scholarly journals The evolutionary dynamics of Oropouche Virus (OROV) in South America

2019 ◽  
Author(s):  
Bernardo Gutierrez ◽  
Emma Wise ◽  
Steven Pullan ◽  
Christopher Logue ◽  
Thomas A. Bowden ◽  
...  
Keyword(s):  
Viral Genome ◽  
Amazon Basin ◽  
Evolutionary Dynamics ◽  
Surface Proteins ◽  
Human Populations ◽  
Evolutionary Processes ◽  
Viral Pathogens ◽  
Viral Genomes ◽  
Glycosylation Sites ◽  
Variable Evolutionary Rates

AbstractThe Amazon basin is host to numerous arthropod-borne viral pathogens that cause febrile disease in humans. Among these,Oropouche orthobunyavirus(OROV) is a relatively understudied member of the Peribunyavirales that causes periodic outbreaks in human populations in Brazil and other South American countries. Although several studies have described the genetic diversity of the virus, the evolutionary processes that shape the viral genome remain poorly understood. Here we present a comprehensive study of the genomic dynamics of OROV that encompasses phylogenetic analysis, evolutionary rate estimates, inference of natural selective pressures, recombination and reassortment, and structural analysis of OROV variants. Our study includes all available published sequences, as well as a set of new OROV genomes sequences obtained from patients in Ecuador, representing the first set of viral genomes from this country. Our results show that differing evolutionary processes on the three segments that encompass the viral genome lead to variable evolutionary rates and TMRCAs that could be explained by cryptic reassortment. We also present the discovery of previously unobserved putative N-linked glycosylation sites, and codons which evolve under positive selection on the viral surface proteins, and discuss the potential role of these features in the evolution of the virus through a combined phylogenetic and structural approach.

scholarly journals Evolutionary Dynamics of Oropouche Virus in South America

2019 ◽  
Vol 94 (5) ◽  
Author(s):  
Bernardo Gutierrez ◽  
Emma L. Wise ◽  
Steven T. Pullan ◽  
Christopher H. Logue ◽  
Thomas A. Bowden ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
South America ◽  
Amazon Basin ◽  
Evolutionary Dynamics ◽  
Yellow Fever Virus ◽  
Surface Proteins ◽  
Human Populations ◽  
Evolutionary Processes ◽  
Public Health Burden ◽  
Evolutionary Forces

ABSTRACT The Amazon basin is home to numerous arthropod-borne viral pathogens that cause febrile disease in humans. Among these, Oropouche orthobunyavirus (OROV) is a relatively understudied member of the genus Orthobunyavirus, family Peribunyaviridae, that causes periodic outbreaks in human populations in Brazil and other South American countries. Although several studies have described the genetic diversity of the virus, the evolutionary processes that shape the OROV genome remain poorly understood. Here, we present a comprehensive study of the genomic dynamics of OROV that encompasses phylogenetic analysis, evolutionary rate estimates, inference of natural selective pressures, recombination and reassortment, and structural analysis of OROV variants. Our study includes all available published sequences, as well as a set of new OROV genome sequences obtained from patients in Ecuador, representing the first set of genomes from this country. Our results show differing evolutionary processes on the three segments that comprise the viral genome. We infer differing times of the most recent common ancestors of the genome segments and propose that this can be explained by cryptic reassortment. We also present the discovery of previously unobserved putative N-linked glycosylation sites, as well as codons that evolve under positive selection on the viral surface proteins, and discuss the potential role of these features in the evolution of OROV through a combined phylogenetic and structural approach. IMPORTANCE The emergence and reemergence of pathogens such as Zika virus, chikungunya virus, and yellow fever virus have drawn attention toward other cocirculating arboviruses in South America. Oropouche virus (OROV) is a poorly studied pathogen responsible for over a dozen outbreaks since the early 1960s and represents a public health burden to countries such as Brazil, Panama, and Peru. OROV is likely underreported since its symptomatology can be easily confounded with other febrile illnesses (e.g., dengue fever and leptospirosis) and point-of-care testing for the virus is still uncommon. With limited data, there is a need to optimize the information currently available. Analysis of OROV genomes can help us understand how the virus circulates in nature and can reveal the evolutionary forces that shape the genetic diversity of the virus, which has implications for molecular diagnostics and the design of potential vaccines.

