1
|
Grybchuk D, Galan A, Klocek D, Macedo DH, Wolf YI, Votýpka J, Butenko A, Lukeš J, Neri U, Záhonová K, Kostygov AY, Koonin EV, Yurchenko V. Identification of diverse RNA viruses in Obscuromonas flagellates (Euglenozoa: Trypanosomatidae: Blastocrithidiinae). Virus Evol 2024; 10:veae037. [PMID: 38774311 PMCID: PMC11108086 DOI: 10.1093/ve/veae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 04/03/2024] [Accepted: 04/29/2024] [Indexed: 05/24/2024] Open
Abstract
Trypanosomatids (Euglenozoa) are a diverse group of unicellular flagellates predominately infecting insects (monoxenous species) or circulating between insects and vertebrates or plants (dixenous species). Monoxenous trypanosomatids harbor a wide range of RNA viruses belonging to the families Narnaviridae, Totiviridae, Qinviridae, Leishbuviridae, and a putative group of tombus-like viruses. Here, we focus on the subfamily Blastocrithidiinae, a previously unexplored divergent group of monoxenous trypanosomatids comprising two related genera: Obscuromonas and Blastocrithidia. Members of the genus Blastocrithidia employ a unique genetic code, in which all three stop codons are repurposed to encode amino acids, with TAA also used to terminate translation. Obscuromonas isolates studied here bear viruses of three families: Narnaviridae, Qinviridae, and Mitoviridae. The latter viral group is documented in trypanosomatid flagellates for the first time. While other known mitoviruses replicate in the mitochondria, those of trypanosomatids appear to reside in the cytoplasm. Although no RNA viruses were detected in Blastocrithidia spp., we identified an endogenous viral element in the genome of B. triatomae indicating its past encounter(s) with tombus-like viruses.
Collapse
Affiliation(s)
- Danyil Grybchuk
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
- Central European Institute of Technology, Masaryk University, Brno 625 00, Czechia
| | - Arnau Galan
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
| | - Donnamae Klocek
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
| | - Diego H Macedo
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
| | - Yuri I Wolf
- National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda 20894, USA
| | - Jan Votýpka
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice 370 05, Czechia
- Department of Parasitology, Faculty of Science, Charles University, Prague 128 00, Czechia
| | - Anzhelika Butenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice 370 05, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice 370 05, Czechia
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice 370 05, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice 370 05, Czechia
| | - Uri Neri
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 39040, Israel
| | - Kristína Záhonová
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice 370 05, Czechia
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec 252 50, Czechia
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Alexei Yu Kostygov
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
- Zoological Institute of the Ruian Academy of Sciences, St. Petersburg 199034, Russia
| | - Eugene V Koonin
- National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda 20894, USA
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
| |
Collapse
|
2
|
Mehta P, Swaminathan A, Yadav A, Chattopadhyay P, Shamim U, Pandey R. Integrative genomics important to understand host-pathogen interactions. Brief Funct Genomics 2024; 23:1-14. [PMID: 35909219 DOI: 10.1093/bfgp/elac021] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/30/2022] [Accepted: 07/11/2022] [Indexed: 01/21/2024] Open
Abstract
Infectious diseases are the leading cause of morbidity and mortality worldwide. Causative pathogenic microbes readily mutate their genome and lead to outbreaks, challenging the healthcare and the medical support. Understanding how certain symptoms manifest clinically is integral for therapeutic decisions and vaccination efficacy/protection. Notably, the interaction between infecting pathogens, host response and co-presence of microbes influence the trajectories of disease progression and clinical outcome. The spectrum of observed symptomatic patients (mild, moderate and severe) and the asymptomatic infections highlight the challenges and the potential for understanding the factors driving protection/susceptibility. With the increasing repertoire of high-throughput tools, such as cutting-edge multi-omics profiling and next-generation sequencing, genetic drivers of factors linked to heterogeneous disease presentations can be investigated in tandem. However, such strategies are not without limits in terms of effectively integrating host-pathogen interactions. Nonetheless, an integrative genomics method (for example, RNA sequencing data) for exploring multiple layers of complexity in host-pathogen interactions could be another way to incorporate findings from high-throughput data. We further propose that a Holo-transcriptome-based technique to capture transcriptionally active microbial units can be used to elucidate functional microbiomes. Thus, we provide holistic perspective on investigative methodologies that can harness the same genomic data to investigate multiple seemingly independent but deeply interconnected functional domains of host-pathogen interaction that modulate disease severity and clinical outcomes.
Collapse
|
3
|
Jang H, Matsuoka M, Freire M. Oral mucosa immunity: ultimate strategy to stop spreading of pandemic viruses. Front Immunol 2023; 14:1220610. [PMID: 37928529 PMCID: PMC10622784 DOI: 10.3389/fimmu.2023.1220610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/11/2023] [Indexed: 11/07/2023] Open
Abstract
Global pandemics are most likely initiated via zoonotic transmission to humans in which respiratory viruses infect airways with relevance to mucosal systems. Out of the known pandemics, five were initiated by respiratory viruses including current ongoing coronavirus disease 2019 (COVID-19). Striking progress in vaccine development and therapeutics has helped ameliorate the mortality and morbidity by infectious agents. Yet, organism replication and virus spread through mucosal tissues cannot be directly controlled by parenteral vaccines. A novel mitigation strategy is needed to elicit robust mucosal protection and broadly neutralizing activities to hamper virus entry mechanisms and inhibit transmission. This review focuses on the oral mucosa, which is a critical site of viral transmission and promising target to elicit sterile immunity. In addition to reviewing historic pandemics initiated by the zoonotic respiratory RNA viruses and the oral mucosal tissues, we discuss unique features of the oral immune responses. We address barriers and new prospects related to developing novel therapeutics to elicit protective immunity at the mucosal level to ultimately control transmission.
Collapse
Affiliation(s)
- Hyesun Jang
- Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, United States
| | - Michele Matsuoka
- Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, United States
| | - Marcelo Freire
- Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, United States
- Division of Infectious Diseases and Global Public Health Department of Medicine, University of California San Diego, La Jolla, CA, United States
| |
Collapse
|
4
|
Cholette F, Lazarus L, Macharia P, Thompson LH, Githaiga S, Mathenge J, Walimbwa J, Kuria I, Okoth S, Wambua S, Albert H, Mwangi P, Adhiambo J, Kasiba R, Juma E, Battacharjee P, Kimani J, Sandstrom P, Meyers AFA, Joy JB, Thomann M, McLaren PJ, Shaw S, Mishra S, Becker ML, McKinnon L, Lorway R. Community Insights in Phylogenetic HIV Research: The CIPHR Project Protocol. Glob Public Health 2023; 18:2269435. [PMID: 37851872 DOI: 10.1080/17441692.2023.2269435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023]
Abstract
Inferring HIV transmission networks from HIV sequences is gaining popularity in the field of HIV molecular epidemiology. However, HIV sequences are often analyzed at distance from those affected by HIV epidemics, namely without the involvement of communities most affected by HIV. These remote analyses often mean that knowledge is generated in absence of lived experiences and socio-economic realities that could inform the ethical application of network-derived information in 'real world' programmes. Procedures to engage communities are noticeably absent from the HIV molecular epidemiology literature. Here we present our team's protocol for engaging community activists living in Nairobi, Kenya in a knowledge exchange process - The CIPHR Project (Community Insights in Phylogenetic HIV Research). Drawing upon a community-based participatory approach, our team will (1) explore the possibilities and limitations of HIV molecular epidemiology for key population programmes, (2) pilot a community-based HIV molecular study, and (3) co-develop policy guidelines on conducting ethically safe HIV molecular epidemiology. Critical dialogue with activist communities will offer insight into the potential uses and abuses of using such information to sharpen HIV prevention programmes. The outcome of this process holds importance to the development of policy frameworks that will guide the next generation of the global response.
Collapse
Affiliation(s)
- François Cholette
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Sexually Transmitted and Blood-Borne Infections, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada
| | - Lisa Lazarus
- Institute for Global Public Health, Department of Community Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Pascal Macharia
- Health Options for Young Men on HIV/AIDS and STIs (HOYMAS), Nairobi, Kenya
| | - Laura H Thompson
- Sexually Transmitted and Blood-Borne Infections Surveillance Division, Centre for Communicable Diseases and Infection Control, Public Health Agency of Canada, Ottawa, Canada
| | - Samuel Githaiga
- Health Options for Young Men on HIV/AIDS and STIs (HOYMAS), Nairobi, Kenya
| | - John Mathenge
- Health Options for Young Men on HIV/AIDS and STIs (HOYMAS), Nairobi, Kenya
| | | | - Irene Kuria
- Key Population Consortium of Kenya, Nairobi, Kenya
| | - Silvia Okoth
- Bar Hostess Empowerment and Support Programme, Nairobi, Kenya
| | | | - Harrison Albert
- Health Options for Young Men on HIV/AIDS and STIs (HOYMAS), Nairobi, Kenya
| | - Peninah Mwangi
- Bar Hostess Empowerment and Support Programme, Nairobi, Kenya
| | - Joyce Adhiambo
- Partners for Health Development in Africa (PHDA), Nairobi, Kenya
- Sex Worker Outreach Programme (SWOP), Nairobi, Kenya
| | | | - Esther Juma
- Sex Worker Outreach Programme (SWOP), Nairobi, Kenya
| | | | - Joshua Kimani
- Sex Worker Outreach Programme (SWOP), Nairobi, Kenya
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Paul Sandstrom
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Sexually Transmitted and Blood-Borne Infections, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada
| | - Adrienne F A Meyers
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Sexually Transmitted and Blood-Borne Infections, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada
| | - Jeffrey B Joy
- British Columbia Centre for Excellence in HIV/AIDS (BCCfE), St. Paul's Hospital, Vancouver, Canada
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, Canada
- Bioinformatics Programme, University of British Columbia, Vancouver, Canada
| | - Matthew Thomann
- Department of Anthropology, University of Maryland, College Park, MD, USA
| | - Paul J McLaren
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Sexually Transmitted and Blood-Borne Infections, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada
| | - Souradet Shaw
- Institute for Global Public Health, Department of Community Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Sharmistha Mishra
- MAP Centre for Urban Health Solutions, St. Michael's Hospital, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Canada
| | - Marissa L Becker
- Institute for Global Public Health, Department of Community Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Lyle McKinnon
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Robert Lorway
- Institute for Global Public Health, Department of Community Health Sciences, University of Manitoba, Winnipeg, Canada
| |
Collapse
|
5
|
Ashall J, Shah S, Biggs JR, Chang JNR, Jafari Y, Brady OJ, Mai HK, Lien LT, Do Thai H, Nguyen HAT, Anh DD, Iwasaki C, Kitamura N, Van Loock M, Herrera-Taracena G, Rasschaert F, Van Wesenbeeck L, Yoshida LM, Hafalla JCR, Hue S, Hibberd ML. A phylogenetic study of dengue virus in urban Vietnam shows long-term persistence of endemic strains. Virus Evol 2023; 9:vead012. [PMID: 36926448 PMCID: PMC10013730 DOI: 10.1093/ve/vead012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 10/31/2022] [Accepted: 02/15/2023] [Indexed: 02/17/2023] Open
Abstract
Dengue virus (DENV) causes repeated outbreaks of disease in endemic areas, with patterns of local transmission strongly influenced by seasonality, importation via human movement, immunity, and vector control efforts. An understanding of how each of these interacts to enable endemic transmission (continual circulation of local virus strains) is largely unknown. There are times of the year when no cases are reported, often for extended periods of time, perhaps wrongly implying the successful eradication of a local strain from that area. Individuals who presented at a clinic or hospital in four communes in Nha Trang, Vietnam, were initially tested for DENV antigen presence. Enrolled positive individuals then had their corresponding household members invited to participate, and those who enrolled were tested for DENV. The presence of viral nucleic acid in all samples was confirmed using quantitative polymerase chain reaction, and positive samples were then whole-genome sequenced using an amplicon and target enrichment library preparation techniques and Illumina MiSeq sequencing technology. Generated consensus genome sequences were then analysed using phylogenetic tree reconstruction to categorise sequences into clades with a common ancestor, enabling investigations of both viral clade persistence and introductions. Hypothetical introduction dates were additionally assessed using a molecular clock model that calculated the time to the most recent common ancestor (TMRCA). We obtained 511 DENV whole-genome sequences covering four serotypes and more than ten distinct viral clades. For five of these clades, we had sufficient data to show that the same viral lineage persisted for at least several months. We noted that some clades persisted longer than others during the sampling time, and by comparison with other published sequences from elsewhere in Vietnam and around the world, we saw that at least two different viral lineages were introduced into the population during the study period (April 2017-2019). Next, by inferring the TMRCA from the construction of molecular clock phylogenies, we predicted that two of the viral lineages had been present in the study population for over a decade. We observed five viral lineages co-circulating in Nha Trang from three DENV serotypes, with two likely to have remained as uninterrupted transmission chains for a decade. This suggests clade cryptic persistence in the area, even during periods of low reported incidence.
