA/Ind2001d gradually, which was dominating since 2008. During the years 2014-2018, the sub-lineage O/ME-SA/Ind2001e was found to be the most predominant one whose mean evolutionary rate was observed to be faster than that of the sub-lineage O/ME-SA/Ind2001d. The codon sites 45 and 85 of VP1 were found to be under diversifying selection in a large proportion of trees. The common ancestor predicted for sub-lineages O/ME-SA/Ind2001e and O/ME-SA/2018 dates back to 2012 and 2016, respectively. The sustenance and spread of the new O/ME-SA/2018 cluster need to be assessed by continued surveillance. The Indian vaccine strain O/INDR2/1975 was found to provide adequate antigenic coverage to the emerging and prevalent serotype O lineages. The trait association tests showed frequent virus exchange among different states, which could be an important confounder in the region-specific assessment of effectiveness of FMD control programme.
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Affiliation(s)
- Shyam Singh Dahiya
- ICAR-Directorate of Foot-and-Mouth Disease, Nainital, Uttarakhand, India
| | | | | | - Biswajit Das
- ICAR-Directorate of Foot-and-Mouth Disease, Nainital, Uttarakhand, India
| | | | - Syed Zeeshan Ali
- ICAR-Directorate of Foot-and-Mouth Disease, Nainital, Uttarakhand, India
| | | | | | - Raj Kumar Singh
- ICAR-Directorate of Foot-and-Mouth Disease, Nainital, Uttarakhand, India
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71
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Global emergence and evolutionary dynamics of bluetongue virus. Sci Rep 2020; 10:21677. [PMID: 33303862 PMCID: PMC7729867 DOI: 10.1038/s41598-020-78673-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 11/24/2020] [Indexed: 12/16/2022] Open
Abstract
Bluetongue virus (BTV) epidemics are responsible for worldwide economic losses of up to US$ 3 billion. Understanding the global evolutionary epidemiology of BTV is critical in designing intervention programs. Here we employed phylodynamic models to quantify the evolutionary characteristics, spatiotemporal origins, and multi-host transmission dynamics of BTV across the globe. We inferred that goats are the ancestral hosts for BTV but are less likely to be important for cross-species transmission, sheep and cattle continue to be important for the transmission and maintenance of infection between other species. Our models pointed to China and India, countries with the highest population of goats, as the likely ancestral country for BTV emergence and dispersal worldwide over 1000 years ago. However, the increased diversification and dispersal of BTV coincided with the initiation of transcontinental livestock trade after the 1850s. Our analysis uncovered important epidemiological aspects of BTV that may guide future molecular surveillance of BTV.
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Yamashita-Kawanishi N, Chambers JK, Uchida K, Tobari Y, Yoshimura H, Yamamoto M, Yumoto N, Aoki H, Sugiura K, Higuchi T, Saito S, Haga T. Genomic characterisation of bovine papillomavirus types 1 and 2 identified in equine sarcoids in Japan. Equine Vet J 2020; 53:1199-1209. [PMID: 33300145 DOI: 10.1111/evj.13398] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 09/07/2020] [Accepted: 11/26/2020] [Indexed: 11/29/2022]
Abstract
BACKGROUND Bovine papillomavirus types 1 and 2 (BPV1/2) infection in horses has been associated with the development of equine sarcoids. Previous findings revealed the presence of sarcoid-associated BPV sequence variants that have been proposed as a key factor of cross-species infection in horses. To verify this hypothesis, sarcoid-associated BPV variants should be identified regardless of geographic location. OBJECTIVES Sequence analyses of BPV1/2 derived from both horses and cattle were conducted to clarify the sarcoid-associated sequence variants. The aim of this study was to clarify the correlation between BPV phylogeny and the geographic origin/host species. STUDY DESIGN Cross-sectional study. METHODS Conventional PCR to detect BPV1/2 was performed with genomic DNA extracted from equine sarcoid (n = 10) and bovine papilloma (n = 10) samples collected in Japan. Direct sequencing results were compared between equine and bovine (equine/bovine)-derived BPV to identify sarcoid-associated variants of two early regions (E2, E5), one late region (L1) and the long control region (LCR). Phylogenetic and phylogeny-trait correlation were analysed using Bayesian Markov chain Monte Carlo (MCMC) method and Bayesian tip-association significance testing (BaTS). RESULTS Seven BPV1 and three BPV2 were identified from equine sarcoids using PCR and direct sequencing. Sequence analysis of equine/bovine-derived samples showed no sarcoid-associated variants in four regions (E2, E5, L1 and LCR) of either BPV1 or BPV2. The phylogenetic tree of BPV1 E2, L1 and LCR tended to cluster within its geographic origins. BaTS analysis demonstrated that BPV1 sequence variability may be due to the geographic origin rather than host species difference. MAIN LIMITATIONS There was a limitation in sample numbers. CONCLUSIONS This study supports the geographic-specific hypothesis of sequence variability, suggesting that BPV1 is shared between local equids and bovids. However, more extensively collected sequences worldwide and functional evaluations are needed to verify the geographic-specific sequence variability of BPV1/2 between equine- and bovine-derived sequence.
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Affiliation(s)
- Nanako Yamashita-Kawanishi
- Division of Infection Control and Disease Prevention, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - James K Chambers
- Laboratory of Veterinary Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazuyuki Uchida
- Laboratory of Veterinary Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yumiko Tobari
- Department of Applied Science, Faculty of Veterinary Science, School of Veterinary Nursing and Technology, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Hisashi Yoshimura
- Department of Applied Science, Faculty of Veterinary Science, School of Veterinary Nursing and Technology, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Masami Yamamoto
- Department of Applied Science, Faculty of Veterinary Science, School of Veterinary Nursing and Technology, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Norio Yumoto
- Department of Applied Science, Faculty of Veterinary Science, School of Veterinary Nursing and Technology, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Hiroshi Aoki
- Department of Basic Science, Faculty of Veterinary Science, School of Veterinary Nursing and Technology, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Katsuaki Sugiura
- Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Tohru Higuchi
- Mitsuishi Animal Medical Center, Hokkaido South Agricultural Mutual Aid Association, Hokkaido, Japan
| | | | - Takeshi Haga
- Division of Infection Control and Disease Prevention, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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Peng X, Xu Y, Wu N. Beijing as the hub of CRF07_BC transmission from the intravenous drug users to men who have sex with men in China. AIDS Res Hum Retroviruses 2020:AID.2020.0147. [PMID: 33287623 DOI: 10.1089/aid.2020.0147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
AIDS Research and Human Retroviruses officially retracts the Instant Online/Just Accepted version of the article entitled, "Beijing as the hub of CRF07_BC transmission from the intravenous drug users to men who have sex with men in China" (epub 7 Dec 2020; doi.org/10.1089/aid.2020.0147). A technical issue caused the unedited, accepted version to post online before all plagiarism checks were finalized. Those checks determined that there was too much duplication from previously published sources which prevented the continuance to final publication. The technical issue that caused the premature posting has since been corrected. AIDS Research and Human Retroviruses and its Publisher are committed to upholding the standards of scientific publishing and the community it serves. BACKGROUND The HIV-1 CRF07_BC strain has been increasing in frequency in China, is now the major recombination subtype in the men who have sex with men (MSM) population. However, to date, the evolutionary history of CRF07_BC in MSM in China has not been explored in greater detail. METHODS All available partial gag, pol and env segments of CRF07_BC were obtained from the Los Alamos HIV database. We performed phylogenetic analysis for these fragments by using the Bayesian Markov Chain Monte Carlo method, as implemented in BEAST. We estimated the history of viral migration between different areas over time using the discrete Bayesian phylogeographical method. RESULTS Spatial reconstruction showed that Yunnan had the highest root state posterior probability (0.89 in pol, 0.60 in gag, 0.87 in env). The virus migrated from Yunnan to Beijing in 1990s through intravenous drug users (IDU). The highest root state posterior probability of MSM cluster is Beijing (0.93 in pol, 0.90 in gag and 0.37 in env). In the beginning of 2000s, Beijing became the primary epicenter as CRF07_BC had expanded their geographical distribution to many provinces in China in MSM population. Guangdong and Shanghai were secondary epicenters, with a large extent of viruses. CONCLUSIONS This study highlighted the spatial and temporal spread of CRF07_BC in MSM population in China. It revealed that Beijing was the hub of CRF07_BC transmission from IDU to MSM in China.