scholarly journals Diversity and host assemblage of avian haemosporidians in different terrestrial ecoregions of Peru

2021 ◽  
Author(s):  
Luz Garcia-Longoria ◽  
Jaime Muriel ◽  
Sergio Magallanes ◽  
Zaira Hellen Villa-Galarce ◽  
Leonila Ricopa ◽  
...  
Keyword(s):  
Amazon Basin ◽  
Evolutionary Dynamics ◽  
Bird Species ◽  
Host Community ◽  
Bird Diversity ◽  
New Host ◽  
Parasite Richness ◽  
Haemosporidian Parasites ◽  
Avian Haemosporidians ◽  
Host Parasite

Abstract Characterizing the diversity and structure of host-parasite communities is crucial to understanding their eco-evolutionary dynamics. Malaria and related haemosporidian parasites are responsible for fitness loss and mortality in bird species worldwide. However, despite exhibiting the greatest ornithological biodiversity, avian haemosporidians from Neotropical regions are quite unexplored. Here, we analyse the genetic diversity of bird haemosporidian parasites (Plasmodium and Haemoproteus) in 1,336 individuals belonging to 206 bird species to explore for differences in diversity of parasite lineages and bird species across five well-differentiated Peruvian ecoregions. We detected 70 different haemosporidian lineages infecting 74 bird species. We showed that 25 out of the 70 haplotypes had not been previously recorded. Moreover, we also identified 81 new host – parasite interactions representing new host records for these haemosporidian parasites. Our outcomes revealed that the effective diversity (as well as the richness, abundance, and Shannon-Weaver index) for both birds and parasite lineages was higher in Amazon basin ecoregions. Furthermore, we also showed that ecoregions with greater diversity of bird species also had high parasite richness, hence suggesting that host community is crucial in explaining parasite richness. Generalist parasites were found in ecoregions with lower bird diversity, implying that the abundance and richness of hosts may shape the exploitation strategy followed by haemosporidian parasites. These outcomes reveal that Neotropical region is a major reservoir of unidentified haemosporidian lineages. Further studies analysing host distribution and specificity of these parasites in the tropics will provide important knowledge about phylogenetic relationships, phylogeography, and patterns of evolution and distribution of haemosporidian parasites.

scholarly journals Latest Advances of Virology Research Using CRISPR/Cas9-Based Gene-Editing Technology and Its Application to Vaccine Development

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 779
Author(s):  
Man Teng ◽  
Yongxiu Yao ◽  
Venugopal Nair ◽  
Jun Luo
Keyword(s):  
Biological Sciences ◽  
Gene Therapy ◽  
Genetic Engineering ◽  
Gene Function ◽  
Viral Genome ◽  
Gene Editing ◽  
Vaccine Development ◽  
Future Prospects ◽  
Dna Viruses ◽  
Viral Genomes

In recent years, the CRISPR/Cas9-based gene-editing techniques have been well developed and applied widely in several aspects of research in the biological sciences, in many species, including humans, animals, plants, and even in viruses. Modification of the viral genome is crucial for revealing gene function, virus pathogenesis, gene therapy, genetic engineering, and vaccine development. Herein, we have provided a brief review of the different technologies for the modification of the viral genomes. Particularly, we have focused on the recently developed CRISPR/Cas9-based gene-editing system, detailing its origin, functional principles, and touching on its latest achievements in virology research and applications in vaccine development, especially in large DNA viruses of humans and animals. Future prospects of CRISPR/Cas9-based gene-editing technology in virology research, including the potential shortcomings, are also discussed.

scholarly journals PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Maria Artesi ◽  
Vincent Hahaut ◽  
Basiel Cole ◽  
Laurens Lambrechts ◽  
Fereshteh Ashrafi ◽  
...  
Keyword(s):  
Viral Genome ◽  
Clonal Expansion ◽  
Endogenous Retroviruses ◽  
Viral Genomes ◽  
Short Read Sequencing ◽  
Long Reads ◽  
Infected Cells ◽  
Insertion Sites ◽  
Viral Insertion ◽  
Hiv 1