Collapse
Affiliation(s)
- James Ashall
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Sonal Shah
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Joseph R Biggs
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Jui-Ning R Chang
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Yalda Jafari
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Oliver J Brady
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.,Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Huynh Kim Mai
- Department of Microbiology and Immunology, Pasteur Institute of Nha Trang, Xương Huân, Nha Trang, 650000, Vietnam
| | - Le Thuy Lien
- Department of Microbiology and Immunology, Pasteur Institute of Nha Trang, Xương Huân, Nha Trang, 650000, Vietnam
| | - Hung Do Thai
- Department of Microbiology and Immunology, Pasteur Institute of Nha Trang, Xương Huân, Nha Trang, 650000, Vietnam
| | - Hien Anh Thi Nguyen
- National Institute of Hygiene and Epidemiology, 1 P. Yec Xanh, Phạm Đình Hổ, Hai Bà Trưng, Hà Nội, 100000, Vietnam
| | - Dang Duc Anh
- National Institute of Hygiene and Epidemiology, 1 P. Yec Xanh, Phạm Đình Hổ, Hai Bà Trưng, Hà Nội, 100000, Vietnam
| | - Chihiro Iwasaki
- Paediatric Infectious Diseases Department, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Noriko Kitamura
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.,Paediatric Infectious Diseases Department, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Marnix Van Loock
- Janssen R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, Beerse B-2340, Belgium
| | - Guillermo Herrera-Taracena
- Janssen Global Public Health, Janssen Research & Development, LLC, 800 Ridgeview Drive, Horsham, PA 19044, USA
| | - Freya Rasschaert
- Janssen R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, Beerse B-2340, Belgium
| | | | - Lay-Myint Yoshida
- Paediatric Infectious Diseases Department, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Julius Clemence R Hafalla
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Stephane Hue
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.,Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Martin L Hibberd
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| |
Collapse
|
6
|
Yu X, Cheng G. Contribution of phylogenetics to understanding the evolution and epidemiology of dengue virus. Animal Model Exp Med 2022; 5:410-417. [PMID: 36245335 PMCID: PMC9610151 DOI: 10.1002/ame2.12283] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/05/2022] [Indexed: 11/18/2022] Open
Abstract
Dengue virus (DENV) is one of the most important arboviral pathogens in the tropics and subtropics, and nearly one‐third of the world's population is at risk of infection. The transmission of DENV involves a sylvatic cycle between nonhuman primates (NHP) and Aedes genus mosquitoes, and an endemic cycle between human hosts and predominantly Aedes aegypti. DENV belongs to the genus Flavivirus of the family Flaviviridae and consists of four antigenically distinct serotypes (DENV‐1‐4). Phylogenetic analyses of DENV have revealed its origin, epidemiology, and the drivers that determine its molecular evolution in nature. This review discusses how phylogenetic research has improved our understanding of DENV evolution and how it affects viral ecology and improved our ability to analyze and predict future DENV emergence.
Collapse
Affiliation(s)
- Xi Yu
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China.,Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, China.,Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Gong Cheng
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China.,Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, China.,Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| |
Collapse
|
7
|
Rodríguez-Aguilar ED, Martínez-Barnetche J, Rodríguez MH. Three highly variable genome regions of the four dengue virus serotypes can accurately recapitulate the CDS phylogeny. MethodsX 2022; 9:101859. [PMID: 36187156 PMCID: PMC9516459 DOI: 10.1016/j.mex.2022.101859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/10/2022] [Indexed: 11/18/2022] Open
Abstract
The circulation of the four-dengue virus (DENV) serotypes has significantly increased in recent years, accompanied by an increase in viral genetic diversity. In order to conduct disease surveillance and understand DENV evolution and its effects on virus transmission and disease, efficient and accurate methods for phylogenetic classification are required. Phylogenetic analysis of different viral genes sequences is the most used method, the envelope gene (E) being the most frequently selected target. We explored the genetic variability of the four DENV serotypes throughout their complete coding sequence (CDS) of sequences available in GenBank and used genomic regions of different variability rate to recapitulate the phylogeny obtained with the DENV CDS. Our results indicate that the use of high or low variable regions accurately recapitulate the phylogeny obtained with CDS of sequences from different DENV genotypes. However, when analyzing the phylogeny of a single genotype, highly variable regions performed better in recapitulating the distance branch length, topology, and support of the CDS phylogeny. The use of three concatenated highly variable regions was not statistically different in distance branch length and support to that obtained in CDS phylogeny.•This study demonstrated the ability of highly variable regions of the DENV genome to recapitulate the phylogeny obtained with the full coding sequence (CDS).•The use of genomic regions of high or low variability did not affect the performance in recapitulating the phylogeny obtained with CDS from different genotypes. However, when phylogeny was analyzed for sequences from a single genotype, highly variable regions performed better in recapitulating the distance branch length, topology, and support of the CDS phylogeny.•The use of concatenated highly variable genome regions represent a useful option for recapitulating genome-wide phylogenies in analyses of sequences belonging to the same DENV genotype.
Collapse
|
8
|
Origin of New Lineages by Recombination and Mutation in Avian Infectious Bronchitis Virus from South America. Viruses 2022; 14:v14102095. [PMID: 36298650 PMCID: PMC9609748 DOI: 10.3390/v14102095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/09/2022] [Accepted: 09/11/2022] [Indexed: 11/17/2022] Open
Abstract
The gammacoronavirus avian infectious bronchitis virus (IBV) is a highly contagious respiratory pathogen of primary economic importance to the global poultry industry. Two IBV lineages (GI-11 and GI-16) have been widely circulating for decades in South America. GI-11 is endemic to South America, and the GI-16 is globally distributed. We obtained full-length IBV genomes from Argentine and Uruguayan farms using Illumina sequencing. Genomes of the GI-11 and GI-16 lineages from Argentina and Uruguay differ in part of the spike coding region. The remaining genome regions are similar to the Chinese and Italian strains of the GI-16 lineage that emerged in Asia or Europe in the 1970s. Our findings support that the indigenous GI-11 strains recombine extensively with the invasive GI-16 strains. During the recombination process, GI-11 acquired most of the sequences of the GI-16, retaining the original S1 sequence. GI-11 strains with recombinant genomes are circulating forms that underwent further local evolution. The current IBV scenario in South America includes the GI-16 lineage, recombinant GI-11 strains sharing high similarity with GI-16 outside S1, and Brazilian GI-11 strains with a divergent genomic background. There is also sporadic recombinant in the GI-11 and GI-16 lineages among vaccine and field strains. Our findings exemplified the ability of IBV to generate emergent lineage by using the S gene in different genomic backgrounds. This unique example of recombinational microevolution underscores the genomic plasticity of IBV in South America.
Collapse
|
9
|
Evolutionary Shift from Purifying Selection towards Divergent Selection of SARS-CoV2 Favors its Invasion into Multiple Human Organs. Virus Res 2022; 313:198712. [PMID: 35176330 PMCID: PMC8843322 DOI: 10.1016/j.virusres.2022.198712] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/10/2022] [Accepted: 02/13/2022] [Indexed: 01/07/2023]
Abstract
SARS-CoV2 virus is believed to be originated from a closely related bat Coronavirus RaTG13 lineage and uses its key entry-point residues in S1 protein to attach with human ACE2 receptor. SARS-CoV2 could enter human from bat with its poorly developed entry-point residues much before its known appearance with slower mutation rate or recently with efficiently developed entry-point residues with higher mutation rate or through an intermediate host. Temporal analysis of SARS-CoV2 genome shows that its nucleotide substitution rate is as low as 27nt/year with an evolutionary rate of 9×10−4/site/year, which is well within the range of other RNA virus (10−4 to 10−6/site/year). TMRCA of SARS-CoV2 from bat RaTG13 lineage appears to be in between 9 and 14 years. Evolution of a critical entry-point residue Y493Q needs two substitutions with an intermediate virus carrying Y493H (Y>H>Q) but has not been identified in known twenty-nine bat CoV virus. Genetic codon analysis indicates that SARS-CoV2 evolution during propagation in human disobeys neutral evolution as nonsynonymous mutations surpass synonymous mutations with the increase of ω (dn/ds). Taken together, genetic data suggests that SARS-CoV2 is originated long time back before its appearance in human in 2019. Increase of ω signifies that SARs-CoV2 evolution is approaching towards diversifying selection from purifying selection predictably for its infection power to evade multiple human organs.
Collapse
|
10
|
Genome analysis suggests HTLV-1aA introduction in Chile related to migrations of ancestral indigenous populations. Virus Res 2022; 311:198687. [DOI: 10.1016/j.virusres.2022.198687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/15/2021] [Accepted: 01/14/2022] [Indexed: 11/19/2022]
|
11
|
Seroprevalence of arboviruses in Ecuador: Implications for improved surveillance. ACTA ACUST UNITED AC 2021; 41:247-259. [PMID: 34214266 PMCID: PMC8382292 DOI: 10.7705/biomedica.5623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Indexed: 11/27/2022]
Abstract
Introduction: Arthropod-borne viruses (arboviruses) cause morbidity and mortality in humans and domestic animals worldwide. The percentage of population immunity or susceptibility to these viruses in Ecuador is unknown. Objectives: To investigate the proportion of Ecuadorian populations with IgG antibodies (Abs) (past exposure/immunity) and IgM Abs (current exposure) against flaviviruses and alphaviruses and to study the activity of these viruses in Ecuador. Materials and methods: During 2009-2011, we conducted a serosurvey for selected arboviruses in humans (n=1,842), equines (n=149), and sentinel hamsters (n=84) at two coastal locations and one in the Amazon basin (Eastern Ecuador) using enzyme-linked immunosorbent assay and hemagglutination inhibition test. Results: From 20.63% to 63.61% of humans showed IgG-antibodies for the flaviviruses: Dengue virus (DENV), yellow fever virus (YFV) Saint Louis encephalitis virus, and West Nile virus (WNV); from 4.67% to 8.63% showed IgG-Abs for the alphaviruses: Venezuelan equine encephalitis virus, eastern equine encephalitis virus, and western equine encephalitis virus. IgM-Abs were found for DENV and WNV. Equines and hamsters showed antibodies to alphaviruses in all locations; two hamsters seroconverted to YFV in the Amazonia. Conclusions: The results show a YFV vaccination history and suggest the activity of arboviruses not included in the current surveillance scheme. Enhanced arbovirus and mosquito surveillance, as well as continued YFV vaccination and evaluation of its coverage/ effectiveness, are recommended.
Collapse
|
12
|
Burrows JTA, Depierreux D, Nibert ML, Pearson BJ. A Novel Taxon of Monosegmented Double-Stranded RNA Viruses Endemic to Triclad Flatworms. J Virol 2020; 94:e00623-20. [PMID: 32907972 PMCID: PMC7592200 DOI: 10.1128/jvi.00623-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 09/01/2020] [Indexed: 12/12/2022] Open
Abstract
Freshwater planarians, flatworms from order Tricladida, are experimental models of stem cell biology and tissue regeneration. An aspect of their biology that remains less well studied is their relationship with viruses that may infect them. In this study, we identified a taxon of monosegmented double-stranded RNA (dsRNA) viruses in five planarian species, including the well-characterized model Schmidtea mediterranea Sequences for the S. mediterranea virus (abbreviated SmedTV for S. mediterranea tricladivirus) were found in public transcriptome data from multiple institutions, indicating that SmedTV is prevalent in S. mediterranea lab colonies, though without causing evident disease. The presence of SmedTV in discrete cells was shown through in situ hybridization methods for detecting the viral RNA. SmedTV-staining cells were found to be concentrated in neural structures (eyes and brain) but were also scattered in other worm tissues as well. In contrast, few SmedTV-staining cells were seen in stem cell compartments (also consistent with RNA sequencing data) or early blastema tissue. RNA interference (RNAi) targeted to the SmedTV sequence led to apparent cure of infection, though effects on worm health or behavior were not observed. Efforts to transmit SmedTV horizontally through microinjection were unsuccessful. Based on these findings, we conclude that SmedTV infects S. mediterranea in a persistent manner and undergoes vertical transmission to progeny worms during serial passage in lab colonies. The utility of S. mediterranea as a regeneration model, coupled with the apparent capacity of SmedTV to evade normal host immune/RNAi defenses under standard conditions, argues that further studies are warranted to explore this newly recognized virus-host system.IMPORTANCE Planarians are freshwater flatworms, related more distantly to tapeworms and flukes, and have been developed as models to study the molecular mechanisms of stem cell biology and tissue regeneration. These worms live in aquatic environments, where they are likely to encounter a variety of viruses, bacteria, and eukaryotic organisms with pathogenic potential. How the planarian immune system has evolved to cope with these potential pathogens is not well understood, and only two types of planarian viruses have been described to date. Here, we report discovery and inaugural studies of a novel taxon of dsRNA viruses in five different planarian species. The virus in the best-characterized model species, Schmidtea mediterranea, appears to persist long term in that host while avoiding endogenous antiviral or RNAi mechanisms. The S. mediterranea virus-host system thus seems to offer opportunity for gaining new insights into host defenses and their evolution in an important lab model.