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Affiliation(s)
- Xiaorong Peng
- Zhejiang University, 12377, 79 qingchun Road, Hangzhou, China, 310058;
| | - Yufan Xu
- Zhejiang University, 12377, Hangzhou, Zhejiang, China;
| | - Nanping Wu
- The First Affiliated Hospital, School of Medicine, Zhejiang University, No.79, Qingchun Road, Hangzhou, Zhejiang, China;
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Han Z, Song Y, Xiao J, Jiang L, Huang W, Wei H, Li J, Zeng H, Yu Q, Li J, Yu D, Zhang Y, Li C, Zhan Z, Shi Y, Xiong Y, Wang X, Ji T, Yang Q, Zhu S, Yan D, Xu W, Zhang Y. Genomic epidemiology of coxsackievirus A16 in mainland of China, 2000-18. Virus Evol 2020; 6:veaa084. [PMID: 33343924 PMCID: PMC7733612 DOI: 10.1093/ve/veaa084] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Hand, foot, and mouth disease (HFMD), which is a frequently reported and concerning disease worldwide, is a severe burden on societies globally, especially in the countries of East and Southeast Asia. Coxsackievirus A16 (CV-A16) is one of the most important causes of HFMD and a severe threat to human health, especially in children under 5 years of age. To investigate the epidemiological characteristics, spread dynamics, recombinant forms (RFs), and other features of CV-A16, we leveraged the continuous surveillance data of CV-A16-related HFMD cases collected over an 18-year period. With the advent of the EV-A71 vaccine since 2016, which targeted the EV-A71-related HFMD cases, EV-A71-related HFMD cases decreased dramatically, whereas the CV-A16-related HFMD cases showed an upward trend from 2017 to October 2019. The CV-A16 strains observed in this study were genetically related and widely distributed in the mainland of China. Our results show that three clusters (B1a-B1c) existed in the mainland of China and that the cluster of B1b dominates the diffusion of CV-A16 in China. We found that eastern China played a decisive role in seeding the diffusion of CV-A16 in China, with a more complex and variant transmission trend. Although EV-A71 vaccine was launched in China in 2016, it did not affect the genetic diversity of CV-A16, and its genetic diversity did not decline, which confirmed the epidemiological surveillance trend of CV-A16. Two discontinuous clusters (2000-13 and 2014-18) were observed in the full-length genome and arranged along the time gradient, which revealed the reason why the relative genetic diversity of CV-A16 increased and experienced more complex fluctuation model after 2014. In addition, the switch from RFs B (RF-B) and RF-C co-circulation to RF-D contributes to the prevalence of B1b cluster in China after 2008. The correlation between genotype and RFs partially explained the current prevalence of B1b. This study provides unprecedented full-length genomic sequences of CV-A16 in China, with a wider geographic distribution and a long-term time scale. The study presents valuable information about CV-A16, aimed at developing effective control strategies, as well as a call for a more robust surveillance system, especially in the Asia-Pacific region.
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Affiliation(s)
- Zhenzhi Han
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, NHC Key Laboratory of Biosafety, NHC Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China
| | - Yang Song
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, NHC Key Laboratory of Biosafety, NHC Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China
| | - Jinbo Xiao
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, NHC Key Laboratory of Biosafety, NHC Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China
| | - Lili Jiang
- Yunnan Center for Disease Control and Prevention, Kunming, Yunnan Province, People's Republic of China
| | - Wei Huang
- Chongqing Center for Disease Control and Prevention, Chongqing City, People's Republic of China
| | - Haiyan Wei
- Henan Center for Disease Control and Prevention, Zhengzhou, Henan Province, People's Republic of China
| | - Jie Li
- Beijing Center for Disease Control and Prevention, Beijing City, People's Republic of China
| | - Hanri Zeng
- Guangdong Center for Disease Control and Prevention, Guangzhou, Guangdong Province, People's Republic of China
| | - Qiuli Yu
- Hebei Center for Disease Control and Prevention, Shijiazhuang, Hebei Province, People's Republic of China
| | - Jiameng Li
- Tianjin Center for Disease Control and Prevention, Tianjin City, People's Republic of China
| | - Deshan Yu
- Gansu Center for Disease Control and Prevention, Lanzhou, Gansu Province, People's Republic of China
| | - Yanjun Zhang
- Zhejiang Center for Disease Control and Prevention, Hangzhou, Zhejiang Province, People's Republic of China
| | - Chonghai Li
- Qinghai Center for Disease Control and Prevention, Xining, Qinghai Province, People's Republic of China
| | - Zhifei Zhan
- Hunan Center for Disease Control and Prevention, Changsha, Hunan Province, People's Republic of China
| | - Yonglin Shi
- Anhui Center for Disease Control and Prevention, Hefei, Anhui Province, People's Republic of China
| | - Ying Xiong
- Jiangxi Center for Disease Control and Prevention, Nanchang, Jiangxi Province, People's Republic of China
| | - Xianjun Wang
- Shandong Center for Disease Control and Prevention, Jinan, Shandong Province, People's Republic of China
| | - Tianjiao Ji
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, NHC Key Laboratory of Biosafety, NHC Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China
| | - Qian Yang
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, NHC Key Laboratory of Biosafety, NHC Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China
| | - Shuangli Zhu
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, NHC Key Laboratory of Biosafety, NHC Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China
| | - Dongmei Yan
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, NHC Key Laboratory of Biosafety, NHC Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China
| | - Wenbo Xu
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, NHC Key Laboratory of Biosafety, NHC Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei Province, People's Republic of China
| | - Yong Zhang
- WHO WPRO Regional Polio Reference Laboratory and National Laboratory for Poliomyelitis, NHC Key Laboratory of Biosafety, NHC Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei Province, People's Republic of China
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75
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Unraveling the Global Phylodynamic and Phylogeographic Expansion of Mycoplasma gallisepticum: Understanding the Origin and Expansion of This Pathogen in Ecuador. Pathogens 2020; 9:pathogens9090674. [PMID: 32825097 PMCID: PMC7557814 DOI: 10.3390/pathogens9090674] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 07/31/2020] [Accepted: 08/18/2020] [Indexed: 12/17/2022] Open
Abstract
Mycoplasma gallisepticum (MG) is among the most significant problems in the poultry industry worldwide, representing a serious threat to international trade. Despite the fact that the mgc2 gene has been widely used for diagnostic and molecular characterization purposes, there is a lack of evidence supporting the reliability of this gene as a marker for molecular epidemiology approaches. Therefore, the current study aimed to assess the accuracy of the mgc2 gene for phylogenetic, phylodynamic, and phylogeographic evaluations. Furthermore, the global phylodynamic expansion of MG is described, and the origin and extension of the outbreak caused by MG in Ecuador were tracked and characterized. The results obtained strongly supported the use of the mgc2 gene as a reliable phylogenetic marker and accurate estimator for the temporal and phylogeographic structure reconstruction of MG. The phylodynamic analysis denoted the failures in the current policies to control MG and highlighted the imperative need to implement more sensitive methodologies of diagnosis and more efficient vaccines. Framed in Ecuador, the present study provides the first piece of evidence of the circulation of virulent field MG strains in Ecuadorian commercial poultry. The findings derived from the current study provide novel and significant insights into the origin, diversification, and evolutionary process of MG globally.
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Gianella S, Chaillon A, Chun TW, Sneller MC, Ignacio C, Vargas-Meneses MV, Caballero G, Ellis RJ, Kovacs C, Benko E, Huibner S, Kaul R. HIV RNA Rebound in Seminal Plasma after Antiretroviral Treatment Interruption. J Virol 2020; 94:e00415-20. [PMID: 32434884 PMCID: PMC7375368 DOI: 10.1128/jvi.00415-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/11/2020] [Indexed: 12/12/2022] Open
Abstract
If strategies currently in development succeed in eradicating HIV reservoirs in peripheral blood and lymphoid tissues, residual sources of virus may remain in anatomic compartments. Paired blood and semen samples were collected from 12 individuals enrolled in a randomized, double-blind, placebo-controlled therapeutic vaccine clinical trial in people with HIV (PWH) who began antiretroviral therapy (ART) during acute or early infection (ClinicalTrials registration no. NCT01859325). After the week 56 visit (postintervention), all participants interrupted ART. At the first available time points after viral rebound, we sequenced HIV-1 env (C2-V3), gag (p24), and pol (reverse transcriptase) regions amplified from cell-free HIV RNA in blood and seminal plasma using the MiSeq Illumina platform. Comprehensive sequence and phylogenetic analyses were performed to evaluate viral population structure, compartmentalization, and viral diversity in blood and seminal plasma. Compared to that in blood, HIV RNA rebound in semen occurred significantly later (median of 66 versus 42 days post-ART interruption, P < 0.01) and reached lower levels (median 164 versus 16,090 copies/ml, P < 0.01). Three of five participants with available sequencing data presented compartmentalized viral rebound between blood and semen in one HIV coding region. Despite early ART initiation, HIV RNA molecular diversity was higher in semen than in blood in all three coding regions for most participants. Higher HIV RNA molecular diversity in the genital tract (compared to that in blood plasma) and evidence of compartmentalization illustrate the distinct evolutionary dynamics between these two compartments after ART interruption. Future research should evaluate whether the genital compartment might contribute to viral rebound in some PWH interrupting ART.IMPORTANCE To cure HIV, we likely need to target the reservoirs in all anatomic compartments. Here, we used sophisticated statistical and phylogenetic methods to analyze blood and semen samples collected from 12 persons with HIV who began antiretroviral therapy (ART) during very early HIV infection and who interrupted their ART as part of a clinical trial. First, we found that HIV RNA rebound in semen occurred significantly later and reached lower levels than in blood. Second, we found that the virus in semen was genetically different in some participants compared to that in blood. Finally, we found increased HIV RNA molecular diversity in semen compared to that in blood in almost all study participants. These data suggest that the HIV RNA populations emerging from the genital compartment after ART interruption might not be the same as those emerging from blood plasma. Future research should evaluate whether the genital compartment might contribute to viral rebound in some people with HIV (PWH) interrupting ART.