AbstractThe integration of a viral genome into the host genome has a major impact on the trajectory of the infected cell. Integration location and variation within the associated viral genome can influence both clonal expansion and persistence of infected cells. Methods based on short-read sequencing can identify viral insertion sites, but the sequence of the viral genomes within remains unobserved. We develop PCIP-seq, a method that leverages long reads to identify insertion sites and sequence their associated viral genome. We apply the technique to exogenous retroviruses HTLV-1, BLV, and HIV-1, endogenous retroviruses, and human papillomavirus.

scholarly journals Systemic Polyomavirus Genome Increase and Dissemination of Capsid-Defective Genomes in Mammary Gland Tumor-Bearing Mice

2000 ◽  
Vol 74 (15) ◽  
pp. 6975-6983 ◽  
Author(s):  
Julie J. Wirth ◽  
Li Chen ◽  
Michele M. Fluck
Keyword(s):  
Mammary Gland ◽  
Viral Genome ◽  
Wild Type Strain ◽  
Neonatal Infection ◽  
Wild Type ◽  
Coding Region ◽  
Live Virus ◽  
Viral Genomes ◽  
Mammary Gland Tumors ◽  
Low Levels

ABSTRACT BALB/c mice that developed tumors 7 to 8 months following neonatal infection by polyomavirus (PYV) wild-type strain A2 were characterized with respect to the abundance and integrity of the viral genome in the tumors and in 12 nontumorous organs. These patterns were compared to those found in tumor-free mice infected in parallel. Six mice were analyzed in detail including four sibling females with mammary gland tumors. In four of five mammary gland tumors, the viral genome had undergone a unique deletion and/or rearrangement. Three tumor-resident genomes with an apparently intact large T coding region were present in abundant levels in an unintegrated state. Two of these had undergone deletions and rearrangements involving the capsid genes and therefore lacked the capacity to produce live virus. In the comparative organ survey, the tumors harboring replication-competent genomes contained by far the highest levels of genomes of any tissue. However, the levels of PYV genomes in other organs were elevated by up to 1 to 2 orders of magnitude compared to those detected in the same organs of tumor-free mice. The genomes found in the nontumorous organs had the same rearrangements as the genomes residing in the tumors. The original wild-type genome was detected at low levels in a few organs, particularly in the kidneys. The data indicate that a systemic increase in the level of viral genomes occurred in conjunction with the induction of tumors by PYV. The results suggest two novel hypotheses: (i) that genomes may spread from the tumors to the usual PYV target tissues and (ii) that this dissemination may take place in the absence of capsids, providing an important path for a virus to escape from the immune response. This situation may offer a useful model for the spread of HPV accompanying HPV-induced oncogenesis.

Integration of viral DNA sequences in cells transformed by adenovirus 2 or SV40

1980 ◽  
Vol 210 (1180) ◽  
pp. 423-435 ◽  
Keyword(s):  
Cell Lines ◽  
Dna Sequences ◽  
Viral Genome ◽  
Viral Dna ◽  
Viral Genomes ◽  
Viral Dnas ◽  
Cellular Dna ◽  
Viral Insertion ◽  
Viral Sequences ◽  
Heteroduplex Formation

We have cloned and propagated in prokaryotic vectors the viral DNA sequences that are integrated in a variety of cells transformed by adenovirus 2 or SV40. Analysis of the clones reveals that the viral DNA sequences sometimes are arranged in a simple fashion, collinear with the viral genome; in other cell lines there are complex arrangements of viral sequences in which tracts of the viral genome are inverted with respect to each other. In several cases the nucleotide sequences at the joints between cell and viral sequences have been determined: usually there is a sharp transition between cellular and viral DNAs. The viral sequences are integrated at different locations within the genomes of different cell lines; likewise there is no specific site on the viral genomes at which integration occurs. Sometimes the viral sequences are integrated within repetitive cellular DNA, and sometimes within unique sequences. In some cases there is evidence that the viral sequences along with the flanking cell DNA have been amplified after integration. The sequences that flank the viral insertion in the line of SV40-transformed rat cells known as 14B have been used as probes to isolate, from untransformed rat cells, clones that carry the region of the chromosome in which integration occurred. Analysis of the structure of these clones by restriction endonuclease digestion and heteroduplex formation shows that a rearrangement of cellular sequences has occurred, presumably as a consequence of integration.

scholarly journals Alien Species vs. Native Species: From Community Ecology to Eco-Evolutionary Dynamics