Collapse
Affiliation(s)
- Jeffrey T A Burrows
- The Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Delphine Depierreux
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Max L Nibert
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Bret J Pearson
- The Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- University of Toronto, Department of Molecular Genetics, Toronto, Ontario, Canada
| |
Collapse
|
13
|
Darcy AW, Kanda S, Dalipanda T, Joshua C, Shimono T, Lamaningao P, Mishima N, Nishiyama T. Multiple arboviral infections during a DENV-2 outbreak in Solomon Islands. Trop Med Health 2020; 48:33. [PMID: 32435149 PMCID: PMC7225641 DOI: 10.1186/s41182-020-00217-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/23/2020] [Indexed: 11/15/2022] Open
Abstract
Background Solomon Islands, a country made up of tropical islands, has suffered cyclic dengue fever (DF) outbreaks in the past three decades. An outbreak of dengue-like illness (DLI) that occurred in April 2016 prompted this study, which aimed to determine the population’s immunity status and identify the arboviruses circulating in the country. Methods A household survey, involving 188 participants in two urban areas (Honiara and Gizo), and a parallel hospital-based clinical survey were conducted in April 2016. The latter was repeated in December after a surge in DLI cases. Arbovirus IgG ELISA were performed on the household blood samples to determine the prevalence of arboviruses in the community, while qPCR testing of the clinical samples was used to identify the circulating arboviruses. Dengue virus (DENV)-positive samples were further characterized by amplifying and sequencing the envelope gene. Results The overall prevalence rates of DENV, Zika virus, and chikungunya virus were 83.4%, 7.6%, and 0.9%, respectively. The qPCR positivity rates of the clinical samples collected in April 2016 were as follows: DENV 39.6%, Zika virus 16.7%, and chikungunya virus 6.3%, which increased to 74%, 48%, and 20% respectively in December 2016. The displacement of the circulating serotype-3, genotype-1, with DENV serotype 2, genotype cosmopolitan was responsible for the outbreak in 2016. Conclusions A DENV outbreak in Solomon Islands was caused by the introduction of a single serotype. The high prevalence of DENV provided transient cross-protection, which prevented the introduction of a new serotype from the hyperendemic region for at least 3 years. The severe outcomes seen in the recent outbreak probably resulted from changes in the causative viruses and the effects of population immunity and changes in the outbreak pattern. Solomon Islands needs to step up surveillance to include molecular tools, increase regional communication, and perform timely interventions.
Collapse
|
14
|
Pollett S, Fauver JR, Berry IM, Melendrez M, Morrison A, Gillis LD, Johansson MA, Jarman RG, Grubaugh ND. Genomic Epidemiology as a Public Health Tool to Combat Mosquito-Borne Virus Outbreaks. J Infect Dis 2020; 221:S308-S318. [PMID: 31711190 PMCID: PMC11095994 DOI: 10.1093/infdis/jiz302] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Next-generation sequencing technologies, exponential increases in the availability of virus genomic data, and ongoing advances in phylogenomic methods have made genomic epidemiology an increasingly powerful tool for public health response to a range of mosquito-borne virus outbreaks. In this review, we offer a brief primer on the scope and methods of phylogenomic analyses that can answer key epidemiological questions during mosquito-borne virus public health emergencies. We then focus on case examples of outbreaks, including those caused by dengue, Zika, yellow fever, West Nile, and chikungunya viruses, to demonstrate the utility of genomic epidemiology to support the prevention and control of mosquito-borne virus threats. We extend these case studies with operational perspectives on how to best incorporate genomic epidemiology into structured surveillance and response programs for mosquito-borne virus control. Many tools for genomic epidemiology already exist, but so do technical and nontechnical challenges to advancing their use. Frameworks to support the rapid sharing of multidimensional data and increased cross-sector partnerships, networks, and collaborations can support advancement on all scales, from research and development to implementation by public health agencies.
Collapse
Affiliation(s)
- S. Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Department of Preventive Medicine and Biostatistics, Uniformed Services University, Bethesda, Maryland
- Marie Bashir Institute, University of Sydney, Camperdown, New South Wales, Australia
| | - J. R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | | | | | - L. D. Gillis
- Bureau of Public Health Laboratories–Miami, Florida Department of Health
| | - M. A. Johansson
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - R. G. Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - N. D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut
| |
Collapse
|
15
|
Chen JT, Qin J, Li K, Xu QY, Wang XP, Plyusnin A, Hou W, Zhang YZ. Identification and characterization of a novel subtype of Tula virus in Microtus arvalis obscurus voles sampled from Xinjiang, China. INFECTION GENETICS AND EVOLUTION 2019; 75:104012. [PMID: 31446137 DOI: 10.1016/j.meegid.2019.104012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 08/16/2019] [Accepted: 08/19/2019] [Indexed: 12/24/2022]
Abstract
Although most of Arvicolinae associated hantaviruses can not cause disease in humans, hemorrhagic fever with renal syndrome (HFRS) cases caused by Tula virus (TULV) have been described in Europe since 2002. In addition to Europe, TULV was also identified in the Microtus arvalis obscurus voles sampled from Kazakhstan, which shares borders with China. To gain more insight into the molecular epidemiology of TULV, a total of 365 rodents representing 7 species of 4 subfamily (Arvicolinae, Murinae, Gerbillinae, and Cricetinae) were captured in Qapqal county, Xinjiang, northwest China. Hantavirus RNA was recovered from 40 lung tissue samples of M. arvalis obscurus, with the prevalence of 10.96%. Genetic analysis revealed that all recovered viral sequences were most closely related to those of TULV, but exhibited >11% nucleotide differences from all currently known TULV, suggesting that they may represent a new subtype of TULV. In the S tree, the newly identified viruses formed a distinct lineage and showed a close evolutionary relationship with those sampled from Southwestern Siberia and Kazakhstan. However, they exhibited a different clustering pattern in both the M and the L trees, suggesting the possibility of genetic reassortment. Finally, the recombination event was also observed in Xinjiang TULV viruses. In sum, all these data reveal a complex evolutionary history of TULV in Central Asia.
Collapse
Affiliation(s)
- Jin-Tao Chen
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping Liuzi 5, 102206 Beijing, China; State Key Laboratory of Virology, Institute of Medical Virology, Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei, China
| | - Jing Qin
- Yili Prefecture Center for Disease Control and Prevention, Yili 835000, China
| | - Kun Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping Liuzi 5, 102206 Beijing, China
| | - Qi-Yi Xu
- Yili Prefecture Center for Disease Control and Prevention, Yili 835000, China
| | - Xiao-Ping Wang
- Yili Prefecture Center for Disease Control and Prevention, Yili 835000, China
| | - Alexander Plyusnin
- Department of Virology, Haartman Institute, University of Helsinki, 00014 Helsinki, Finland
| | - Wei Hou
- State Key Laboratory of Virology, Institute of Medical Virology, Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei, China.
| | - Yong-Zhen Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping Liuzi 5, 102206 Beijing, China; Shanghai Public Health Clinical Center, Institute of Biomedical Sciences, Fudan University, Shanghai, China.
| |
Collapse
|
16
|
Multiple introductions of dengue virus strains contribute to dengue outbreaks in East Kalimantan, Indonesia, in 2015-2016. Virol J 2019; 16:93. [PMID: 31345242 PMCID: PMC6659258 DOI: 10.1186/s12985-019-1202-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/18/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Dengue fever is a febrile disease caused by dengue virus (DENV), which affects people throughout the tropical and subtropical regions of the world, including Indonesia. East Kalimantan (Borneo) province suffered a dramatic increase in dengue cases in 2015 and 2016, making it the province with the second highest incidence of dengue in Indonesia. Despite this, dengue in East Kalimantan is understudied; leaving transmission dynamics of the disease in the area are mostly unknown. In this study, we investigate the factors contributing to the outbreaks in East Kalimantan. METHODS Prospective clinical and molecular virology study was conducted in two main cities in the province, namely Samarinda and Balikpapan, in 2015-2016. Patients' clinical, hematological, and demographic data were recorded. Dengue detection and confirmation was performed using NS1-antigen and IgG/IgM antibody detection. RT-PCR was conducted to determine the serotypes of the virus. Phylogenetic analysis was performed based on envelope gene sequences. RESULTS Three hundred patients with suspected dengue were recruited. Among these, 132 (44%) were diagnosed with dengue by NS1 antigen and/or nucleic acid detection. The majority of the infections (60%) were primary, with dengue hemorrhagic fever (DHF) the predominant manifestation (71.9%). Serotyping detected all four DENV serotypes in 112 (37.3%) cases, with the majority of patients (58.9%) infected by DENV-3. Phylogenetic analysis based on envelope gene sequences revealed the genotypes of the viruses as DENV-1 Genotype I, DENV-2 Cosmopolitan, and DENV-3 Genotype I. Most virus strains were closely-related to strains from cities in Indonesia. CONCLUSIONS Our observations indicate that multiple introductions of endemic DENV from surrounding cities in Indonesia, coupled with relatively low herd immunity, were likely responsible for the outbreak of the dominant viruses. The study provides information on the clinical spectrum of the disease, together with serology, viral genetics, and demographic data, which will be useful for better understanding of dengue disease in Borneo.
Collapse
|
17
|
Sacramento CQ, Fintelman-Rodrigues N, Miranda M, Siqueira MM, Souza TML. Influenza virus RNA polymerase may be activated inside the virion. J Gen Virol 2018; 99:1608-1613. [PMID: 30394870 DOI: 10.1099/jgv.0.001168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Influenza A and B virions are packaged with their polymerases to catalyse RNA-dependent RNA polymerase activity. Since there is no evidence to rule in or out the permissiveness of influenza virions to triphosphate ribonucleotides, we functionally evaluated this. We found the means to stimulate influenza A and B RNA polymerase activity inside the virion, called natural endogenous RNA polymerase (NERP) activity. Stimulation of NERP activity increased up to 3 log10 viral RNA content, allowing the detection of influenza virus in otherwise undetectable clinical samples. NERP activation also improved our capacity to sequence misidentified regions of the influenza genome from clinical samples. By treating the samples with the ribavirin triphosphate we inhibited NERP activity, which confirms our hypothesis and highlights that this assay could be used to screen antiviral drugs. Altogether, our data show that NERP activity could be explored to increase molecular diagnostic sensitivity and/or to develop antiviral screening assays.
Collapse
Affiliation(s)
- Carolina Q Sacramento
- 2Laboratório de Vírus Respiratório e do Sarampo, Pavilhão Helio Peggy e Pereira, IOC, Fiocruz, Av. Brasil 4365, Manguinhos, Rio de Janeiro/RJ, Brazil.,3National Institute for Science and Technology on Innovation on Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Av. Brasil 4036, Manguinhos, Rio de Janeiro/RJ, Brazil.,1Laboratório de Imunofarmacologia, Pavilhão Osório de Almeida, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Av. Brasil 4365, Manguinhos, Rio de Janeiro/RJ, Brazil
| | - Natalia Fintelman-Rodrigues
- 3National Institute for Science and Technology on Innovation on Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Av. Brasil 4036, Manguinhos, Rio de Janeiro/RJ, Brazil.,2Laboratório de Vírus Respiratório e do Sarampo, Pavilhão Helio Peggy e Pereira, IOC, Fiocruz, Av. Brasil 4365, Manguinhos, Rio de Janeiro/RJ, Brazil.,1Laboratório de Imunofarmacologia, Pavilhão Osório de Almeida, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Av. Brasil 4365, Manguinhos, Rio de Janeiro/RJ, Brazil
| | - Milene Miranda
- 2Laboratório de Vírus Respiratório e do Sarampo, Pavilhão Helio Peggy e Pereira, IOC, Fiocruz, Av. Brasil 4365, Manguinhos, Rio de Janeiro/RJ, Brazil
| | - Marilda M Siqueira
- 2Laboratório de Vírus Respiratório e do Sarampo, Pavilhão Helio Peggy e Pereira, IOC, Fiocruz, Av. Brasil 4365, Manguinhos, Rio de Janeiro/RJ, Brazil
| | - Thiago Moreno L Souza
- 2Laboratório de Vírus Respiratório e do Sarampo, Pavilhão Helio Peggy e Pereira, IOC, Fiocruz, Av. Brasil 4365, Manguinhos, Rio de Janeiro/RJ, Brazil.,1Laboratório de Imunofarmacologia, Pavilhão Osório de Almeida, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Av. Brasil 4365, Manguinhos, Rio de Janeiro/RJ, Brazil.,3National Institute for Science and Technology on Innovation on Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Av. Brasil 4036, Manguinhos, Rio de Janeiro/RJ, Brazil
| |
Collapse
|
18
|
Masyeni S, Yohan B, Somia IKA, Myint KSA, Sasmono RT. Dengue infection in international travellers visiting Bali, Indonesia. J Travel Med 2018; 25:5065180. [PMID: 30113689 PMCID: PMC6118167 DOI: 10.1093/jtm/tay061] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 08/10/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND Dengue, an acute febrile illness caused by infection with dengue virus (DENV), is endemic in Bali, Indonesia. As one of the world's most popular tourist destinations, Bali is regularly visited by domestic and international travellers, who are prone to infection by endemic pathogens, including DENV. Currently, limited data are available on the characteristics of dengue in travellers visiting Bali. Information on the epidemiology and virological aspects of dengue in these tourists is important to gain a better understanding of the dengue disease in international travellers. METHODS We performed a prospective cross-sectional dengue study involving foreign travellers visiting Bali, Indonesia in the period of 2015-17. Patients presenting at Kasih Ibu Hospital with fever and clinical symptoms of dengue were asked to participate in the study. Clinical and laboratory assessments were performed and sera were collected for molecular analysis, which included DENV serotyping, genome sequencing and phylogenetic analysis. RESULTS Among the 201 patients recruited, dengue was confirmed in 133 (66.2%) of them, based on detection of NS1 antigen and/or viral RNA. Of these, 115 (86.5%) manifested dengue fever (DF) and 18 (13.5%) dengue haemorrhagic fever (DHF). The temporal predominance of infecting DENV serotype was DENV-2 (48.7%), followed by DENV-3 (36.1%), DENV-1 (9.2%) and DENV-4 (3.4%). Phylogenetic analysis of DENV based on envelope gene sequences revealed that the source of DENVs was local endemic viruses. CONCLUSION Our study confirms that dengue is one of the causes of fever in travellers visiting Bali. Although it is a cause of significant morbidity, the majority of patients only experienced mild DF, with only a small proportion developing DHF. We revealed that DENVs isolated were autochthonous. Accurate diagnosis, preventive measures and continuous disease surveillance will be useful for better management of dengue infection in travellers.