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Affiliation(s)
- Sara Gianella
- University of California, San Diego, La Jolla, California, USA
| | | | - Tae-Wook Chun
- National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Michael C Sneller
- National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | | | | | - Gemma Caballero
- University of California, San Diego, La Jolla, California, USA
| | - Ronald J Ellis
- University of California, San Diego, La Jolla, California, USA
| | - Colin Kovacs
- Maple Leaf Medical Clinic, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Erika Benko
- Maple Leaf Medical Clinic, Toronto, Ontario, Canada
| | - Sanja Huibner
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Rupert Kaul
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
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Kamau E, Otieno JR, Murunga N, Oketch JW, Ngoi JM, de Laurent ZR, Mwema A, Nyiro JU, Agoti CN, Nokes DJ. Genomic epidemiology and evolutionary dynamics of respiratory syncytial virus group B in Kilifi, Kenya, 2015-17. Virus Evol 2020; 6:veaa050. [PMID: 32913665 PMCID: PMC7474930 DOI: 10.1093/ve/veaa050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Respiratory syncytial virus (RSV) circulates worldwide, occurring seasonally in communities, and is a leading cause of acute respiratory illness in young children. There is paucity of genomic data from purposively sampled populations by which to investigate evolutionary dynamics and transmission patterns of RSV. Here we present an analysis of 295 RSV group B (RSVB) genomes from Kilifi, coastal Kenya, sampled from individuals seeking outpatient care in nine health facilities across a defined geographical area (∼890 km2), over two RSV epidemics between 2015 and 2017. RSVB diversity was characterized by multiple virus introductions into the area and co-circulation of distinct genetic clusters, which transmitted and diversified locally with varying frequency. Increase in relative genetic diversity paralleled seasonal virus incidence. Importantly, we identified a cluster of viruses that emerged in the 2016/17 epidemic, carrying distinct amino-acid signatures including a novel nonsynonymous change (K68Q) in antigenic site ∅ in the Fusion protein. RSVB diversity was additionally marked by signature nonsynonymous substitutions that were unique to particular genomic clusters, some under diversifying selection. Our findings provide insights into recent evolutionary and epidemiological behaviors of RSVB, and highlight possible emergence of a novel antigenic variant, which has implications on current prophylactic strategies in development.
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Affiliation(s)
- Everlyn Kamau
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - James R Otieno
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Nickson Murunga
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - John W Oketch
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Joyce M Ngoi
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Zaydah R de Laurent
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Anthony Mwema
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Joyce U Nyiro
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Charles N Agoti
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.,School of Health and Human Sciences, Pwani University, Kilifi, Kenya
| | - D James Nokes
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.,School of Life Sciences and Zeeman Institute (SBIDER), University of Warwick, Coventry, UK
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78
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Peláez A, McLeish MJ, Paswan RR, Dubay B, Fraile A, García-Arenal F. Ecological fitting is the forerunner to diversification in a plant virus with broad host range. J Evol Biol 2020; 34:1917-1931. [PMID: 32618008 DOI: 10.1111/jeb.13672] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 04/23/2020] [Accepted: 06/24/2020] [Indexed: 11/29/2022]
Abstract
The evolution and diversification of ssRNA plant viruses are often examined under reductionist conditions that ignore potentially much wider biotic interactions. The host range of a plant virus is central to interactions at higher levels that are organized by both fitness and ecological criteria. Here we employ a strategy to minimize sampling biases across distinct plant communities and combine it with a high-throughput sequencing approach to examine the influence of four habitats on the evolution of Watermelon mosaic virus (WMV). Local, regional and global levels of genetic diversity that correspond to spatial and temporal extents are used to infer haplotype relationships using network and phylogenetic approaches. We find that the incidence and genetic diversity of WMV were structured significantly by host species and habitat type. A single haplotype that infected 11 host species of a total of 24 showed that few constraints on host species use exist in the crop communities. When the evolution of WMV was examined at broader levels of organization, we found variation in genetic diversity and contrasting host use footprints that broadly corresponded to habitat effects. The findings demonstrated that nondeterministic ecological factors structured the genetic diversity of WMV. Habitat-driven constraints underlie host use preferences.
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Affiliation(s)
- Adrián Peláez
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, Madrid, Spain
| | - Michael J McLeish
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, Madrid, Spain
| | - Ricky R Paswan
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, Madrid, Spain
| | - Bhumika Dubay
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, Madrid, Spain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, Madrid, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, Madrid, Spain
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79
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Bradshaw D, Vasylyeva TI, Davis C, Pybus OG, Thézé J, Thomson EC, Martinello M, Matthews GV, Burholt R, Gilleece Y, Cooke GS, Page EE, Waters L, Nelson M. Transmission of hepatitis C virus in HIV-positive and PrEP-using MSM in England. J Viral Hepat 2020; 27:721-730. [PMID: 32115809 DOI: 10.1111/jvh.13286] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 12/12/2019] [Accepted: 02/18/2020] [Indexed: 12/14/2022]
Abstract
We sought to characterize risk factors and patterns of HCV transmission amongst men who have sex with men (MSM). MSM with recently acquired HCV (AHCV) were prospectively recruited ('clinic cohort') between January and September 2017. Clinical data and risk behaviours were identified and blood obtained for HCV whole genome sequencing. Phylogenetic analyses were performed, using sequences from this cohort and two other AHCV cohorts, to identify transmission clusters. Sixteen (40.0%) men in the clinic cohort were HIV-negative MSM. HIV-negative MSM were younger than HIV-positive MSM; most (81.3%) had taken HIV PrEP in the preceding year. Eighteen men (45.0%) reported injection drug use; most (34, 85.0%) reported noninjection drug use in the last year. Most in both groups reported condomless anal sex, fisting and sex in a group environment. Few (7, 17.5%) men thought partners may have had HCV. There were 52 sequences in the HCV genotype 1a phylogeny, 18 from the clinic cohort and 34 from other AHCV cohorts; 47 (90.4%) clustered with ≥1 other sequence. There were 7 clusters of 2-27 sequences; 6 clusters contained HIV-negative and HIV-positive MSM and 1 cluster only HIV-positive MSM. Four of these clusters were part of larger clusters first described in 2007. PrEP-using MSM are at risk of HCV, sharing similar risk factors to HIV-positive MSM. Phylogenetics highlights that PrEP-using and HIV-positive MSM are involved in the same HCV transmission networks. Few men demonstrated HCV awareness and risk reduction strategies should be expanded.
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Affiliation(s)
- Daniel Bradshaw
- Department of HIV and Sexual Health, Chelsea and Westminster Hospital NHS Foundation Trust, London, UK
| | | | - Chris Davis
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Julien Thézé
- Department of Zoology, University of Oxford, Oxford, UK
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Gail V Matthews
- Kirby Institute, University of New South Wales, Sydney, Australia
| | - Ruth Burholt
- Brighton and Sussex University Hospitals NHS Trust, Brighton, UK
| | - Yvonne Gilleece
- Brighton and Sussex University Hospitals NHS Trust, Brighton, UK
| | | | - Emma E Page
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | | | - Mark Nelson
- Department of HIV and Sexual Health, Chelsea and Westminster Hospital NHS Foundation Trust, London, UK
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80
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Mazzetto E, Bortolami A, Fusaro A, Mazzacan E, Maniero S, Vascellari M, Beato MS, Schiavon E, Chiapponi C, Terregino C, Monne I, Bonfante F. Replication of Influenza D Viruses of Bovine and Swine Origin in Ovine Respiratory Explants and Their Attachment to the Respiratory Tract of Bovine, Sheep, Goat, Horse, and Swine. Front Microbiol 2020; 11:1136. [PMID: 32523585 PMCID: PMC7261881 DOI: 10.3389/fmicb.2020.01136] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 05/05/2020] [Indexed: 12/30/2022] Open
Abstract
Bovine is considered the main reservoir of influenza D virus (IDV), however, low levels of seropositivity in other farmed species suggest a wide range of potential hosts. Nevertheless, it is not clear whether this scenario is the result of rare spillover events upon contact with bovines, or a lack of adaptation of IDV to these hosts. Among these species, sheep represents a crucial component of the rural economy in many developing countries, but little is known about its role in the ecology of the disease. To evaluate the susceptibility of sheep to IDV viruses of different origin, we used ovine respiratory tissues as an ex vivo model and investigated the infective phenotype of two IDV strains isolated from either bovine (IDV-BOV) or swine (IDV-SW). For translatability purposes, we included a parainfluenza type 3 virus, as positive control, given its known respiratory tropism in sheep. We performed a timed evaluation of the viral infectivity, cell tropism and the associated histopathology, by means of tissue culture infectious dose assays on supernatants and histological/immunohistochemical analyses on explanted tissues, respectively. To further investigate differences in the phenotype of these two strains and to identify the potential targets of replication in the most commonly land-based farmed mammalian species, we carried out virus binding assays on histological sections of the respiratory tract of bovine, caprine, ovine, horse and swine. Our results demonstrated that IDV successfully replicates in nasal, tracheal and lung ovine tissues, suggesting a moderate susceptibility of this species to IDV infection. Interestingly, despite the high genetic identity of these strains, IDV- BOV consistently replicated to higher titers than IDV-SW in all respiratory tracts, suggesting IDV viruses might display considerable levels of variability in their phenotype when crossing the species barrier. Virus binding assays confirmed a superior affinity of the IDV viruses for the bovine upper respiratory tract, and a preference for the pharyngeal epithelium of small ruminants, indicating possible targets to improve the sensitivity of virological sampling for diagnostic and post-mortem purposes. Further pathogenesis and cross-species transmission studies will be necessary to elucidate the ecology of IDV and eventually allow the design of cost-effective surveillance strategies.