2019 ◽  
Author(s):  
Andersonn Silveira Prestes
Keyword(s):  
Alien Species ◽  
Exotic Species ◽  
Native Species ◽  
Evolutionary Dynamics ◽  
Evolutionary Processes ◽  
Native Communities ◽  
Individualized Approach ◽  
History Of ◽  
Relationship Of ◽  
The Relationship

The establishment and spread of exotic species is a contemporary major concern. Alien species may become invasive in their new habitat, leading to both/either environmental and/or economic impacts. I briefly reviewed the literature in the last decade about the relationship of exotic species and native communities. I identified that professionals usually approach the subject in two main points of view: (1) researchers tend to point out the impacts of alien species on entire communities, evaluating if the relationship is positive, negative or neutral; (2) they focus on the eco-evolutionary processes involved in the introductions, the dynamics of invasion, and individual study cases. When evaluating the response of introductions to entire communities, evidence seems to be ambiguous and may support positive, negative or neutral relationship, especially depending on the scale approached. The unique eco-evolutionary pathways of each introduction may be a great shortcoming in the searching for generalities. On the other hand, advances have been made in understanding the dynamics of invasion on different lineages through a more selective/individualized approach. I suggest that the dynamics of invasion might be studied through a perspective in which different eco-evolutionary processes, levels of organization (from gene to entire communities), the history of the organism(s) and time are taken into account. Individual cases might be compared in attempt to understand how the relationship exotic and native works and in the search for generalities.

scholarly journals Utilizing the VirIdAl Pipeline to Search for Viruses in the Metagenomic Data of Bat Samples

Viruses ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 2006
Author(s):  
Anna Y Budkina ◽  
Elena V Korneenko ◽  
Ivan A Kotov ◽  
Daniil A Kiselev ◽  
Ilya V Artyushin ◽  
...  
Keyword(s):  
Large Scale ◽  
High Throughput Sequencing ◽  
Metagenomic Data ◽  
Sequencing Data ◽  
Viral Pathogens ◽  
Genomic Databases ◽  
Bioinformatic Pipeline ◽  
Viral Genomes ◽  
Sequencing Technologies ◽  
Viral Screening

According to various estimates, only a small percentage of existing viruses have been discovered, naturally much less being represented in the genomic databases. High-throughput sequencing technologies develop rapidly, empowering large-scale screening of various biological samples for the presence of pathogen-associated nucleotide sequences, but many organisms are yet to be attributed specific loci for identification. This problem particularly impedes viral screening, due to vast heterogeneity in viral genomes. In this paper, we present a new bioinformatic pipeline, VirIdAl, for detecting and identifying viral pathogens in sequencing data. We also demonstrate the utility of the new software by applying it to viral screening of the feces of bats collected in the Moscow region, which revealed a significant variety of viruses associated with bats, insects, plants, and protozoa. The presence of alpha and beta coronavirus reads, including the MERS-like bat virus, deserves a special mention, as it once again indicates that bats are indeed reservoirs for many viral pathogens. In addition, it was shown that alignment-based methods were unable to identify the taxon for a large proportion of reads, and we additionally applied other approaches, showing that they can further reveal the presence of viral agents in sequencing data. However, the incompleteness of viral databases remains a significant problem in the studies of viral diversity, and therefore necessitates the use of combined approaches, including those based on machine learning methods.

scholarly journals The Dynamics of Influenza A H3N2 Defective Viral Genomes from a Human Challenge Study

2019 ◽  
Author(s):  
Michael A. Martin ◽  
Drishti Kaul ◽  
Gene S. Tan ◽  
Christopher W. Woods ◽  
Katia Koelle
Keyword(s):  
Genetic Drift ◽  
Influenza A ◽  
Evolutionary Dynamics ◽  
De Novo ◽  
Gene Segment ◽  
Influenza Viruses ◽  
Genomic Variation ◽  
Wild Type Virus ◽  
Single Nucleotide Variants ◽  
Viral Genomes