Collapse
Affiliation(s)
- Sri Masyeni
- Department of Internal Medicine, Faculty of Medicine and Health Sciences, Warmadewa University, Denpasar, Bali, Indonesia
| | | | - I Ketut Agus Somia
- Department of Internal Medicine, Faculty of Medicine and Health Sciences, Udayana University, Denpasar, Bali, Indonesia
| | - Khin S A Myint
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | | |
Collapse
|
19
|
McCrone JT, Woods RJ, Martin ET, Malosh RE, Monto AS, Lauring AS. Stochastic processes constrain the within and between host evolution of influenza virus. eLife 2018; 7:e35962. [PMID: 29683424 PMCID: PMC5933925 DOI: 10.7554/elife.35962] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 04/18/2018] [Indexed: 12/12/2022] Open
Abstract
The evolutionary dynamics of influenza virus ultimately derive from processes that take place within and between infected individuals. Here we define influenza virus dynamics in human hosts through sequencing of 249 specimens from 200 individuals collected over 6290 person-seasons of observation. Because these viruses were collected from individuals in a prospective community-based cohort, they are broadly representative of natural infections with seasonal viruses. Consistent with a neutral model of evolution, sequence data from 49 serially sampled individuals illustrated the dynamic turnover of synonymous and nonsynonymous single nucleotide variants and provided little evidence for positive selection of antigenic variants. We also identified 43 genetically-validated transmission pairs in this cohort. Maximum likelihood optimization of multiple transmission models estimated an effective transmission bottleneck of 1-2 genomes. Our data suggest that positive selection is inefficient at the level of the individual host and that stochastic processes dominate the host-level evolution of influenza viruses.
Collapse
Affiliation(s)
- John T McCrone
- Department of Microbiology and ImmunologyUniversity of MichiganAnn ArborUnited States
| | - Robert J Woods
- Division of Infectious Diseases, Department of Internal MedicineUniversity of MichiganAnn ArborUnited States
| | - Emily T Martin
- Department of EpidemiologyUniversity of MichiganAnn ArborUnited States
| | - Ryan E Malosh
- Department of EpidemiologyUniversity of MichiganAnn ArborUnited States
| | - Arnold S Monto
- Department of EpidemiologyUniversity of MichiganAnn ArborUnited States
| | - Adam S Lauring
- Department of Microbiology and ImmunologyUniversity of MichiganAnn ArborUnited States
- Division of Infectious Diseases, Department of Internal MedicineUniversity of MichiganAnn ArborUnited States
| |
Collapse
|
20
|
Pollett S, Melendrez MC, Maljkovic Berry I, Duchêne S, Salje H, Cummings DAT, Jarman RG. Understanding dengue virus evolution to support epidemic surveillance and counter-measure development. INFECTION GENETICS AND EVOLUTION 2018; 62:279-295. [PMID: 29704626 DOI: 10.1016/j.meegid.2018.04.032] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 04/20/2018] [Accepted: 04/24/2018] [Indexed: 11/30/2022]
Abstract
Dengue virus (DENV) causes a profound burden of morbidity and mortality, and its global burden is rising due to the co-circulation of four divergent DENV serotypes in the ecological context of globalization, travel, climate change, urbanization, and expansion of the geographic range of the Ae.aegypti and Ae.albopictus vectors. Understanding DENV evolution offers valuable opportunities to enhance surveillance and response to DENV epidemics via advances in RNA virus sequencing, bioinformatics, phylogenetic and other computational biology methods. Here we provide a scoping overview of the evolution and molecular epidemiology of DENV and the range of ways that evolutionary analyses can be applied as a public health tool against this arboviral pathogen.
Collapse
Affiliation(s)
- S Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Marie Bashir Institute, University of Sydney, NSW, Australia; Institute for Global Health Sciences, University of California at San Francisco, CA, USA.
| | - M C Melendrez
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - I Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - S Duchêne
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Australia
| | - H Salje
- Institut Pasteur, Paris, France; Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - D A T Cummings
- Johns Hopkins School of Public Health, Baltimore, MD, USA; University of Florida, FL, USA
| | - R G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| |
Collapse
|
21
|
Genomic analysis of dengue virus serotype 1 (DENV-1) genotypes from Surabaya, Indonesia. Virus Genes 2018; 54:461-465. [PMID: 29616396 DOI: 10.1007/s11262-018-1558-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 03/29/2018] [Indexed: 10/17/2022]
Abstract
Dengue has caused a significant public health impact globally. With the diverse genetic of the causative viruses, analysis of dengue virus (DENV) genomes is important to supplement epidemiological data with information that can be used to reconstruct the history of epidemics in time and space. We have reported the clinical and virological characteristics of dengue in Surabaya, Indonesia and revealed the presence of all four DENV serotypes and the predominance of DENV-1. The further classification of Surabaya DENV-1 into two different genotypes warrants in-depth genomic analysis to study the dynamics of both genotypes and their contribution to virus evolution, virus transmission, and disease. We performed full-length genome sequencing to nine isolates' representatives from DENV-1 Genotype I and Genotype IV. Phylogenetic and evolutionary analyses suggested the more recent introduction of Genotype I viruses compared to the more endemic Genotype IV. Comparative analysis of Surabaya DENV-1 genomes and other sequences available publicly revealed that the majority of the DENV-1 codons were under strong purifying selection, while seven codon sites identified to be under positive selection. We highlight a unique codon site under the positive pressure in the NS1 gene of DENV-1. Our results provide additional genomic data of DENV from Indonesia that may contribute to the better understanding of dengue disease dynamics.
Collapse
|
22
|
Host-associated selection of a P3 mutant of zucchini yellow mosaic virus affects viral infectivity in watermelon. Arch Virol 2018; 163:1449-1454. [PMID: 29426994 DOI: 10.1007/s00705-018-3719-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 12/11/2017] [Indexed: 10/18/2022]
Abstract
In this study, we found that the infectivity of zucchini yellow mosaic virus (ZYMV) in watermelon lines H1 and K6 changed from partial to complete after propagation in the susceptible watermelon line ZXG637. When using cucumber infected with strain ZYMV-CH87 as an inoculum (named ZYMV-CH87C), the mean incidences of infection in lines H1 and K6 were 6% and 11%, respectively. However, when these lines were inoculated with ZXG637 infected with ZYMV-CH87C (named ZYMV-637), 100% of the plants became infected. Sequencing of ZYMV from these different inoculums revealed two nucleotide changes in the P3 cistron in ZYMV-637, which resulted in changes in the amino acids at positions 768 and 857 of the P3 protein, compared with the original strain ZYMV-CH87. We named this variant the M768I857-variant. The M768I857-variant was detected at low levels (3.9%) in ZYMV-CH87C. When ZYMV-CH87C was passaged with ZXG637, the M768I857-variant was selected by the host, and the original sequence was replaced entirely after two passages. These results may be explained by host-associated selection due to an unknown host-encoded factor. Using the M768I857-variant as an inoculum, 100% of the H1 and K6 plants showed systemic symptoms. These results suggest that (1) changing the individual amino acids at the end of the P3 N-terminus induces resistance-breaking, and (2) the P3 N-terminus may be involved in host recognition.
Collapse
|
23
|
Kusmintarsih ES, Hayati RF, Turnip ON, Yohan B, Suryaningsih S, Pratiknyo H, Denis D, Sasmono RT. Molecular characterization of dengue viruses isolated from patients in Central Java, Indonesia. J Infect Public Health 2017; 11:617-625. [PMID: 29056517 DOI: 10.1016/j.jiph.2017.09.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 08/14/2017] [Accepted: 09/09/2017] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Dengue is hyper-endemic in Indonesia. Purwokerto city in Central Java province is routinely ravaged by the disease. Despite the endemicity of dengue in this city, there is still no data on the virological aspects of dengue in the city. We conducted a molecular surveillance study of the circulating dengue viruses (DENV) in Purwokerto city to gain information on the virus origin, serotype and genotype distribution, and phylogenetic characteristics of DENV. METHODS A cross-sectional dengue molecular surveillance study was conducted in Purwokerto. Sera were collected from dengue-suspected patients attending three hospitals in the city. Diagnosis was performed using dengue NS1 antigen and IgG/IgM antibodies detection. DENV serotyping was performed using Simplexa Dengue real-time RT-PCR. Sequencing was conducted to obtain full-length DENV Envelope (E) gene sequences, which were then used in phylogenetic and genotypic analyses. Patients' clinical and demographic data were collected and analyzed. RESULTS A total of 105 dengue-suspected patients' sera were collected, in which 80 (76.2%) were positive for IgM and/or IgG, and 57 (54.2%) were confirmed as dengue by NS1 antigen and/or DENV RNA detection using RT-PCR. Serotyping was successful for 47 isolates. All four serotypes circulated in the area with DENV-3 as the predominant serotype. Phylogenetic analyses grouped the isolates into Genotype I for DENV-1, Cosmopolitan genotype for DENV-2, and Genotype I and II for DENV-3 and -4, respectively. The analyses also revealed the close relatedness of Purwokerto isolates to other DENV strains from Indonesia and neighboring countries. CONCLUSION We reveal the molecular and virological characteristics of DENV in Purwokerto, Banyumas regency, Central Java. The genotype and phylogenetic analyses indicate the endemicity of the circulating DENV in the city. Our serotype and genotype data provide references for future dengue molecular epidemiology studies and disease management in the region.
Collapse
Affiliation(s)
- Endang S Kusmintarsih
- Fakultas Biologi, Universitas Jenderal Soedirman, Jl. dr. Soeparno No. 63, Purwokerto, 53122, Indonesia
| | - Rahma F Hayati
- Eijkman Institute for Molecular Biology, Jl. Diponegoro 69, Jakarta, 10430, Indonesia
| | - Oktaviani N Turnip
- Fakultas Biologi, Universitas Jenderal Soedirman, Jl. dr. Soeparno No. 63, Purwokerto, 53122, Indonesia; Eijkman Institute for Molecular Biology, Jl. Diponegoro 69, Jakarta, 10430, Indonesia
| | - Benediktus Yohan
- Eijkman Institute for Molecular Biology, Jl. Diponegoro 69, Jakarta, 10430, Indonesia
| | - Suhestri Suryaningsih
- Fakultas Biologi, Universitas Jenderal Soedirman, Jl. dr. Soeparno No. 63, Purwokerto, 53122, Indonesia
| | - Hery Pratiknyo
- Fakultas Biologi, Universitas Jenderal Soedirman, Jl. dr. Soeparno No. 63, Purwokerto, 53122, Indonesia
| | - Dionisius Denis
- Eijkman Institute for Molecular Biology, Jl. Diponegoro 69, Jakarta, 10430, Indonesia
| | - R Tedjo Sasmono
- Eijkman Institute for Molecular Biology, Jl. Diponegoro 69, Jakarta, 10430, Indonesia.
| |
Collapse
|
24
|
Franco LS, Holechek SA, Caplan MR, Blattman JN. Sequence-specific detection of different strains of LCMV in a single sample using tentacle probes. Virol J 2017; 14:197. [PMID: 29029641 PMCID: PMC5640925 DOI: 10.1186/s12985-017-0863-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/05/2017] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Virus infections often result in quasispecies of viral strains that can have dramatic impacts on disease outcomes. However, sequencing of viruses to determine strain composition is time consuming and often cost-prohibitive. Rapid, cost-effective methods are needed for accurate measurement of virus diversity to understand virus evolution and can be useful for experimental systems. METHODS We have developed a novel molecular method for sequence-specific detection of RNA virus genetic variants called Tentacle Probes. The probes are modified molecular beacons that have dramatically improved false positive rates and specificity in routine qPCR. To validate this approach, we have designed Tentacle Probes for two different strains of Lymphocytic Choriomeningitis Virus (LCMV) that differ by only 3 nucleotide substitutions, the parental Armstrong and the more virulent Clone-13 strain. One of these mutations is a missense mutation in the receptor protein GP1 that leads to the Armstrong strain to cause an acute infection and Clone-13 to cause a chronic infection instead. The probes were designed using thermodynamic calculations for hybridization between target or non-target sequences and the probe. RESULTS Using this approach, we were able to distinguish these two strains of LCMV individually by a single nucleotide mutation. The assay showed high reproducibility among different concentrations of viral cDNA, as well as high specificity and sensitivity, especially for the Clone-13 Tentacle Probe. Furthermore, in virus mixing experiments we were able to detect less than 10% of Clone-13 cDNA diluted in Armstrong cDNA. CONCLUSIONS Thus, we have developed a fast, cost-effective approach for identifying Clone-13 strain in a mix of other LCMV strains.