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Affiliation(s)
- Eva Mazzetto
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Alessio Bortolami
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Alice Fusaro
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Elisa Mazzacan
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Silvia Maniero
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Marta Vascellari
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Maria Serena Beato
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Eliana Schiavon
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Chiara Chiapponi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Brescia, Italy
| | - Calogero Terregino
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Isabella Monne
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Francesco Bonfante
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
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81
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Chen X, Adam DC, Chughtai AA, Stelzer-Braid S, Scotch M, MacIntyre CR. The Phylogeography of MERS-CoV in Hospital Outbreak-Associated Cases Compared to Sporadic Cases in Saudi Arabia. Viruses 2020; 12:E540. [PMID: 32422937 PMCID: PMC7290704 DOI: 10.3390/v12050540] [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: 04/14/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 12/30/2022] Open
Abstract
This study compared the phylogeography of MERS-CoV between hospital outbreak-associated cases and sporadic cases in Saudi Arabia. We collected complete genome sequences from human samples in Saudi Arabia and data on the multiple risk factors of human MERS-CoV in Saudi Arabia reported from 2012 to 2018. By matching each sequence to human cases, we identified isolates as hospital outbreak-associated cases or sporadic cases. We used Bayesian phylogenetic methods including temporal, discrete trait analysis and phylogeography to uncover transmission routes of MERS-CoV isolates between hospital outbreaks and sporadic cases. Of the 120 sequences collected between 19 June 2012 and 23 January 2017, there were 64 isolates from hospital outbreak-associated cases and 56 from sporadic cases. Overall, MERS-CoV is fast evolving at 7.43 × 10-4 substitutions per site per year. Isolates from hospital outbreaks showed unusually fast evolutionary speed in a shorter time-frame than sporadic cases. Multiple introductions of different MERS-CoV strains occurred in three separate hospital outbreaks. MERS-CoV appears to be mutating in humans. The impact of mutations on viruses transmissibility in humans is unknown.
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Affiliation(s)
- Xin Chen
- Biosecurity Research Program, Kirby Institute, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia; (D.C.A.); (C.R.M.)
| | - Dillon Charles Adam
- Biosecurity Research Program, Kirby Institute, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia; (D.C.A.); (C.R.M.)
| | - Abrar Ahmad Chughtai
- School of Public Health and Community Medicine, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia;
| | - Sacha Stelzer-Braid
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia;
- Virology Research Laboratory, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Matthew Scotch
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA;
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA
| | - Chandini Raina MacIntyre
- Biosecurity Research Program, Kirby Institute, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia; (D.C.A.); (C.R.M.)
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA
- College of Public Service and Community Solutions, Arizona State University, Tempe, AZ 85004, USA
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82
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Zhang Y, Tian P, Duan G, Gao F, Schnabel G, Zhan J, Chen F. Histone H3 gene is not a suitable marker to distinguish Alternaria tenuissima from A. alternata affecting potato. PLoS One 2020; 15:e0231961. [PMID: 32324785 PMCID: PMC7179870 DOI: 10.1371/journal.pone.0231961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 04/03/2020] [Indexed: 11/21/2022] Open
Abstract
Potato Alternaria leaf blight is one of the economically most important disease in potato production worldwide. A recent study reported a quick method to distinguish main Alternaria pathogens A. tenuissima, A. alternata, and A. solani using partial histone H3 gene sequences. Using this method, our collection of 79 isolates from 8 provinces in China were presumably separated into A. tenussima and A. alternata. But in depth morphological and genetic analysis casted doubt on this identification. Culture morphologies of six presumed A. alternata isolates (PresA_alt) and six presumed A. tenuissima isolates (PresA_ten) were not significantly different. PresA_ten isolates also produced conidia in branched chains which supposed to be A. aternata. Phylogenetic analyses were conducted using internal transcribed spacer region (ITS) and five genes commonly used for species identification including glyceraldehyde-3-phosphate dehydrogenase (GPDH), translation elongation factor 1-alpha (TEF1), β-tubulin, plasma membrane ATPase (ATPase), and calmodulin genes. The results showed that GPDH and TEF1 sequences of PresA_alt and PresA_ten isolates were identical. The 12 isolates did not cluster by presumed species neither by individual or concatenated sequence comparisons. The phylogeny–trait association analysis confirmed that the two group isolates were undistinguishable by those molecular markers. Analysis of histone H3 gene sequences revealed variable intron sequences between PresA_ten and PresA_alt isolates, but the amino acid sequences were identical. Our results indicate that the previously published method to distinguish Alternaria species based on histone H3 gene sequence variation is inaccurate and that the prevalence of A. tenuissima isolates in China was likely overestimated.
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Affiliation(s)
- Yue Zhang
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Peiyu Tian
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guohua Duan
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Fangluan Gao
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guido Schnabel
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States of America
| | - Jiasui Zhan
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- * E-mail: (FC); (JZ)
| | - Fengping Chen
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
- * E-mail: (FC); (JZ)
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83
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Chaillon A, Gianella S, Dellicour S, Rawlings SA, Schlub TE, De Oliveira MF, Ignacio C, Porrachia M, Vrancken B, Smith DM. HIV persists throughout deep tissues with repopulation from multiple anatomical sources. J Clin Invest 2020; 130:1699-1712. [PMID: 31910162 PMCID: PMC7108926 DOI: 10.1172/jci134815] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/19/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUNDUnderstanding HIV dynamics across the human body is important for cure efforts. This goal has been hampered by technical difficulties and the challenge of obtaining fresh tissues.METHODSThis observational study evaluated 6 individuals with HIV (n = 4 with viral suppression using antiretroviral [ART] therapy; n = 2 with rebound viremia after stopping ART), who provided serial blood samples before death and their bodies for rapid autopsy. HIV reservoirs were characterized by digital droplet PCR, single-genome amplification, and sequencing of full-length (FL) envelope HIV. Phylogeographic methods were used to reconstruct HIV spread, and generalized linear models were tested for viral factors associated with dispersal.RESULTSAcross participants, HIV DNA levels varied from approximately 0 to 659 copies/106 cells (IQR: 22.9-126.5). A total of 605 intact FL env sequences were recovered in antemortem blood cells and across 28 tissues (IQR: 5-9). Sequence analysis showed (a) the emergence of large, identical, intact HIV RNA populations in blood after cessation of therapy, which repopulated tissues throughout the body; (b) that multiple sites acted as hubs for HIV dissemination but that blood and lymphoid tissues were the main source; (c) that viral exchanges occurred within brain areas and across the blood-brain barrier; and (d) that migration was associated with low HIV divergence between sites and greater diversity at the recipient site.CONCLUSIONHIV reservoirs persisted in all deep tissues, and blood was the main source of dispersal. This may explain why eliminating HIV susceptibility in circulating T cells via bone marrow transplants allowed some individuals with HIV to experience therapy-free remission, even though deeper tissue reservoirs were not targeted.TRIAL REGISTRATIONNot applicable.FUNDINGNIH grants P01 AI31385, P30 AI036214, AI131971-01, AI120009AI036214, HD094646, AI027763, AI134295, and AI68636.
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Affiliation(s)
| | - Sara Gianella
- Department of Medicine, UCSD, La Jolla, California, USA
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Laboratory of Computational and Evolutionary Virology, Leuven, Belgium
| | | | - Timothy E. Schlub
- University of Sydney, Faculty of Medicine and Health, Sydney School of Public Health, Sydney, Australia
| | | | | | | | - Bram Vrancken
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Laboratory of Computational and Evolutionary Virology, Leuven, Belgium
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84
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Dobelmann J, Felden A, Lester PJ. Genetic Strain Diversity of Multi-Host RNA Viruses that Infect a Wide Range of Pollinators and Associates is Shaped by Geographic Origins. Viruses 2020; 12:E358. [PMID: 32213950 PMCID: PMC7150836 DOI: 10.3390/v12030358] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 03/16/2020] [Accepted: 03/21/2020] [Indexed: 01/29/2023] Open
Abstract
Emerging viruses have caused concerns about pollinator population declines, as multi-host RNA viruses may pose a health threat to pollinators and associated arthropods. In order to understand the ecology and impact these viruses have, we studied their host range and determined to what extent host and spatial variation affect strain diversity. Firstly, we used RT-PCR to screen pollinators and associates, including honey bees (Apis mellifera) and invasive Argentine ants (Linepithema humile), for virus presence and replication. We tested for the black queen cell virus (BQCV), deformed wing virus (DWV), and Kashmir bee virus (KBV) that were initially detected in bees, and the two recently discovered Linepithema humile bunya-like virus 1 (LhuBLV1) and Moku virus (MKV). DWV, KBV, and MKV were detected and replicated in a wide range of hosts and commonly co-infected hymenopterans. Secondly, we placed KBV and DWV in a global phylogeny with sequences from various countries and hosts to determine the association of geographic origin and host with shared ancestry. Both phylogenies showed strong geographic rather than host-specific clustering, suggesting frequent inter-species virus transmission. Transmission routes between hosts are largely unknown. Nonetheless, avoiding the introduction of non-native species and diseased pollinators appears important to limit spill overs and disease emergence.