AbstractThe rapid evolution of influenza is an important contributing factor to its high worldwide incidence. The emergence and spread of genetic point mutations has been thoroughly studied both within populations and within individual hosts. In addition, influenza viruses are also known to generate genomic variation during their replication in the form of defective viral genomes (DVGs). These DVGs are formed by internal deletions in at least one gene segment that render them incapable of replication without the presence of wild-type virus. DVGs have previously been identified in natural human infections and may be associated with less severe clinical outcomes. These studies have not been able to address how DVG populations evolve in vivo in individual infections due to their cross-sectional design. Here we present an analysis of DVGs present in samples from two longitudinal influenza A H3N2 human challenge studies. We observe the generation of DVGs in almost all subjects. Although the genetic composition of DVG populations was highly variable, identical DVGs were observed both between multiple samples within single hosts as well as between hosts. Most likely due to stochastic effects, we did not observe clear instances of selection for specific DVGs or for shorter DVGs over the course of infection. Furthermore, DVG presence was not found to be associated with peak viral titer or peak symptom scores. Our analyses highlight the diversity of DVG populations within a host over the course of infection and the apparent role that genetic drift plays in their population dynamics.ImportanceThe evolution of influenza virus, in terms of single nucleotide variants and the reassortment of gene segments, has been studied in detail. However, influenza is known to generate defective viral genomes (DVGs) during replication, and little is known about how these genomes evolve both within hosts and at the population level. Studies in animal models have indicated that prophylactically or therapeutically administered DVGs can impact patterns of disease progression. However, the formation of naturally-occurring DVGs, their evolutionary dynamics, and their contribution to disease severity in human hosts is not well understood. Here, we identify the formation of de novo DVGs in samples from human challenge studies throughout the course of infection. We analyze their evolutionary trajectories, revealing the important role of genetic drift in shaping DVG populations during acute infections with well-adapted viral strains.

Abstract 20433: Viral Myocarditis: Viral Genome Detection Yield on Endomyocardial Biopsy is Influenced by Methodological Factors

Circulation ◽  
2014 ◽  
Vol 130 (suppl_2) ◽  
Author(s):  
Elisa Carturan ◽  
Stefania Rizzo ◽  
Gaetano Thiene ◽  
Cristina Basso
Keyword(s):  
Endomyocardial Biopsy ◽  
Viral Genome ◽  
Viral Myocarditis ◽  
Molecular Techniques ◽  
Time Interval ◽  
Tissue Fixation ◽  
Viral Genomes ◽  
Consensus Document ◽  
Significant Difference

Introduction: Myocarditis is diagnosed on endomyocardial biopsy (EMB) by histological, immune-histochemical and molecular techniques to detect viral genomes. The role of EMB for the diagnosis and its contribution to patient management has been addressed by a Consensus document of American and European Cardiovascular Pathology Societies. Hypothesis: Different methods of tissue fixation and the number of myocardial samples could impact on viral genome yield on EMB. Methods: Consecutive EMBs referred at our Institution for histology/ immunohistochemistry evaluation in the time interval 1996-2012 were enrolled. Molecular investigation by RT-PCR and PCR technique was performed in all EMBs with inflammatory cardiomyopathy diagnosis at histology and immunohistochemistry. Results: A total of 467 EMBs have been diagnosed as myocarditis: 79 in pediatric (1 month to 18 years; 47M/ 32F) and 388 adult (19 to 75 years; 256M/132 F) patients (pts.). Viral etiology was identified in 28 (36%) pediatric and 101 (26%) adult pts, and the most prevalent type of viruses were enterovirus (8/28, 36%; 26/101, 24%). In a more recent subgroup of 137 EMBs (virus positive 30/137, 22%) seasonality, type of fixation and number of EMB samples were assessed. The seasonal distribution of myocarditis was higher in winter than in other seasons (33% vs. autumn 28%, spring 20% and summer 19%) without any significant difference in terms of virus positive EMBs. The number of EMB samples per pt. was ≤3 (either formalin or RNAlater) in 94/137 (69%) and >3 in 43/137 (31%), with a lower prevalence of virus positive in the former (17/94, 18% vs. 13/43, 30%). Eighty-one EMB samples were frozen while 56 were paraffin embedded, with a higher prevalence of viral genome in the former (26/81, 32% vs. 4/56, 7%; p=0.001). Conclusions: The diagnosis of myocarditis on EMB samples requires standardized protocols including molecular techniques. Viral genomes are identifiable in more than one third of pediatric and one fourth of adult cases. Methodological factors like the type of tissue fixation and the number of samples could impact on viral genome detection on EMB.

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