Collapse
Affiliation(s)
- Lina S Franco
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Susan A Holechek
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Simon A. Levin Mathematical, Computational and Modeling Sciences Center, Arizona State University, Tempe, AZ, USA
| | - Michael R Caplan
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | | |
Collapse
|
25
|
Yudhaputri FA, Trimarsanto H, Perkasa A, Yohan B, Haryanto S, Wiyatno A, Soebandrio A, Myint KS, Ledermann JP, Rosenberg R, Powers AM, Sasmono RT. Genomic characterization of Zika virus isolated from Indonesia. Virology 2017; 510:248-251. [PMID: 28755588 DOI: 10.1016/j.virol.2017.07.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 07/10/2017] [Accepted: 07/20/2017] [Indexed: 01/06/2023]
Abstract
Zika virus (ZIKV) JMB-185 strain was isolated from a febrile patient in Jambi, Indonesia in 2014. To understand its genetic characteristics, we performed whole genome sequencing using the Ion Torrent PGM platform on the supernatant of the first passage. The phylogenetic analysis showed that the isolate was not closely related to the Brazilian ZIKV associated with microcephaly or isolates from the recent Singapore Zika outbreak. Molecular evolution analysis indicated that JMB-185 strain may have been circulating in the Southeast Asia region, including Indonesia since 2000. We observed high nucleotide sequence identity between Indonesia, Thailand, Singapore, and American strains although unique amino acid substitutions were also observed. This report provides information on the genomic characteristics of Indonesian ZIKV which may be used for further studies.
Collapse
Affiliation(s)
| | - Hidayat Trimarsanto
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia; Agency for Assessment and Application of Technology, Jakarta, Indonesia
| | - Aditya Perkasa
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | | | | | - Ageng Wiyatno
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | | | - Khin Saw Myint
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | | | - Ronald Rosenberg
- Centers for Disease Control and Prevention, Fort Collins, Colorado, USA
| | - Ann M Powers
- Centers for Disease Control and Prevention, Fort Collins, Colorado, USA
| | - R Tedjo Sasmono
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia.
| |
Collapse
|
26
|
Lestari CSW, Yohan B, Yunita A, Meutiawati F, Hayati RF, Trimarsanto H, Sasmono RT. Phylogenetic and evolutionary analyses of dengue viruses isolated in Jakarta, Indonesia. Virus Genes 2017; 53:778-788. [PMID: 28600724 DOI: 10.1007/s11262-017-1474-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/03/2017] [Indexed: 02/01/2023]
Abstract
Dengue has affected Indonesia for the last five decades and become a major health problem in many cities in the country. Jakarta, the capital of Indonesia, reports dengue cases annually, with several outbreaks documented. To gain information on the dynamic and evolutionary history of dengue virus (DENV) in Jakarta, we conducted phylogenetic and evolutionary analyses of DENV isolated in 2009. Three hundred thirty-three dengue-suspected patients were recruited. Our data revealed that dengue predominantly affected young adults, and the majority of cases were due to secondary infection. A total of 171 virus isolates were successfully serotyped. All four DENV serotypes were circulating in the city, and DENV-1 was the predominant serotype. The DENV genotyping of 17 isolates revealed the presence of Genotypes I and IV in DENV-1, while DENV-2 isolates were grouped into the Cosmopolitan genotype. The grouping of isolates into Genotype I and II was seen for DENV-3 and DENV-4, respectively. Evolutionary analysis revealed the relatedness of Jakarta isolates with other isolates from other cities in Indonesia and isolates from imported cases in other countries. We revealed the endemicity of DENV and the role of Jakarta as the potential source of imported dengue cases in other countries. Our study provides genetic information regarding DENV from Jakarta, which will be useful for upstream applications, such as the study of DENV epidemiology and evolution and transmission dynamics.
Collapse
Affiliation(s)
- C S Whinie Lestari
- Center for Research and Development of Biomedical and Basic Health Technology, National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Benediktus Yohan
- Eijkman Institute for Molecular Biology, Ministry of Research, Technology, and Higher Education, Jakarta, Indonesia
| | - Anisa Yunita
- Center for Research and Development of Biomedical and Basic Health Technology, National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Febrina Meutiawati
- Eijkman Institute for Molecular Biology, Ministry of Research, Technology, and Higher Education, Jakarta, Indonesia
| | - Rahma Fitri Hayati
- Eijkman Institute for Molecular Biology, Ministry of Research, Technology, and Higher Education, Jakarta, Indonesia
| | - Hidayat Trimarsanto
- Eijkman Institute for Molecular Biology, Ministry of Research, Technology, and Higher Education, Jakarta, Indonesia
| | - R Tedjo Sasmono
- Eijkman Institute for Molecular Biology, Ministry of Research, Technology, and Higher Education, Jakarta, Indonesia.
| |
Collapse
|
27
|
Wardhani P, Aryati A, Yohan B, Trimarsanto H, Setianingsih TY, Puspitasari D, Arfijanto MV, Bramantono B, Suharto S, Sasmono RT. Clinical and virological characteristics of dengue in Surabaya, Indonesia. PLoS One 2017; 12:e0178443. [PMID: 28575000 PMCID: PMC5456069 DOI: 10.1371/journal.pone.0178443] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Accepted: 05/12/2017] [Indexed: 01/28/2023] Open
Abstract
Dengue disease is still a major health problem in Indonesia. Surabaya, the second largest city in the country, is endemic for dengue. We report here on dengue disease in Surabaya, investigating the clinical manifestations, the distribution of dengue virus (DENV) serotypes, and the relationships between clinical manifestations and the genetic characteristics of DENV. A total of 148 patients suspected of having dengue were recruited during February-August 2012. One hundred one (68%) of them were children, and 47 (32%) were adults. Dengue fever (DF) and Dengue hemorrhagic fever (DHF) were equally manifested in all of the patients. We performed DENV serotyping on all of the samples using real-time RT-PCR. Of 148, 79 (53%) samples were detected as DENV positive, with DENV-1 as the predominant serotype (73%), followed by DENV-2 (8%), DENV-4 (8%), and DENV-3 (6%), while 5% were mixed infections. Based on the Envelope gene sequences, we performed phylogenetic analyses of 24 isolates to genotype the DENV circulating in Surabaya in 2012, and the analysis revealed that DENV-1 consisted of Genotypes I and IV, DENV-2 was of the Cosmopolitan genotype, the DENV-3 viruses were of Genotype I, and DENV-4 was detected as Genotype II. We correlated the infecting DENV serotypes with clinical manifestations and laboratory parameters; however, no significant correlations were found. Amino acid analysis of Envelope protein did not find any unique mutations related to disease severity.
Collapse
Affiliation(s)
- Puspa Wardhani
- Department of Clinical Pathology, School of Medicine, Universitas Airlangga, Surabaya, Indonesia
- Institute for Tropical Diseases, Universitas Airlangga, Surabaya, Indonesia
| | - Aryati Aryati
- Department of Clinical Pathology, School of Medicine, Universitas Airlangga, Surabaya, Indonesia
- Institute for Tropical Diseases, Universitas Airlangga, Surabaya, Indonesia
| | | | | | | | - Dwiyanti Puspitasari
- Department of Pediatric, School of Medicine, Universitas Airlangga, Surabaya, Indonesia
| | | | - Bramantono Bramantono
- Department of Internal Medicine, School of Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Suharto Suharto
- Department of Internal Medicine, School of Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - R. Tedjo Sasmono
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- * E-mail:
| |
Collapse
|
28
|
Debbink K, McCrone JT, Petrie JG, Truscon R, Johnson E, Mantlo EK, Monto AS, Lauring AS. Vaccination has minimal impact on the intrahost diversity of H3N2 influenza viruses. PLoS Pathog 2017; 13:e1006194. [PMID: 28141862 PMCID: PMC5302840 DOI: 10.1371/journal.ppat.1006194] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 02/10/2017] [Accepted: 01/19/2017] [Indexed: 12/19/2022] Open
Abstract
While influenza virus diversity and antigenic drift have been well characterized on a global scale, the factors that influence the virus’ rapid evolution within and between human hosts are less clear. Given the modest effectiveness of seasonal vaccination, vaccine-induced antibody responses could serve as a potent selective pressure for novel influenza variants at the individual or community level. We used next generation sequencing of patient-derived viruses from a randomized, placebo-controlled trial of vaccine efficacy to characterize the diversity of influenza A virus and to define the impact of vaccine-induced immunity on within-host populations. Importantly, this study design allowed us to isolate the impact of vaccination while still studying natural infection. We used pre-season hemagglutination inhibition and neuraminidase inhibition titers to quantify vaccine-induced immunity directly and to assess its impact on intrahost populations. We identified 166 cases of H3N2 influenza over 3 seasons and 5119 person-years. We obtained whole genome sequence data for 119 samples and used a stringent and empirically validated analysis pipeline to identify intrahost single nucleotide variants at ≥1% frequency. Phylogenetic analysis of consensus hemagglutinin and neuraminidase sequences showed no stratification by pre-season HAI and NAI titer, respectively. In our study population, we found that the vast majority of intrahost single nucleotide variants were rare and that very few were found in more than one individual. Most samples had fewer than 15 single nucleotide variants across the entire genome, and the level of diversity did not significantly vary with day of sampling, vaccination status, or pre-season antibody titer. Contrary to what has been suggested in experimental systems, our data indicate that seasonal influenza vaccination has little impact on intrahost diversity in natural infection and that vaccine-induced immunity may be only a minor contributor to antigenic drift at local scales. Influenza is a significant global health problem. Vaccination is the best way to prevent influenza virus infection, and seasonal influenza vaccines are considered for reformulation each year in order to keep up with the virus’ evolution. Despite these efforts, vaccine recipients often develop an immune response that does not protect from infection. Given the current recommendation that all people over 6 months of age get vaccinated, it is important to understand how vaccination itself may impact viral evolution during natural human infection. We studied how vaccination may alter viral evolution within individuals, as each person harbors many highly-related influenza variants that differ in their ability to escape the immune response. We compared groups of people in a vaccine trial to determine the impact that vaccination has on viral diversity and variant selection within individuals. We did not detect significant differences in the number of variants detected or in the prevalence of mutations that could impact antibody binding based on vaccination group or antibody response. Our work suggests that vaccination is not a major factor in driving the emergence of new influenza strains at the level of the individual host.
Collapse
Affiliation(s)
- Kari Debbink
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - John T McCrone
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Joshua G Petrie
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Rachel Truscon
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Emileigh Johnson
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Emily K Mantlo
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Arnold S Monto
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Adam S Lauring
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America.,Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| |
Collapse
|
29
|
Wang J, Chen H, Huang M, Zhang Y, Xie J, Yan Y, Zheng K, Weng Y. Epidemiological and etiological investigation of dengue fever in the Fujian province of China during 2004–2014. SCIENCE CHINA-LIFE SCIENCES 2016; 60:72-80. [DOI: 10.1007/s11427-016-0021-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 04/14/2016] [Indexed: 10/20/2022]
|
30
|
Haryanto S, Hayati RF, Yohan B, Sijabat L, Sihite IF, Fahri S, Meutiawati F, Halim JAN, Halim SN, Soebandrio A, Sasmono RT. The molecular and clinical features of dengue during outbreak in Jambi, Indonesia in 2015. Pathog Glob Health 2016; 110:119-29. [PMID: 27215933 DOI: 10.1080/20477724.2016.1184864] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Dengue is hyperendemic in Indonesia. In 2015, reported cases of dengue fever doubled those of 2014 in the Jambi municipality of Sumatra. We examined viral aetiology and its relationship with disease outcome in Jambi. Dengue-suspected patients' sera were collected and NS1 detection and IgM/IgG serology were performed. Dengue virus (DENV) serotyping was performed using real-time RT-PCR. Envelope genes were sequenced to determine the genotypes of DENV. Clinical, haematologic, and demographic data were recorded. Of 210 dengue-suspected patients, 107 were confirmed. The disease manifested as Dengue Fever (62%), Dengue Haemorrhagic Fever (36%), and Dengue Shock Syndrome (2%). The serotypes of 94 DENV were determined. All DENV serotypes were detected with DENV-1 as the predominant serotype (66%). Genotypically, the DENV-1 viruses belong to Genotype I, DENV-2 was of Cosmopolitan genotype, DENV-3 as Genotype I, and DENV-4 belonged to Genotype II. Comparison with historical data revealed serotype predominance switched from DENV-3 to DENV-1, and the replacement of Genotype IV of DENV-1 with Genotype I. In summary, DENV-1 predominated during the 2015 dengue outbreak in Jambi. The full spectrum of dengue disease occurred and was characterized by a switch in predominant serotypes.