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Affiliation(s)
- Jana Dobelmann
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; (A.F.); (P.J.L.)
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85
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Abstract
To investigate the genetic diversity, spatiotemporal dynamics, and transmission networks of HIV-1 CRF55_01B epidemic in China. A total of 209 partial pol gene sequences of HIV-1 CRF55_01B were sampled during 2007–2015 from 7 provinces of China. Phylogenetic analyses and trait diffusion process of these sequences were performed using Bayesian methods. Distance-based molecular network analyses were performed to infer putative relationships. Characteristics of genetically linked individuals were analyzed. Our study identified that HIV-1 CRF55_01B likely originated among men who have sex with men (MSM) in Guangdong province in January 2003 (April 2000–April 2005), and that Guangdong province and MSM are major hubs for the spread of the HIV-1 CRF55_01B epidemic in China. A Bayesian Skygrid plot revealed that the effective population size of HIV-1 CRF55_01B experienced increased phase followed by a plateau. All sequences from persons of unknown risk clustered within groups who reported MSM risk. This could be because Chinese MSM may not report such risk due to HIV/AIDS-related stigmatization and discrimination. This study inferred the transmission dynamics of the HIV-1 CRF55_01B epidemic in China at high resolution. The methods developed in this study may be critical for designing effective HIV prevention strategies in China and beyond.
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86
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Genotyping Porcine Circovirus 3 (PCV-3) Nowadays: Does It Make Sense? Viruses 2020; 12:v12030265. [PMID: 32121102 PMCID: PMC7150946 DOI: 10.3390/v12030265] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/20/2020] [Accepted: 02/25/2020] [Indexed: 02/07/2023] Open
Abstract
The discovery of a globally distributed porcine circovirus (Porcine circovirus 3; PCV-3) has led to intense research activity and the production of a large amount of molecular data. Different research groups have proposed several, not always concordant, genotypes for this virus. While such categories could aid an easier interpretation of PCV-3 molecular epidemiology, any classification, to be useful in practical settings, must be univocal and of help in the understanding of underlying biological features and epidemiology. Based on these premises, the possibility of defining PCV-3 genotypes was evaluated on the broadest available dataset of PCV-3 complete genome (n = 357) and open reading frame 2 (ORF2, n = 653) sequences. Genetic distance and phylogenetic clustering were selected as the main objective criteria. Additional factors, including the number of within-cluster sequences, host and geographic clustering, concordance between different genomic regions, and analysis method were also taken in account to generate a classification that could be effectively applied in research and diagnostic settings. A maximum within-genotype genetic distance of 3% at the complete genome and 6% at the ORF2 levels, bootstrap support higher than 90%, and concordance between analysis methods allowed us to clearly define two clades which could be potentially defined as genotypes. Further subdivision was not suggested due to the absence of a meaningful association between PCV-3 and its biological/epidemiological features. Nevertheless, since one of the clades included two strains only, thus far we formally propose the definition of only one PCV-3 genotype (PCV-3a). The established criteria will allow us to automatically recognize other genotypes when more strain sequences are characterized.
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87
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Vasylyeva TI, du Plessis L, Pineda-Peña AC, Kühnert D, Lemey P, Vandamme AM, Gomes P, Camacho RJ, Pybus OG, Abecasis AB, Faria NR. Tracing the Impact of Public Health Interventions on HIV-1 Transmission in Portugal Using Molecular Epidemiology. J Infect Dis 2020; 220:233-243. [PMID: 30805610 PMCID: PMC6581889 DOI: 10.1093/infdis/jiz085] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/21/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Estimation of temporal changes in human immunodeficiency virus (HIV) transmission patterns can help to elucidate the impact of preventive strategies and public health policies. METHODS Portuguese HIV-1 subtype B and G pol genetic sequences were appended to global reference data sets to identify country-specific transmission clades. Bayesian birth-death models were used to estimate subtype-specific effective reproductive numbers (Re). Discrete trait analysis (DTA) was used to quantify mixing among transmission groups. RESULTS We identified 5 subtype B Portuguese clades (26-79 sequences) and a large monophyletic subtype G Portuguese clade (236 sequences). We estimated that major shifts in HIV-1 transmission occurred around 1999 (95% Bayesian credible interval [BCI], 1998-2000) and 2000 (95% BCI, 1998-2001) for subtypes B and G, respectively. For subtype B, Re dropped from 1.91 (95% BCI, 1.73-2.09) to 0.62 (95% BCI,.52-.72). For subtype G, Re decreased from 1.49 (95% BCI, 1.39-1.59) to 0.72 (95% BCI, .63-.8). The DTA suggests that people who inject drugs (PWID) and heterosexuals were the source of most (>80%) virus lineage transitions for subtypes G and B, respectively. CONCLUSIONS The estimated declines in Re coincide with the introduction of highly active antiretroviral therapy and the scale-up of harm reduction for PWID. Inferred transmission events across transmission groups emphasize the importance of prevention efforts for bridging populations.
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Affiliation(s)
- Tetyana I Vasylyeva
- Department of Zoology, University of Oxford, United Kingdom.,New College, University of Oxford, United Kingdom
| | | | - Andrea C Pineda-Peña
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa.,Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia.,Basic Sciences Department, Universidad del Rosario, Bogotá, Colombia
| | - Denise Kühnert
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Philippe Lemey
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Anne-Mieke Vandamme
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa.,Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Perpétua Gomes
- Laboratory of Molecular Biology, LMCBM, SPC, Hospital de Egas Moniz-Centro Hospitalar de Lisboa Ocidental, Lisbon.,Center for Interdisciplinary Research Egas Moniz, CiiEM, Almada, Portugal
| | - Ricardo J Camacho
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, United Kingdom
| | - Ana B Abecasis
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa
| | - Nuno R Faria
- Department of Zoology, University of Oxford, United Kingdom
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88
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Rodríguez-Nevado C, G Gavilán R, Pagán I. Host Abundance and Identity Determine the Epidemiology and Evolution of a Generalist Plant Virus in a Wild Ecosystem. PHYTOPATHOLOGY 2020; 110:94-105. [PMID: 31589103 DOI: 10.1094/phyto-07-19-0271-fi] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Increasing evidence indicates that in wild ecosystems plant viruses are important ecological agents, and with potential to jump into crops, but only recently have the diversity and population dynamics of wild plant viruses begun to be explored. Theory proposes that biotic factors (e.g., ecosystem biodiversity, host abundance, and host density) and climatic conditions would determine the epidemiology and evolution of wild plant viruses. However, these predictions seldom have been empirically tested. For 3 years, we analyzed the prevalence and genetic diversity of Potyvirus species in preserved riparian forests of Spain. Results indicated that potyviruses were always present in riparian forests, with a novel generalist potyvirus species provisionally named Iberian hop mosaic virus (IbHMV), explaining the largest fraction of infected plants. Focusing on this potyvirus, we analyzed the biotic and climatic factors affecting virus infection risk and population genetic diversity in its native ecosystem. The main predictors of IbHMV infection risk were host relative abundance and species richness. Virus prevalence and host relative abundance were the major factors determining the genetic diversity and selection pressures in the virus population. These observations support theoretical predictions assigning these ecological factors a key role in parasite epidemiology and evolution. Finally, our phylogenetic analysis indicated that the viral population was genetically structured according to host and location of origin, as expected if speciation is largely sympatric. Thus, this work contributes to characterizing viral diversity and provides novel information on the determinants of plant virus epidemiology and evolution in wild ecosystems.
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Affiliation(s)
- Cristina Rodríguez-Nevado
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Departamento de Biotecnología-Biología Vegetal, Universidad Politécnica de Madrid, Madrid, Spain
| | - Rosario G Gavilán
- Facultad de Farmacia, Departamento de Farmacología, Farmacognosia y Botánica, unidad de Botánica, Universidad Complutense de Madrid, Madrid, Spain
| | - Israel Pagán
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Departamento de Biotecnología-Biología Vegetal, Universidad Politécnica de Madrid, Madrid, Spain
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89
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Bittar C, Machado RRG, Comelis MT, Bueno LM, Beguelini MR, Morielle-Versute E, Nogueira ML, Rahal P. Alphacoronavirus Detection in Lungs, Liver, and Intestines of Bats from Brazil. MICROBIAL ECOLOGY 2020; 79:203-212. [PMID: 31144002 PMCID: PMC7080140 DOI: 10.1007/s00248-019-01391-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/15/2019] [Indexed: 05/08/2023]
Abstract
Bats are flying mammals distributed worldwide known to host several types of Coronavirus (CoV). Since they were reported as the probable source of spillover of highly pathogenic CoV into the human population, investigating the circulation of this virus in bats around the world became of great importance. We analyzed samples from 103 bats from two distinct regions in Brazil. Coronavirus from the Alphacoronavirus genus was detected in 12 animals, 11 from São José do Rio Preto-SP region and 1 from Barreiras-BA region, resulting in a prevalence of 17.18% and 2.56% respectively. The virus was detected not only in intestines but also in lungs and liver. Phylogenetic analysis based on nsP12 genomic region suggests that the sequences group according to host family and sampling location. Studies on the circulation of these viruses in bats remain important to understand the ecology and evolutionary relationship of these pathogens.