Collapse
Affiliation(s)
- Sotianingsih Haryanto
- a Siloam Hospital , Jambi , Indonesia.,d Faculty of Medicine , Jambi University , Jambi , Indonesia
| | - Rahma F Hayati
- b Eijkman Institute for Molecular Biology , Jakarta , Indonesia
| | | | | | | | - Sukmal Fahri
- c Health Polytechnic , Jambi Provincial Health Office , Jambi , Indonesia
| | | | | | - Stefanie N Halim
- e Faculty of Medicine , Diponegoro University , Semarang , Indonesia
| | - Amin Soebandrio
- b Eijkman Institute for Molecular Biology , Jakarta , Indonesia
| | - R Tedjo Sasmono
- b Eijkman Institute for Molecular Biology , Jakarta , Indonesia
| |
Collapse
|
31
|
Incomplete Protection against Dengue Virus Type 2 Re-infection in Peru. PLoS Negl Trop Dis 2016; 10:e0004398. [PMID: 26848841 PMCID: PMC4746126 DOI: 10.1371/journal.pntd.0004398] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 12/29/2015] [Indexed: 12/27/2022] Open
Abstract
Background Nearly half of the world’s population is at risk for dengue, yet no licensed vaccine or anti-viral drug is currently available. Dengue is caused by any of four dengue virus serotypes (DENV-1 through DENV-4), and infection by a DENV serotype is assumed to provide life-long protection against re-infection by that serotype. We investigated the validity of this fundamental assumption during a large dengue epidemic caused by DENV-2 in Iquitos, Peru, in 2010–2011, 15 years after the first outbreak of DENV-2 in the region. Methodology/Principal Findings We estimated the age-dependent prevalence of serotype-specific DENV antibodies from longitudinal cohort studies conducted between 1993 and 2010. During the 2010–2011 epidemic, active dengue cases were identified through active community- and clinic-based febrile surveillance studies, and acute inapparent DENV infections were identified through contact tracing studies. Based on the age-specific prevalence of DENV-2 neutralizing antibodies, the age distribution of DENV-2 cases was markedly older than expected. Homologous protection was estimated at 35.1% (95% confidence interval: 0%–65.2%). At the individual level, pre-existing DENV-2 antibodies were associated with an incomplete reduction in the frequency of symptoms. Among dengue cases, 43% (26/66) exhibited elevated DENV-2 neutralizing antibody titers for years prior to infection, compared with 76% (13/17) of inapparent infections (age-adjusted odds ratio: 4.2; 95% confidence interval: 1.1–17.7). Conclusions/Significance Our data indicate that protection from homologous DENV re-infection may be incomplete in some circumstances, which provides context for the limited vaccine efficacy against DENV-2 in recent trials. Further studies are warranted to confirm this phenomenon and to evaluate the potential role of incomplete homologous protection in DENV transmission dynamics. Dengue is a mosquito-borne viral illness that imposes a tremendous public health burden on tropical and sub-tropical regions. An estimated 390 million infections occur globally each year, and up to 4 billion people are at risk. Dengue is caused by four dengue virus (DENV) serotypes (DENV-1 to DENV-4). Infection with any DENV can lead to a range of disease outcomes, from mild febrile illness to severe, hemorrhagic manifestations and death. Infection by one serotype has been assume to provide complete and lifelong protection against re-infection by the same serotype, and to our knowledge, instances of re-infection by the same serotype have not been rigorously documented. However, few long-term studies have been conducted in such a way that re-infection by the same serotype could be observed, if it did in fact occur. Our study provides evidence that re-infection may occur in certain circumstances. We draw from data collected during a 2010–2011 DENV-2 epidemic in northeastern Peru, 15 years after the initial DENV-2 outbreak in the region. This finding has significant implications for our understanding of dengue epidemiology and for dengue vaccine formulation, which may need to consider multiple genotypes of each serotype. Data from other long-term dengue epidemiology studies should be analyzed to determine if homologous re-infection is a more widespread phenomenon.
Collapse
|
32
|
Abraham R, Manakkadan A, Mudaliar P, Joseph I, Sivakumar KC, Nair RR, Sreekumar E. Correlation of phylogenetic clade diversification and in vitro infectivity differences among Cosmopolitan genotype strains of Chikungunya virus. INFECTION GENETICS AND EVOLUTION 2016; 37:174-84. [DOI: 10.1016/j.meegid.2015.11.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 11/16/2015] [Accepted: 11/19/2015] [Indexed: 02/05/2023]
|
33
|
Abstract
Until recently, members of the monogeneric family Arenaviridae (arenaviruses) have been known to infect only muroid rodents and, in one case, possibly phyllostomid bats. The paradigm of arenaviruses exclusively infecting small mammals shifted dramatically when several groups independently published the detection and isolation of a divergent group of arenaviruses in captive alethinophidian snakes. Preliminary phylogenetic analyses suggest that these reptilian arenaviruses constitute a sister clade to mammalian arenaviruses. Here, the members of the International Committee on Taxonomy of Viruses (ICTV) Arenaviridae Study Group, together with other experts, outline the taxonomic reorganization of the family Arenaviridae to accommodate reptilian arenaviruses and other recently discovered mammalian arenaviruses and to improve compliance with the Rules of the International Code of Virus Classification and Nomenclature (ICVCN). PAirwise Sequence Comparison (PASC) of arenavirus genomes and NP amino acid pairwise distances support the modification of the present classification. As a result, the current genus Arenavirus is replaced by two genera, Mammarenavirus and Reptarenavirus, which are established to accommodate mammalian and reptilian arenaviruses, respectively, in the same family. The current species landscape among mammalian arenaviruses is upheld, with two new species added for Lunk and Merino Walk viruses and minor corrections to the spelling of some names. The published snake arenaviruses are distributed among three new separate reptarenavirus species. Finally, a non-Latinized binomial species name scheme is adopted for all arenavirus species. In addition, the current virus abbreviations have been evaluated, and some changes are introduced to unequivocally identify each virus in electronic databases, manuscripts, and oral proceedings.
Collapse
|
34
|
Mehta SR, Vinterbo SA, Little SJ. Ensuring privacy in the study of pathogen genetics. THE LANCET. INFECTIOUS DISEASES 2014; 14:773-777. [PMID: 24721230 DOI: 10.1016/s1473-3099(14)70016-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Rapid growth in the genetic sequencing of pathogens in recent years has led to the creation of large sequence databases. This aggregated sequence data can be very useful for tracking and predicting epidemics of infectious diseases. However, the balance between the potential public health benefit and the risk to personal privacy for individuals whose genetic data (personal or pathogen) are included in such work has been difficult to delineate, because neither the true benefit nor the actual risk to participants has been adequately defined. Existing approaches to minimise the risk of privacy loss to participants are based on de-identification of data by removal of a predefined set of identifiers. These approaches neither guarantee privacy nor protect the usefulness of the data. We propose a new approach to privacy protection that will quantify the risk to participants, while still maximising the usefulness of the data to researchers. This emerging standard in privacy protection and disclosure control, which is known as differential privacy, uses a process-driven rather than data-centred approach to protecting privacy.
Collapse
Affiliation(s)
- Sanjay R Mehta
- Division of Infectious Diseases, University of California, San Diego, CA, USA.
| | - Staal A Vinterbo
- Division of Biomedical Informatics, University of California, San Diego, CA, USA
| | - Susan J Little
- Division of Infectious Diseases, University of California, San Diego, CA, USA
| |
Collapse
|
35
|
Bhattacharjee S. Role of genomic and proteomic tools in the study of host-virus interactions and virus evolution. INDIAN JOURNAL OF VIROLOGY : AN OFFICIAL ORGAN OF INDIAN VIROLOGICAL SOCIETY 2013; 24:306-11. [PMID: 24426292 PMCID: PMC3832694 DOI: 10.1007/s13337-013-0150-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 07/24/2013] [Indexed: 01/05/2023]
Abstract
Viruses have short replication cycles and produce genomic variants within a host, a process that seems to adapt to their specific host and also enable them to infect new hosts. The recent emergence of viral genomic variants from the circulating pool within the host population and re-emergence of the old ones are posing serious threat to agriculture, animal husbandry and humanity as a whole. This review assesses the potential role of genomic and proteomic tools that can monitor not only the course of infection and pathogenesis, but also predict the pandemic or zoonotic epidemic potential of a virus in a previously exposed or immunologically naive biological population.
Collapse
Affiliation(s)
- Soumen Bhattacharjee
- Cell and Molecular Biology Laboratory, Department of Zoology, University of North Bengal, Raja Rammohunpur, P.O. North Bengal University, Siliguri, 734 013 District Darjeeling, West Bengal India
| |
Collapse
|
36
|
Fahri S, Yohan B, Trimarsanto H, Sayono S, Hadisaputro S, Dharmana E, Syafruddin D, Sasmono RT. Molecular surveillance of dengue in Semarang, Indonesia revealed the circulation of an old genotype of dengue virus serotype-1. PLoS Negl Trop Dis 2013; 7:e2354. [PMID: 23951374 PMCID: PMC3738473 DOI: 10.1371/journal.pntd.0002354] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 06/17/2013] [Indexed: 11/18/2022] Open
Abstract
Dengue disease is currently a major health problem in Indonesia and affects all provinces in the country, including Semarang Municipality, Central Java province. While dengue is endemic in this region, only limited data on the disease epidemiology is available. To understand the dynamics of dengue in Semarang, we conducted clinical, virological, and demographical surveillance of dengue in Semarang and its surrounding regions in 2012. Dengue cases were detected in both urban and rural areas located in various geographical features, including the coastal and highland areas. During an eight months' study, a total of 120 febrile patients were recruited, of which 66 were serologically confirmed for dengue infection using IgG/IgM ELISA and/or NS1 tests. The cases occurred both in dry and wet seasons. Majority of patients were under 10 years old. Most patients were diagnosed as dengue hemorrhagic fever, followed by dengue shock syndrome and dengue fever. Serotyping was performed in 31 patients, and we observed the co-circulation of all four dengue virus (DENV) serotypes. When the serotypes were correlated with the severity of the disease, no direct correlation was observed. Phylogenetic analysis of DENV based on Envelope gene sequence revealed the circulation of DENV-2 Cosmopolitan genotype and DENV-3 Genotype I. A striking finding was observed for DENV-1, in which we found the co-circulation of Genotype I with an old Genotype II. The Genotype II was represented by a virus strain that has a very slow mutation rate and is very closely related to the DENV strain from Thailand, isolated in 1964 and never reported in other countries in the last three decades. Moreover, this virus was discovered in a cool highland area with an elevation of 1,001 meters above the sea level. The discovery of this old DENV strain may suggest the silent circulation of old virus strains in Indonesia. We studied dengue disease in Semarang municipality, Central Java, one of the endemic regions in Indonesia. The disease occurred in wide geographical regions which include urban, rural, coastal, and highland areas. All four dengue virus serotypes were found. The infecting serotypes were not associated with disease severities. We also determined the genotype of the circulating viruses. One of the interesting findings was the presence of an old genotype of DENV-1 which has never been reported in the last three decades, which may suggest the silent circulation of this particular genotype in Semarang. These findings offer the first information of the clinical, virological and demographical aspects of the dengue disease in Semarang, Indonesia.
Collapse
Affiliation(s)
- Sukmal Fahri
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- Health Polytechnic, Jambi Provincial Health Office, Ministry of Health of the Republic of Indonesia, Kotabaru, Jambi, Indonesia
- Graduate School in Medicine and Health, Faculty of Medicine, Universitas Diponegoro, Semarang, Indonesia
| | | | - Hidayat Trimarsanto
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- The Agency for the Assessment and Application of Technology, Ministry of Research and Technology of the Republic of Indonesia, Jakarta, Indonesia
| | - S. Sayono
- Graduate School in Medicine and Health, Faculty of Medicine, Universitas Diponegoro, Semarang, Indonesia
- Faculty of Public Health, Universitas Muhammadiyah Semarang, Semarang, Indonesia
| | - Suharyo Hadisaputro
- Graduate School in Medicine and Health, Faculty of Medicine, Universitas Diponegoro, Semarang, Indonesia
| | - Edi Dharmana
- Graduate School in Medicine and Health, Faculty of Medicine, Universitas Diponegoro, Semarang, Indonesia
| | - Din Syafruddin
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - R. Tedjo Sasmono
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- * E-mail:
| |
Collapse
|
37
|
Rodriguez-Roche R, Gould EA. Understanding the dengue viruses and progress towards their control. BIOMED RESEARCH INTERNATIONAL 2013; 2013:690835. [PMID: 23936833 PMCID: PMC3722981 DOI: 10.1155/2013/690835] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 05/08/2013] [Indexed: 01/12/2023]
Abstract
Traditionally, the four dengue virus serotypes have been associated with fever, rash, and the more severe forms, haemorrhagic fever and shock syndrome. As our knowledge as well as understanding of these viruses increases, we now recognise not only that they are causing increasing numbers of human infections but also that they may cause neurological and other clinical complications, with sequelae or fatal consequences. In this review we attempt to highlight some of these features in the context of dengue virus pathogenesis. We also examine some of the efforts currently underway to control this "scourge" of the tropical and subtropical world.
Collapse
Affiliation(s)
- Rosmari Rodriguez-Roche
- Pedro Kouri Tropical Medicine Institute, WHO/PAHO Collaborating Centre for the Study of Dengue and Its Vector, Havana, Cuba.
| | | |
Collapse
|
38
|
Téllez-Sosa J, Rodríguez MH, Gómez-Barreto RE, Valdovinos-Torres H, Hidalgo AC, Cruz-Hervert P, Luna RS, Carrillo-Valenzo E, Ramos C, García-García L, Martínez-Barnetche J. Using high-throughput sequencing to leverage surveillance of genetic diversity and oseltamivir resistance: a pilot study during the 2009 influenza A(H1N1) pandemic. PLoS One 2013; 8:e67010. [PMID: 23843978 PMCID: PMC3699567 DOI: 10.1371/journal.pone.0067010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 05/17/2013] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Influenza viruses display a high mutation rate and complex evolutionary patterns. Next-generation sequencing (NGS) has been widely used for qualitative and semi-quantitative assessment of genetic diversity in complex biological samples. The "deep sequencing" approach, enabled by the enormous throughput of current NGS platforms, allows the identification of rare genetic viral variants in targeted genetic regions, but is usually limited to a small number of samples. METHODOLOGY AND PRINCIPAL FINDINGS We designed a proof-of-principle study to test whether redistributing sequencing throughput from a high depth-small sample number towards a low depth-large sample number approach is feasible and contributes to influenza epidemiological surveillance. Using 454-Roche sequencing, we sequenced at a rather low depth, a 307 bp amplicon of the neuraminidase gene of the Influenza A(H1N1) pandemic (A(H1N1)pdm) virus from cDNA amplicons pooled in 48 barcoded libraries obtained from nasal swab samples of infected patients (n = 299) taken from May to November, 2009 pandemic period in Mexico. This approach revealed that during the transition from the first (May-July) to second wave (September-November) of the pandemic, the initial genetic variants were replaced by the N248D mutation in the NA gene, and enabled the establishment of temporal and geographic associations with genetic diversity and the identification of mutations associated with oseltamivir resistance. CONCLUSIONS NGS sequencing of a short amplicon from the NA gene at low sequencing depth allowed genetic screening of a large number of samples, providing insights to viral genetic diversity dynamics and the identification of genetic variants associated with oseltamivir resistance. Further research is needed to explain the observed replacement of the genetic variants seen during the second wave. As sequencing throughput rises and library multiplexing and automation improves, we foresee that the approach presented here can be scaled up for global genetic surveillance of influenza and other infectious diseases.
Collapse
Affiliation(s)
- Juan Téllez-Sosa
- Centro de Investigaciones sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
| | - Mario Henry Rodríguez
- Centro de Investigaciones sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
| | - Rosa E. Gómez-Barreto
- Centro de Investigaciones sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
| | - Humberto Valdovinos-Torres
- Centro de Investigaciones sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
| | - Ana Cecilia Hidalgo
- Centro de Investigaciones sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
| | - Pablo Cruz-Hervert
- Centro de Investigaciones sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
| | - René Santos Luna
- Centro de Información para Decisiones en Salud Pública, Instituto Nacional de Salud Pública, Cuernavaca, México
| | | | - Celso Ramos
- Centro de Investigaciones sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
| | - Lourdes García-García
- Centro de Investigaciones sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
| | - Jesús Martínez-Barnetche
- Centro de Investigaciones sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
- * E-mail:
| |
Collapse
|
39
|
Velez Rueda AJ, Mistchenko AS, Viegas M. Phylogenetic and phylodynamic analyses of human metapneumovirus in Buenos Aires (Argentina) for a three-year period (2009-2011). PLoS One 2013; 8:e63070. [PMID: 23646177 PMCID: PMC3639999 DOI: 10.1371/journal.pone.0063070] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 03/27/2013] [Indexed: 12/26/2022] Open
Abstract
Human metapneumovirus, which belongs to the Paramyxoviridae family and has been classified as a member of the Pneumovirus genus, is genetically and clinically similar to other family members such as human respiratory syncytial virus. A total of 1146 nasopharyngeal aspirates from pediatric patients with moderate and severe acute lower respiratory tract infections, hospitalized at the Ricardo Gutierrez Childreńs Hospital (Buenos Aires, Argentina), were tested by real time RT-PCR for human metapneumovirus. Results showed that 168 (14.65%) were positive. Thirty-six of these 168 samples were randomly selected to characterize positive cases molecularly. The phylogenetic analysis of the sequences of the G and F genes showed that genotypes A2 and B2 cocirculated during 2009 and 2010 and that only genotype A2 circulated in 2011 in Argentina. Genotype A2 prevailed during the study period, a fact supported by a higher effective population size (Neτ) and higher diversity as compared to that of genotype B2 (10.9% (SE 1.3%) vs. 1.7% (SE 0.4%), respectively). The phylogeographic analysis of the G protein gene sequences showed that this virus has no geographical restrictions and can travel globally harbored in hosts. The selection pressure analysis of the F protein showed that although this protein has regions with polymorphisms, it has vast structural and functional constraints. In addition, the predicted B-linear epitopes and the sites recognized by previously described monoclonal antibodies were conserved in all Argentine sequences. This points out this protein as a potential candidate to be the target of future humanized antibodies or vaccines.
Collapse
Affiliation(s)
- Ana Julia Velez Rueda
- Laboratorio de Virología, Hospital de Niños “Dr. Ricardo Gutiérrez”, Ciudad Autónoma de Buenos Aires, Argentina
- Comisión de Investigaciones Científicas (CIC), La Plata, Provincia de Buenos Aires, Argentina
| | - Alicia Susana Mistchenko
- Laboratorio de Virología, Hospital de Niños “Dr. Ricardo Gutiérrez”, Ciudad Autónoma de Buenos Aires, Argentina
- Comisión de Investigaciones Científicas (CIC), La Plata, Provincia de Buenos Aires, Argentina
| | - Mariana Viegas
- Laboratorio de Virología, Hospital de Niños “Dr. Ricardo Gutiérrez”, Ciudad Autónoma de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
- * E-mail:
| |
Collapse
|
40
|
Huang SSH, Lin Z, Banner D, León AJ, Paquette SG, Rubin B, Rubino S, Guan Y, Kelvin DJ, Kelvin AA. Immunity toward H1N1 influenza hemagglutinin of historical and contemporary strains suggests protection and vaccine failure. Sci Rep 2013; 3:1698. [PMID: 23608887 PMCID: PMC3633051 DOI: 10.1038/srep01698] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 04/05/2013] [Indexed: 11/09/2022] Open
Abstract
Evolution of H1N1 influenza A outbreaks of the past 100 years is interesting and significantly complex and details of H1N1 genetic drift remains unknown. Here we investigated the clinical characteristics and immune cross-reactivity of significant historical H1N1 strains. We infected ferrets with H1N1 strains from 1943, 1947, 1977, 1986, 1999, and 2009 and showed each produced a unique clinical signature. We found significant cross-reactivity between viruses with similar HA sequences. Interestingly, A/FortMonmouth/1/1947 antisera cross-reacted with A/USSR/90/1977 virus, thought to be a 1947 resurfaced virus. Importantly, our immunological data that didn't show cross-reactivity can be extrapolated to failure of past H1N1 influenza vaccines, ie. 1947, 1986 and 2009. Together, our results help to elucidate H1N1 immuno-genetic alterations that occurred in the past 100 years and immune responses caused by H1N1 evolution. This work will facilitate development of future influenza therapeutics and prophylactics such as influenza vaccines.
Collapse
Affiliation(s)
- Stephen S. H. Huang
- Division of Experimental Therapeutics, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- These authors contributed equally to this work
| | - Zhen Lin
- Division of Experimental Therapeutics, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
- International Institute of Infection and Immunity, Shantou University Medical College, Shantou, Guangdong, China
- These authors contributed equally to this work
| | - David Banner
- Division of Experimental Therapeutics, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Alberto J. León
- Division of Experimental Therapeutics, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
- International Institute of Infection and Immunity, Shantou University Medical College, Shantou, Guangdong, China
| | - Stéphane G. Paquette
- Division of Experimental Therapeutics, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Barry Rubin
- Division of Vascular Surgery, Peter Munk Cardiac Centre, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Salvatore Rubino
- Universita' degli Studi di Sassari, Sezione di Microbiologia Sperimentale e Clinica, Dipartimento di Scienze Biomediche, Viale San Pietro 43/b, 07100 Sassari, Italia
| | - Yi Guan
- International Institute of Infection and Immunity, Shantou University Medical College, Shantou, Guangdong, China
| | - David J. Kelvin
- Division of Experimental Therapeutics, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Universita' degli Studi di Sassari, Sezione di Microbiologia Sperimentale e Clinica, Dipartimento di Scienze Biomediche, Viale San Pietro 43/b, 07100 Sassari, Italia
- International Institute of Infection and Immunity, Shantou University Medical College, Shantou, Guangdong, China
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | | |
Collapse
|
41
|
Determination of spontaneous mutation frequencies in measles virus under nonselective conditions. J Virol 2012; 87:2686-92. [PMID: 23255805 DOI: 10.1128/jvi.02146-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
There is a paradox between the remarkable genetic stability of measles virus (MV) in the field and the high mutation rates implied by the frequency of the appearance of monoclonal antibody escape mutants generated when the virus is pressured to revert in vitro (S. J. Schrag, P. A. Rota, and W. J. Bellini, J. Virol. 73:51-54, 1999). We established a highly sensitive assay to determine frequencies of various categories of mutations in large populations of wild-type and laboratory-adapted MVs using recombinant viruses containing an additional transcription unit (ATU) encoding enhanced green fluorescent protein (EGFP). Single and double mutations were made in the fluorophore of EGFP to ablate fluorescence. The frequencies of reversion mutants in the population were determined by measuring the appearance of fluorescence indicating a revertant virus. This allows mutation rates to be measured under nonselective conditions, as phenotypic reversion to fluorescence requires only either a single- or a double-nucleotide change and amino acid substitution, which does not affect the length of the nonessential reporter protein expressed from the ATU. Mutation rates in MV are the same for wild-type and laboratory-adapted viruses, and they are an order of magnitude lower than the previous measurement assessed under selective conditions. The actual mutation rate for MV is approximately 1.8 × 10(-6) per base per replication event.
Collapse
|
42
|
Kolekar P, Kale M, Kulkarni-Kale U. Alignment-free distance measure based on return time distribution for sequence analysis: applications to clustering, molecular phylogeny and subtyping. Mol Phylogenet Evol 2012; 65:510-22. [PMID: 22820020 DOI: 10.1016/j.ympev.2012.07.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Accepted: 07/08/2012] [Indexed: 11/30/2022]
Abstract
The data deluge in post-genomic era demands development of novel data mining tools. Existing molecular phylogeny analyses (MPAs) developed for individual gene/protein sequences are alignment-based. However, the size of genomic data and uncertainties associated with alignments, necessitate development of alignment-free methods for MPA. Derivation of distances between sequences is an important step in both, alignment-dependant and alignment-free methods. Various alignment-free distance measures based on oligo-nucleotide frequencies, information content, compression techniques, etc. have been proposed. However, these distance measures do not account for relative order of components viz. nucleotides or amino acids. A new distance measure, based on the concept of 'return time distribution' (RTD) of k-mers is proposed, which accounts for the sequence composition and their relative orders. Statistical parameters of RTDs are used to derive a distance function. The resultant distance matrix is used for clustering and phylogeny using Neighbor-joining. Its performance for MPA and subtyping was evaluated using simulated data generated by block-bootstrap, receiver operating characteristics and leave-one-out cross validation methods. The proposed method was successfully applied for MPA of family Flaviviridae and subtyping of Dengue viruses. It is observed that method retains resolution for classification and subtyping of viruses at varying levels of sequence similarity and taxonomic hierarchy.
Collapse
|
43
|
Abstract
Evolution of RNA viruses occurs through disequilibria of collections of closely related mutant spectra or mutant clouds termed viral quasispecies. Here we review the origin of the quasispecies concept and some biological implications of quasispecies dynamics. Two main aspects are addressed: (i) mutant clouds as reservoirs of phenotypic variants for virus adaptability and (ii) the internal interactions that are established within mutant spectra that render a virus ensemble the unit of selection. The understanding of viruses as quasispecies has led to new antiviral designs, such as lethal mutagenesis, whose aim is to drive viruses toward low fitness values with limited chances of fitness recovery. The impact of quasispecies for three salient human pathogens, human immunodeficiency virus and the hepatitis B and C viruses, is reviewed, with emphasis on antiviral treatment strategies. Finally, extensions of quasispecies to nonviral systems are briefly mentioned to emphasize the broad applicability of quasispecies theory.