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Affiliation(s)
- Cíntia Bittar
- Instituto de Biociências, Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP) - Campus de São José do Rio Preto, Rua Cristóvão Colombo, 2265, Jardim Nazareth, São Jose do Rio Preto, SP, 15054-000, Brazil.
| | - Rafael Rahal Guaragna Machado
- Instituto de Biociências, Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP) - Campus de São José do Rio Preto, Rua Cristóvão Colombo, 2265, Jardim Nazareth, São Jose do Rio Preto, SP, 15054-000, Brazil
| | - Manuela Tosi Comelis
- Instituto de Biociências, Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP) - Campus de São José do Rio Preto, Rua Cristóvão Colombo, 2265, Jardim Nazareth, São Jose do Rio Preto, SP, 15054-000, Brazil
| | - Larissa Mayumi Bueno
- Instituto de Biociências, Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP) - Campus de São José do Rio Preto, Rua Cristóvão Colombo, 2265, Jardim Nazareth, São Jose do Rio Preto, SP, 15054-000, Brazil
| | - Mateus Rodrigues Beguelini
- Instituto de Biociências, Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP) - Campus de São José do Rio Preto, Rua Cristóvão Colombo, 2265, Jardim Nazareth, São Jose do Rio Preto, SP, 15054-000, Brazil
- Centro das Ciências Biológicas e da Saúde (CCBS), Universidade Federal do Oeste da Bahia (UFOB), Rua Professor José Seabra de Lemos, 316, Recanto dos Pássaros, Barreiras, BA, 47808-021, Brazil
| | - Eliana Morielle-Versute
- Instituto de Biociências, Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP) - Campus de São José do Rio Preto, Rua Cristóvão Colombo, 2265, Jardim Nazareth, São Jose do Rio Preto, SP, 15054-000, Brazil
| | - Maurício Lacerda Nogueira
- Faculdade de Medicina de São José do Rio Preto (FAMERP), Avenida Brigadeiro Faria Lima, 5416, Vila São Pedro, Sao Jose do Rio Preto, SP, 15090-000, Brazil
| | - Paula Rahal
- Instituto de Biociências, Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP) - Campus de São José do Rio Preto, Rua Cristóvão Colombo, 2265, Jardim Nazareth, São Jose do Rio Preto, SP, 15054-000, Brazil
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90
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Swift evolutionary response of microbes to a rise in anthropogenic mercury in the Northern Hemisphere. ISME JOURNAL 2019; 14:788-800. [PMID: 31831837 PMCID: PMC7031220 DOI: 10.1038/s41396-019-0563-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 11/17/2019] [Indexed: 01/22/2023]
Abstract
Anthropogenic mercury remobilization has considerably increased since the Industrial Revolution in the late 1700s. The Minamata Convention on Mercury is a United Nations treaty (2017) aiming at curbing mercury emissions. Unfortunately, evaluating the effectiveness of such a global treaty is hampered by our inability to determine the lag in aquatic ecosystem responses to a change in atmospheric mercury deposition. Whereas past metal concentrations are obtained from core samples, there are currently no means of tracking historical metal bioavailability or toxicity. Here, we recovered DNA from nine dated sediment cores collected in Canada and Finland, and reconstructed the past demographics of microbes carrying genes coding for the mercuric reductase (MerA)—an enzyme involved in Hg detoxification—using Bayesian relaxed molecular clocks. We found that the evolutionary dynamics of merA exhibited a dramatic increase in effective population size starting from 1783.8 ± 3.9 CE, which coincides with both the Industrial Revolution, and with independent measurements of atmospheric Hg concentrations. We show that even low levels of anthropogenic mercury affected the evolutionary trajectory of microbes in the Northern Hemisphere, and that microbial DNA encoding for detoxification determinants stored in environmental archives can be used to track historical pollutant toxicity.
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91
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Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa. PLoS Pathog 2019; 15:e1007976. [PMID: 31809523 PMCID: PMC6897401 DOI: 10.1371/journal.ppat.1007976] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 07/11/2019] [Indexed: 12/21/2022] Open
Abstract
Since the ignition of the HIV-1 group M pandemic in the beginning of the 20th century, group M lineages have spread heterogeneously throughout the world. Subtype C spread rapidly through sub-Saharan Africa and is currently the dominant HIV lineage worldwide. Yet the epidemiological and evolutionary circumstances that contributed to its epidemiological expansion remain poorly understood. Here, we analyse 346 novel pol sequences from the DRC to compare the evolutionary dynamics of the main HIV-1 lineages, subtypes A1, C and D. Our results place the origins of subtype C in the 1950s in Mbuji-Mayi, the mining city of southern DRC, while subtypes A1 and D emerged in the capital city of Kinshasa, and subtypes H and J in the less accessible port city of Matadi. Following a 15-year period of local transmission in southern DRC, we find that subtype C spread at least three-fold faster than other subtypes circulating in Central and East Africa. In conclusion, our results shed light on the origins of HIV-1 main lineages and suggest that socio-historical rather than evolutionary factors may have determined the epidemiological fate of subtype C in sub-Saharan Africa.
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92
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Zhai X, Zhao W, Li K, Zhang C, Wang C, Su S, Zhou J, Lei J, Xing G, Sun H, Shi Z, Gu J. Genome Characteristics and Evolution of Pseudorabies Virus Strains in Eastern China from 2017 to 2019. Virol Sin 2019; 34:601-609. [PMID: 31278605 PMCID: PMC6888805 DOI: 10.1007/s12250-019-00140-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 04/24/2019] [Indexed: 11/29/2022] Open
Abstract
Since late 2011, outbreaks of pseudorabies virus (PRV) have occurred in southern China causing major economic losses to the pig industry. We previously reported that variant PRV forms and recombination in China could be the source of continued epidemics. Here, we analyzed samples from intensive pig farms in eastern China between 2017 and 2019, and sequenced the main glycoproteins (gB, gC, gD, and gE) to study the evolution characteristics of PRV. Based on the gC gene, we found that PRV variants belong to clade 2 and detected a founder effect during by the PRV epidemic. In addition, we detected inter- and intra-clade recombination; in particular, inter-clade recombination in the gB genes of strains FJ-ZXF and FJ-W2, which were recombinant with clade 1 strains. We also found specific amino-acid changes and positively selected sites, possibly associated with functional changes. This analysis of the emergence of PRV in China illustrates the need for continuous monitoring and the development of vaccines against specific variants of PRV.
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Affiliation(s)
- Xiaofeng Zhai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210000, China
| | - Wen Zhao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210000, China
| | - Kemang Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210000, China
| | - Cheng Zhang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210000, China
| | - Congcong Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210000, China
| | - Shuo Su
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210000, China.
| | - Jiyong Zhou
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, Hangzhou, 310058, China
| | - Jing Lei
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210000, China
| | - Gang Xing
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, Hangzhou, 310058, China
| | - Haifeng Sun
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210000, China
| | - Zhiyu Shi
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210000, China
| | - Jinyan Gu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210000, China
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93
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Wang L, Wu X, Wang C, Song C, Bao J, Du J. Origin and transmission of bovine viral diarrhea virus type 1 in China revealed by phylodynamic analysis. Res Vet Sci 2019; 128:162-169. [PMID: 31809973 DOI: 10.1016/j.rvsc.2019.11.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 11/22/2019] [Accepted: 11/27/2019] [Indexed: 01/12/2023]
Abstract
Bovine viral diarrhea virus type 1 (BVDV-1) is prevalent worldwide and causes significant economic loss in animal husbandry. Since its first report in the 1980s in China, several genotypes of BVDV-1 had been reported, but an in-depth phylogenetic analysis on the BVDV isolates from China is lacking. To investigate the molecular evolution and phylodynamics of BVDV-1 genotypes circulating in China, comprehensive phylogenetic and phylodynamic analyses were performed to reconstruct the origin and spatial-temporal distribution, and to trace main viral flows among different areas. BVDV-1 5'-UTR sequences from China and Mongolia were collected from Genbank, and the phylogeny was built using the maximum likelihood method. The Bayesian Skygrid was used to estimate the evolution and population dynamics of BVDV-1. Eight BVDV-1 genotypes were identified, of which 1b and 1 m are the main genotypes. The results indicated that BVDV-1 might be introduced in China in the 1960s, and after a long period of population growth, it gradually leveled off after 2010. The phylodynamic inference clearly shows a more steady BVDV-1 population growth, and the transmission of BVDV-1 may be confined to specific regions. This study will help to understand the molecular epidemiology and long-term evolutionary dynamics of BVDV-1 in China, therefore providing a scientific basis for the prevention and controlof the virus.