Collapse
Affiliation(s)
- Esteban Domingo
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), C/ Nicolás Cabrera, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain.
| | | | | |
Collapse
|
44
|
Identification of novel positive-strand RNA viruses by metagenomic analysis of archaea-dominated Yellowstone hot springs. J Virol 2012; 86:5562-73. [PMID: 22379100 DOI: 10.1128/jvi.07196-11] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
There are no known RNA viruses that infect Archaea. Filling this gap in our knowledge of viruses will enhance our understanding of the relationships between RNA viruses from the three domains of cellular life and, in particular, could shed light on the origin of the enormous diversity of RNA viruses infecting eukaryotes. We describe here the identification of novel RNA viral genome segments from high-temperature acidic hot springs in Yellowstone National Park in the United States. These hot springs harbor low-complexity cellular communities dominated by several species of hyperthermophilic Archaea. A viral metagenomics approach was taken to assemble segments of these RNA virus genomes from viral populations isolated directly from hot spring samples. Analysis of these RNA metagenomes demonstrated unique gene content that is not generally related to known RNA viruses of Bacteria and Eukarya. However, genes for RNA-dependent RNA polymerase (RdRp), a hallmark of positive-strand RNA viruses, were identified in two contigs. One of these contigs is approximately 5,600 nucleotides in length and encodes a polyprotein that also contains a region homologous to the capsid protein of nodaviruses, tetraviruses, and birnaviruses. Phylogenetic analyses of the RdRps encoded in these contigs indicate that the putative archaeal viruses form a unique group that is distinct from the RdRps of RNA viruses of Eukarya and Bacteria. Collectively, our findings suggest the existence of novel positive-strand RNA viruses that probably replicate in hyperthermophilic archaeal hosts and are highly divergent from RNA viruses that infect eukaryotes and even more distant from known bacterial RNA viruses. These positive-strand RNA viruses might be direct ancestors of RNA viruses of eukaryotes.
Collapse
|
45
|
Falconar AKI, Romero-Vivas CME. Simple Prognostic Criteria can Definitively Identify Patients who Develop Severe Versus Non-Severe Dengue Disease, or Have Other Febrile Illnesses. J Clin Med Res 2012; 4:33-44. [PMID: 22383925 PMCID: PMC3279499 DOI: 10.4021/jocmr694w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2011] [Indexed: 11/26/2022] Open
Abstract
Background Severe dengue disease (SDD) (DHF/DSS: dengue hemorrhagic fever/dengue shock syndrome) results from either primary or secondary dengue virus (DENV) infections, which occur 4 - 6 days after the onset of fever. As yet, there are no definitive clinical or hematological criteria that can specifically identify SDD patients during the early acute febrile-phase of disease (day 0 - 3: < 72 hours). This study was performed during a SDD (DHF/DSS) epidemic to: 1) identify the DENV serotypes that caused SDD during primary or secondary DENV infections; 2) identify simple clinical and hematological criteria that could significantly discriminate between patients who subsequently developed SDD versus non-SDD (N-SDD), or had a non-DENV fever of unknown origin (FUO) during day 0 - 3 of fever; 3) assess whether DENV serotype co-infections resulted in SDD. Methods First serum samples, with clinical and hematological criteria, were collected from 100 patients during the early acute febrile-phase (day 0 - 3: < 72 hours), assessed for DENV or FUO infections by IgM- and IgG-capture ELISAs on paired serum samples and by DENV isolations, and subsequently graded as SDD, N-SDD or FUO patients. Results In this study: 1) Thirty-three patients had DENV infections, predominantly secondary DENV-2 infections, including each SDD (DHF/DSS) case; 2) Secondary DENV-2/-3 and DENV-2/-4 serotype co-infections however resulted in N-SDD; 3) Each patient who subsequently developed SDD, but none of the others, displayed three clinical criteria: abdominal pain, conjunctival injection and veni-puncture bleeding, therefore each of these criteria provided definitively significant prognostic (P < 0.001) values; 4) Petechia, positive tourniquet tests and hepatomegaly, and neutrophilia or leukopenia also significantly identified those who: a) subsequently developed SDD versus N-SDD, or had a FUO; b) subsequently developed SDD versus N-SDD; c) subsequently developed N-SDD versus FUOs, respectively. Conclusions This is the first report of simple definitively prognostic criteria for SDD patients, including the first assessment and confirmation of conjunctival injection. The three definitive clinical criteria used alone, or supported by the other four criteria, could be essential for specifically identifying those patients needing prompt hospital-based therapies to lessen or avert SDD, without unnecessary hospitalization of the other patients. Keywords Dengue virus; Severe dengue; Dengue fever; Diagnostic; Criteria; Hemorrhage; Shock
Collapse
Affiliation(s)
- Andrew K I Falconar
- Laboratorio de Enfermedades Tropicales, Departamento de Medicina, Fundacion Universidad del Norte Km5 Antigua Via a Puerto Colombia, Barranquilla, Colombia, South America
| | | |
Collapse
|
46
|
Viral Genomics: Implications for the Understanding and Control of Emerging Viral Diseases. ADVANCES IN MICROBIAL ECOLOGY 2012. [PMCID: PMC7120675 DOI: 10.1007/978-1-4614-2182-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In recent decades, many infectious diseases have significantly increased in incidence and/or geographic range, in some cases impacting heavily on human, animal or plant populations. Some of these ‘emerging infectious diseases’ are associated with pathogens that have appeared in populations for the first time as a result of cross-species transmission (e.g. human immunodeficiency virus—acquired immunodeficiency syndrome (HIV-AIDS), severe acute respiratory syndrome (SARS)), while others were previously known but are rapidly increasing in incidence or geographic range as a result of underlying epidemiological changes (e.g. multi-drug resistant Staphylococcus aureus (MRSA) infection, dengue, West Nile encephalitis, foot and mouth disease, cassava mosaic disease). The latter include prominent diseases as tuberculosis, malaria and yellow fever that were once on the decline but are now ‘re-emerging diseases’.
Collapse
|
47
|
Rodriguez-Roche R, Villegas E, Cook S, Poh Kim PAW, Hinojosa Y, Rosario D, Villalobos I, Bendezu H, Hibberd ML, Guzman MG. Population structure of the dengue viruses, Aragua, Venezuela, 2006-2007. Insights into dengue evolution under hyperendemic transmission. INFECTION GENETICS AND EVOLUTION 2011; 12:332-44. [PMID: 22197765 PMCID: PMC3919160 DOI: 10.1016/j.meegid.2011.12.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 12/08/2011] [Accepted: 12/10/2011] [Indexed: 12/16/2022]
Abstract
During the past three decades there has been a notable increase in dengue disease severity in Venezuela. Nevertheless, the population structure of the viruses being transmitted in this country is not well understood. Here, we present a molecular epidemiological study on dengue viruses (DENV) circulating in Aragua State, Venezuela during 2006-2007. Twenty-one DENV full-length genomes representing all of the four serotypes were amplified and sequenced directly from the serum samples. Notably, only DENV-2 was associated with severe disease. Phylogenetic trees constructed using Bayesian methods indicated that only one genotype was circulating for each serotype. However, extensive viral genetic diversity was found in DENV isolated from the same area during the same period, indicating significant in situ evolution since the introduction of these genotypes. Collectively, the results suggest that the non-structural (NS) proteins may play an important role in DENV evolution, particularly NS1, NS2A and NS4B proteins. The phylogenetic data provide evidence to suggest that multiple introductions of DENV have occurred from the Latin American region into Venezuela and vice versa. The implications of the significant viral genetic diversity generated during hyperendemic transmission, particularly in NS protein are discussed and considered in the context of future development and use of human monoclonal antibodies as antivirals and tetravalent vaccines.
Collapse
|
48
|
Hedskog C, Mild M, Albert J. Transmission of the X4 phenotype of HIV-1: is there evidence against the "random transmission" hypothesis? J Infect Dis 2011; 205:163-5. [PMID: 22147793 DOI: 10.1093/infdis/jir719] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
|
49
|
The human antibody response to dengue virus infection. Viruses 2011; 3:2374-95. [PMID: 22355444 PMCID: PMC3280510 DOI: 10.3390/v3122374] [Citation(s) in RCA: 239] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 11/12/2011] [Accepted: 11/15/2011] [Indexed: 12/11/2022] Open
Abstract
Dengue viruses (DENV) are the causative agents of dengue fever (DF) and dengue hemorrhagic fever (DHF). Here we review the current state of knowledge about the human antibody response to dengue and identify important knowledge gaps. A large body of work has demonstrated that antibodies can neutralize or enhance DENV infection. Investigators have mainly used mouse monoclonal antibodies (MAbs) to study interactions between DENV and antibodies. These studies indicate that antibody neutralization of DENVs is a “multi-hit” phenomenon that requires the binding of multiple antibodies to neutralize a virion. The most potently neutralizing mouse MAbs bind to surface exposed epitopes on domain III of the dengue envelope (E) protein. One challenge facing the dengue field now is to extend these studies with mouse MAbs to better understand the human antibody response. The human antibody response is complex as it involves a polyclonal response to primary and secondary infections with 4 different DENV serotypes. Here we review studies conducted with immune sera and MAbs isolated from people exposed to dengue infections. Most dengue-specific antibodies in human immune sera are weakly neutralizing and bind to multiple DENV serotypes. The human antibodies that potently and type specifically neutralize DENV represent a small fraction of the total DENV-specific antibody response. Moreover, these neutralizing antibodies appear to bind to novel epitopes including complex, quaternary epitopes that are only preserved on the intact virion. These studies establish that human and mouse antibodies recognize distinct epitopes on the dengue virion. The leading theory proposed to explain the increased risk of severe disease in secondary cases is antibody dependent enhancement (ADE), which postulates that weakly neutralizing antibodies from the first infection bind to the second serotype and enhance infection of FcγR bearing myeloid cells such as monocytes and macrophages. Here we review results from human, animal and cell culture studies relevant to the ADE hypothesis. By understanding how human antibodies neutralize or enhance DENV, it will be possible to better evaluate existing vaccines and develop the next generation of novel vaccines.
Collapse
|
50
|
Huang SSH, Banner D, Fang Y, Ng DCK, Kanagasabai T, Kelvin DJ, Kelvin AA. Comparative analyses of pandemic H1N1 and seasonal H1N1, H3N2, and influenza B infections depict distinct clinical pictures in ferrets. PLoS One 2011; 6:e27512. [PMID: 22110664 PMCID: PMC3217968 DOI: 10.1371/journal.pone.0027512] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Accepted: 10/18/2011] [Indexed: 11/18/2022] Open
Abstract
Influenza A and B infections are a worldwide health concern to both humans and animals. High genetic evolution rates of the influenza virus allow the constant emergence of new strains and cause illness variation. Since human influenza infections are often complicated by secondary factors such as age and underlying medical conditions, strain or subtype specific clinical features are difficult to assess. Here we infected ferrets with 13 currently circulating influenza strains (including strains of pandemic 2009 H1N1 [H1N1pdm] and seasonal A/H1N1, A/H3N2, and B viruses). The clinical parameters were measured daily for 14 days in stable environmental conditions to compare clinical characteristics. We found that H1N1pdm strains had a more severe physiological impact than all season strains where pandemic A/California/07/2009 was the most clinically pathogenic pandemic strain. The most serious illness among seasonal A/H1N1 and A/H3N2 groups was caused by A/Solomon Islands/03/2006 and A/Perth/16/2009, respectively. Among the 13 studied strains, B/Hubei-Wujiagang/158/2009 presented the mildest clinical symptoms. We have also discovered that disease severity (by clinical illness and histopathology) correlated with influenza specific antibody response but not viral replication in the upper respiratory tract. H1N1pdm induced the highest and most rapid antibody response followed by seasonal A/H3N2, seasonal A/H1N1 and seasonal influenza B (with B/Hubei-Wujiagang/158/2009 inducing the weakest response). Our study is the first to compare the clinical features of multiple circulating influenza strains in ferrets. These findings will help to characterize the clinical pictures of specific influenza strains as well as give insights into the development and administration of appropriate influenza therapeutics.
Collapse
Affiliation(s)
- Stephen S. H. Huang
- Division of Experimental Therapeutics, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - David Banner
- Division of Experimental Therapeutics, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Yuan Fang
- Division of Experimental Therapeutics, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Derek C. K. Ng
- Division of Experimental Therapeutics, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Thirumagal Kanagasabai
- Division of Experimental Therapeutics, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - David J. Kelvin
- Division of Experimental Therapeutics, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Immune Diagnostics and Research, Toronto, Ontario, Canada
- International Institute of Infection and Immunity, Shantou University Medical College, Shantou, Guangdong, China
- Dipartimento di Scienze Biomediche, Universita' degli Studi di Sassari, Sassari, Sardinia, Italia
- * E-mail:
| | | |
Collapse
|