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Affiliation(s)
- Lina Wang
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xiaoming Wu
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Chengbao Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Changxin Song
- Department of Computer, Qinghai Normal University, Xining, Qinghai, China
| | - Junpeng Bao
- Department of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jianqiang Du
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China.
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94
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Stelzer-Braid S, Wynn M, Chatoor R, Scotch M, Ramachandran V, Teoh HL, Farrar MA, Sampaio H, Andrews PI, Craig ME, MacIntyre CR, Varadhan H, Kesson A, Britton PN, Newcombe J, Rawlinson WD. Next generation sequencing of human enterovirus strains from an outbreak of enterovirus A71 shows applicability to outbreak investigations. J Clin Virol 2019; 122:104216. [PMID: 31790967 DOI: 10.1016/j.jcv.2019.104216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 10/08/2019] [Accepted: 11/11/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND The most recent documented Australian outbreak of enterovirus A71 (EV-A71) occurred in Sydney from 2012 to 2013. Over a four-month period more than 100 children presented to four paediatric hospitals with encephalitic presentations including fever and myoclonic jerks. The heterogeneous presentations included typical encephalomyelitis, and cardiopulmonary complications. OBJECTIVES To characterise the genomes of enterovirus strains circulating during the 2013 Sydney EV-A71 outbreak and determine their phylogeny, phylogeography and association between genome and clinical phenotype. STUDY DESIGN We performed an analysis of enterovirus (EV) positive specimens from children presenting to hospitals in the greater Sydney region of Australia during the 2013 outbreak. We amplified near full-length genomes of EV, and used next generation sequencing technology to sequence the virus. We used phylogenetic/phylogeographic analysis to characterize the outbreak viruses. RESULTS We amplified and sequenced 23/63 (37 %) genomes, and identified the majority (61 %) as EV-A71. The EV-A71 sequences showed high level sequence homology to C4a genogroups of EV-A71 circulating in China and Vietnam during 2012-13. Phylogenetic analysis showed EV-A71 strains associated with more severe symptoms, including encephalitis or cardiopulmonary failure, grouped together more closely than those from patients with hand, foot and mouth disease. Amongst the non-EV-A71 sequences were five other EV subtypes (representing enterovirus subtypes A and B), reflecting the diversity of EV co-circulation within the community. CONCLUSIONS This is the first Australian study investigating the near full-length genome of EV strains identified during a known outbreak of EV-A71. EV-A71 sequences were very similar to strains circulating in Asia during the same time period. Whole genome sequencing offers additional information over routine diagnostic testing such as characterisation of emerging recombinant strains and inform vaccine design.
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Affiliation(s)
- Sacha Stelzer-Braid
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia; School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Matthew Wynn
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Richard Chatoor
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Matthew Scotch
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA; Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Public Health and Community Medicine, University of New South Wales, Sydney, NSW 2033, Australia
| | - Vidiya Ramachandran
- Serology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Hooi-Ling Teoh
- Department of Neurology, Sydney Children's Hospital, Sydney, Australia; School of Women's and Children's Health, University of New South Wales Medicine, Sydney, NSW 2052, Australia
| | - Michelle A Farrar
- Department of Neurology, Sydney Children's Hospital, Sydney, Australia; School of Women's and Children's Health, University of New South Wales Medicine, Sydney, NSW 2052, Australia
| | - Hugo Sampaio
- Department of Neurology, Sydney Children's Hospital, Sydney, Australia; School of Women's and Children's Health, University of New South Wales Medicine, Sydney, NSW 2052, Australia
| | - Peter Ian Andrews
- Department of Neurology, Sydney Children's Hospital, Sydney, Australia; School of Women's and Children's Health, University of New South Wales Medicine, Sydney, NSW 2052, Australia
| | - Maria E Craig
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia; School of Women's and Children's Health, University of New South Wales Medicine, Sydney, NSW 2052, Australia
| | - C Raina MacIntyre
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA; Biosecurity Program, Kirby Institute, University of New South Wales, Sydney, NSW 2052, Australia; Watts College of Public Service and Community Solutions, Arizona State University, Phoenix, AZ 85004, USA
| | | | - Alison Kesson
- Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Sydney, Australia
| | - Philip N Britton
- Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Sydney, Australia; Marie Bashir Institute, University of Sydney, Australia
| | - James Newcombe
- Pathology North, Royal North Shore Hospital, St Leonards, Sydney, Australia
| | - William D Rawlinson
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia; School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia; Serology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Sydney, NSW 2031, Australia; School of Women's and Children's Health, University of New South Wales Medicine, Sydney, NSW 2052, Australia
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95
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Zeghbib S, Herczeg R, Kemenesi G, Zana B, Kurucz K, Urbán P, Madai M, Földes F, Papp H, Somogyi B, Jakab F. Genetic characterization of a novel picornavirus in Algerian bats: co-evolution analysis of bat-related picornaviruses. Sci Rep 2019; 9:15706. [PMID: 31673141 PMCID: PMC6823487 DOI: 10.1038/s41598-019-52209-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 10/15/2019] [Indexed: 12/13/2022] Open
Abstract
Bats are reservoirs of numerous zoonotic viruses. The Picornaviridae family comprises important pathogens which may infect both humans and animals. In this study, a bat-related picornavirus was detected from Algerian Minioptreus schreibersii bats for the first time in the country. Molecular analyses revealed the new virus originates to the Mischivirus genus. In the operational use of the acquired sequence and all available data regarding bat picornaviruses, we performed a co-evolutionary analysis of mischiviruses and their hosts, to authentically reveal evolutionary patterns within this genus. Based on this analysis, we enlarged the dataset, and examined the co-evolutionary history of all bat-related picornaviruses including their hosts, to effectively compile all possible species jumping events during their evolution. Furthermore, we explored the phylogeny association with geographical location, host-genus and host-species in both data sets.
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Affiliation(s)
- Safia Zeghbib
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Róbert Herczeg
- Bioinformatics Research Group, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Gábor Kemenesi
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Brigitta Zana
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Kornélia Kurucz
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Péter Urbán
- Bioinformatics Research Group, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Mónika Madai
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Fanni Földes
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Henrietta Papp
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Balázs Somogyi
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Ferenc Jakab
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary.
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary.
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96
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Hall MD, Holden MT, Srisomang P, Mahavanakul W, Wuthiekanun V, Limmathurotsakul D, Fountain K, Parkhill J, Nickerson EK, Peacock SJ, Fraser C. Improved characterisation of MRSA transmission using within-host bacterial sequence diversity. eLife 2019; 8:46402. [PMID: 31591959 PMCID: PMC6954020 DOI: 10.7554/elife.46402] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 10/01/2019] [Indexed: 12/31/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) transmission in the hospital setting has been a frequent subject of investigation using bacterial genomes, but previous approaches have not yet fully utilised the extra deductive power provided when multiple pathogen samples are acquired from each host. Here, we used a large dataset of MRSA sequences from multiply-sampled patients to reconstruct colonisation of individuals in a high-transmission setting in a hospital in Thailand. We reconstructed transmission trees for MRSA. We also investigated transmission between anatomical sites on the same individual, finding that this either occurs repeatedly or involves a wide transmission bottleneck. We examined the between-subject bottleneck, finding considerable variation in the amount of diversity transmitted. Finally, we compared our approach to the simpler method of identifying transmission pairs using single nucleotide polymorphism (SNP) counts. This suggested that the optimum threshold for identifying a pair is 39 SNPs, if sensitivities and specificities are equally weighted.
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Affiliation(s)
- Matthew D Hall
- Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Matthew Tg Holden
- School of Medicine, University of St Andrews, St Andrews, United Kingdom
| | - Pramot Srisomang
- Department of Pediatrics, Sunpasitthiprasong Hospital, Ubon Ratchathani, Thailand
| | - Weera Mahavanakul
- Department of Medicine, Sunpasitthiprasong Hospital, Ubon Ratchathani, Thailand
| | - Vanaporn Wuthiekanun
- Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Salaya, Thailand
| | | | - Kay Fountain
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Emma K Nickerson
- Department of Infectious Diseases, Cambridge University Hospitals NHS Foundation, Cambridge, United Kingdom
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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97
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Wei S, He X, Wang D, Xiang J, Yang Y, Yuan S, Shang J, Yang H. Genetic structure and variability of tobacco vein banding mosaic virus populations. Arch Virol 2019; 164:2459-2467. [PMID: 31286220 DOI: 10.1007/s00705-019-04342-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 06/03/2019] [Indexed: 10/26/2022]
Abstract
Tobacco vein banding mosaic virus (TVBMV) is of increasing importance in tobacco production. Knowledge of the genetic structure and variability of the virus population is vital for developing sustainable management. In this study, 24 new TVBMV isolates from Sichuan Province together with 46 previous isolates were studied based on their coat protein sequences. Two distinguishable clades were supported by phylogenetic analysis. The summary statistics PS, AI and MC showed a strong TVBMV-geography association between the isolates from Southwest China (SW) and Mainland China (MC). Further analysis indicated that the spatial genetic structure of TVBMV populations is likely to have been caused by natural selection. Phylogeographic analysis provided strong support for spatial diffusion pathways between the Southwest and Northwest tobacco-producing regions. The TVBMV CP gene was found to be under negative selection, and no significant positive selection of amino acids was detected in the SW group; however, the isolates of the MC group experienced significant positive selection pressure at the first and third amino acid sites of CP. This study suggests that natural selection and habitat heterogeneity are important evolutionary mechanisms affecting the genetic structure of the TVBMV population.
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Affiliation(s)
- Shiqing Wei
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaorong He
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Die Wang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jinyou Xiang
- Sichuan Tobacco Company Yibin Company, Yibin, 644000, China
| | - Yide Yang
- Sichuan Tobacco Company Yibin Company, Yibin, 644000, China
| | - Shu Yuan
- College of Resources, Sichuan Agricultural University Chengdu Campus, Chengdu, 611130, China
| | - Jing Shang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hui Yang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China.
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98
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Tseng SP, Wetterer JK, Suarez AV, Lee CY, Yoshimura T, Shoemaker D, Yang CCS. Genetic Diversity and Wolbachia Infection Patterns in a Globally Distributed Invasive Ant. Front Genet 2019; 10:838. [PMID: 31608104 PMCID: PMC6758599 DOI: 10.3389/fgene.2019.00838] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 08/13/2019] [Indexed: 11/23/2022] Open
Abstract
Understanding the phylogeographic history of an invasive species may facilitate reconstructing the history and routes of its invasion. The longhorn crazy ant, Paratrechina longicornis, is a ubiquitous agricultural and household pest throughout much of the tropics and subtropics, but little is known about the history of its spread. Here, we examine worldwide genetic variation in P. longicornis and its associated Wolbachia bacterial symbionts. Analyses of mtDNA sequences of 248 P. longicornis workers (one per colony) from 13 geographic regions reveal two highly diverged mtDNA clades that co-occur in most of the geographic regions. These two mtDNA clades are associated with different Wolbachia infection patterns, but are not congruent with patterns of nDNA (microsatellite) variation. Multilocus sequence typing reveals two distinct Wolbachia strains in P. longicornis, namely, wLonA and wLonF. The evolutionary histories of these two strains differ; wLonA appears to be primarily transmitted maternally, and patterns of mtDNA and nDNA variation and wLonA infection status are consistent with a relatively recent Wolbachia-induced selective sweep. In contrast, the observed patterns of mtDNA variation and wLonF infections suggest frequent horizontal transfer and losses of wLonF infections. The lack of nDNA structure among sampled geographic regions coupled with the finding that numerous mtDNA haplotypes are shared among regions implies that inadvertent long-distance movement through human commerce is common in P. longicornis and has shaped the genetic structure of this invasive ant worldwide.
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Affiliation(s)
- Shu-Ping Tseng
- Research Institute for Sustainable Humanosphere, Kyoto University, Kyoto, Japan
| | - James K. Wetterer
- Wilkes Honors College, Florida Atlantic University, Jupiter, FL, United States
| | - Andrew V. Suarez
- Department of Evolution, Ecology and Behavior and Department of Entomology, University of Illinois Urbana-Champaign, IL, United States
| | - Chow-Yang Lee
- Department of Entomology, University of California, Riverside, CA, United States
| | - Tsuyoshi Yoshimura
- Research Institute for Sustainable Humanosphere, Kyoto University, Kyoto, Japan
| | - DeWayne Shoemaker
- Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, United States
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99
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De Scheerder MA, Vrancken B, Dellicour S, Schlub T, Lee E, Shao W, Rutsaert S, Verhofstede C, Kerre T, Malfait T, Hemelsoet D, Coppens M, Dhondt A, De Looze D, Vermassen F, Lemey P, Palmer S, Vandekerckhove L. HIV Rebound Is Predominantly Fueled by Genetically Identical Viral Expansions from Diverse Reservoirs. Cell Host Microbe 2019; 26:347-358.e7. [PMID: 31471273 PMCID: PMC11021134 DOI: 10.1016/j.chom.2019.08.003] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/16/2019] [Accepted: 07/31/2019] [Indexed: 02/01/2023]
Abstract
Viral rebound upon stopping combined antiretroviral therapy poses a major barrier toward an HIV cure. Cellular and anatomical sources responsible for reinitiating viral replication remain a subject of ardent debate, despite extensive research efforts. To unravel the source of rebounding viruses, we conducted a large-scale HIV-STAR (HIV-1 sequencing before analytical treatment interruption to identify the anatomically relevant HIV reservoir) clinical trial. We collected samples from 11 participants and compared the genetic composition of (pro)viruses collected under treatment from different cellular and anatomical compartments with that of plasma viruses sampled during analytical treatment interruption. We found a remarkably heterogeneous source of viral rebound. In addition, irrespective of the compartment or cell subset, genetically identical viral expansions played a significant role in viral rebound. Our study suggests that although there does not seem to be a primary source for rebound HIV, cellular proliferation is an important driver of HIV persistence and should therefore be considered in future curative strategies.
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Affiliation(s)
- Marie-Angélique De Scheerder
- HIV Cure Research Center, Department of General Internal Medicine, Ghent University Hospital, Ghent University, Ghent 9000, Belgium.
| | - Bram Vrancken
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Laboratory of Evolutionary and Computational Virology, Herestraat 49, Leuven 3000 Belgium
| | - Simon Dellicour
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Laboratory of Evolutionary and Computational Virology, Herestraat 49, Leuven 3000 Belgium; Spatial Epidemiology Laboratory (SpELL), Université Libre de Bruxelles, CP160/12 50, av. FD Roosevelt, 1050 Bruxelles, Belgium
| | - Timothy Schlub
- University of Sydney, Faculty of Medicine and Health, Sydney School of Public Health, Sydney 2000, NSW, Australia
| | - Eunok Lee
- Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney 2145, NSW, Australia
| | - Wei Shao
- Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD, USA
| | - Sofie Rutsaert
- HIV Cure Research Center, Department of General Internal Medicine, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Chris Verhofstede
- Aids Reference Laboratory, Ghent University Hospital, Ghent 9000, Belgium
| | - Tessa Kerre
- Department of Hematology, Ghent University Hospital, Ghent 9000, Belgium
| | - Thomas Malfait
- Department of Pulmonology, Ghent University Hospital, Ghent 9000, Belgium
| | - Dimitri Hemelsoet
- Department of Neurology, Ghent University Hospital, Ghent 9000, Belgium
| | - Marc Coppens
- Department of Anesthesiology, Ghent University Hospital, Ghent 9000, Belgium
| | - Annemieke Dhondt
- Department of Nephrology, Ghent University Hospital, Ghent 9000, Belgium
| | - Danny De Looze
- Department of Gastro-Enterology, Ghent University Hospital, Ghent 9000, Belgium
| | - Frank Vermassen
- Department of Vascular Surgery, Ghent University Hospital, Ghent 9000, Belgium
| | - Philippe Lemey
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Laboratory of Evolutionary and Computational Virology, Herestraat 49, Leuven 3000 Belgium
| | - Sarah Palmer
- Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney 2145, NSW, Australia
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of General Internal Medicine, Ghent University Hospital, Ghent University, Ghent 9000, Belgium.
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100
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Li K, Yan S, Wang N, He W, Guan H, He C, Wang Z, Lu M, He W, Ye R, Veit M, Su S. Emergence and adaptive evolution of Nipah virus. Transbound Emerg Dis 2019; 67:121-132. [PMID: 31408582 PMCID: PMC7168560 DOI: 10.1111/tbed.13330] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 07/24/2019] [Accepted: 07/27/2019] [Indexed: 12/11/2022]
Abstract
Since its first emergence in 1998 in Malaysia, Nipah virus (NiV) has become a great threat to domestic animals and humans. Sporadic outbreaks associated with human-to-human transmission caused hundreds of human fatalities. Here, we collected all available NiV sequences and combined phylogenetics, molecular selection, structural biology and receptor analysis to study the emergence and adaptive evolution of NiV. NiV can be divided into two main lineages including the Bangladesh and Malaysia lineages. We formly confirmed a significant association with geography which is probably the result of long-term evolution of NiV in local bat population. The two NiV lineages differ in many amino acids; one change in the fusion protein might be involved in its activation via binding to the G protein. We also identified adaptive and positively selected sites in many viral proteins. In the receptor-binding G protein, we found that sites 384, 386 and especially 498 of G protein might modulate receptor-binding affinity and thus contribute to the host jump from bats to humans via the adaption to bind the human ephrin-B2 receptor. We also found that site 1645 in the connector domain of L was positive selected and involved in adaptive evolution; this site might add methyl groups to the cap structure present at the 5'-end of the RNA and thus modulate its activity. This study provides insight to assist the design of early detection methods for NiV to assess its epidemic potential in humans.
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Affiliation(s)
- Kemang Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Shiyu Yan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Ningning Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Wanting He
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Haifei Guan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Chengxi He
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Zhixue Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Meng Lu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Wei He
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Rui Ye
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Michael Veit
- Institute for Virology, Center for Infection Medicine, Veterinary Faculty, Free University Berlin, Berlin, Germany
| | - Shuo Su
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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