scholarly journals Vertically transmitted rhabdoviruses are found across three insect families and have dynamic interactions with their hosts

2017 ◽  
Vol 284 (1847) ◽  
pp. 20162381 ◽  
Author(s):  
Ben Longdon ◽  
Jonathan P. Day ◽  
Nora Schulz ◽  
Philip T. Leftwich ◽  
Maaike A. de Jong ◽  
...  
Keyword(s):  
Vertical Transmission ◽  
Ceratitis Capitata ◽  
Sequence Data ◽  
Viral Sequence ◽  
Maternal Transmission ◽  
Free Living ◽  
Dynamic Interactions ◽  
Paternal Transmission ◽  
Pararge Aegeria ◽  
Mode Of Transmission

A small number of free-living viruses have been found to be obligately vertically transmitted, but it remains uncertain how widespread vertically transmitted viruses are and how quickly they can spread through host populations. Recent metagenomic studies have found several insects to be infected with sigma viruses ( Rhabdoviridae ). Here, we report that sigma viruses that infect Mediterranean fruit flies ( Ceratitis capitata ), Drosophila immigrans , and speckled wood butterflies ( Pararge aegeria ) are all vertically transmitted. We find patterns of vertical transmission that are consistent with those seen in Drosophila sigma viruses, with high rates of maternal transmission, and lower rates of paternal transmission. This mode of transmission allows them to spread rapidly in populations, and using viral sequence data we found the viruses in D. immigrans and C. capitata had both recently swept through host populations. The viruses were common in nature, with mean prevalences of 12% in C. capitata , 38% in D. immigrans and 74% in P. aegeria . We conclude that vertically transmitted rhabdoviruses may be widespread in a broad range of insect taxa, and that these viruses can have dynamic interactions with their hosts.

scholarly journals Vertically transmitted rhabdoviruses are found across three insect families and have dynamic interactions with their hosts

2016 ◽  
Author(s):  
Ben Longdon ◽  
Jonathan P Day ◽  
Nora Schulz ◽  
Philip T Leftwich ◽  
Maaike A de Jong ◽  
...  
Keyword(s):  
Vertical Transmission ◽  
Ceratitis Capitata ◽  
Sequence Data ◽  
Viral Sequence ◽  
Maternal Transmission ◽  
Free Living ◽  
Dynamic Interactions ◽  
Paternal Transmission ◽  
Pararge Aegeria ◽  
Mode Of Transmission

AbstractA small number of free-living viruses have been found to be obligately vertically transmitted, but it remains uncertain how widespread vertically transmitted viruses are and how quickly they can spread through host populations. Recent metagenomic studies have found several insects to be infected with sigma viruses (Rhabdoviridae). Here, we report that sigma viruses that infect Mediterranean fruit flies (Ceratitis capitata),Drosophila immigrans, and speckled wood butterflies (Pararge aegeria) are all vertically transmitted. We find patterns of vertical transmission that are consistent with those seen inDrosophilasigma viruses, with high rates of maternal transmission, and lower rates of paternal transmission. This mode of transmission allows them to spread rapidly in populations, and using viral sequence data we found the viruses inD. immigransandC. capitatahad both recently swept through host populations. The viruses were common in nature, with mean prevalences of 12% inC. capitata,38% inD. immigransand 74% inP. aegeria. We conclude that vertically transmitted rhabdoviruses may be widespread in insects, and that these viruses can have dynamic interactions with their hosts.

scholarly journals Challenges in evaluating the use of viral sequence data to identify HIV transmission networks for public health

2020 ◽  
Vol 12 (s1) ◽  
Author(s):  
Rami Kantor ◽  
John P. Fulton ◽  
Jon Steingrimsson ◽  
Vladimir Novitsky ◽  
Mark Howison ◽  
...  
Keyword(s):  
Public Health ◽  
United States ◽  
Hiv Transmission ◽  
Sequence Data ◽  
The United States ◽  
Viral Sequence ◽  
Transmission Networks ◽  
New Methods ◽  
Hiv Epidemic ◽  
The World

AbstractGreat efforts are devoted to end the HIV epidemic as it continues to have profound public health consequences in the United States and throughout the world, and new interventions and strategies are continuously needed. The use of HIV sequence data to infer transmission networks holds much promise to direct public heath interventions where they are most needed. As these new methods are being implemented, evaluating their benefits is essential. In this paper, we recognize challenges associated with such evaluation, and make the case that overcoming these challenges is key to the use of HIV sequence data in routine public health actions to disrupt HIV transmission networks.

scholarly journals VirusDIP: Virus Data Integration Platform

2020 ◽  
Author(s):  
Lina Wang ◽  
Fengzhen Chen ◽  
Xueqin Guo ◽  
Lijin You ◽  
Xiaoxia Yang ◽  
...  
Keyword(s):  
Sequence Alignment ◽  
Sequence Data ◽  
Data Retrieval ◽  
Viral Sequence ◽  
Origin And Evolution ◽  
Alignment Tool ◽  
Public Data ◽  
Virus Research ◽  
Global Initiative ◽  
Tree Building

AbstractMotivationThe Coronavirus Disease 2019 (COVID-19) pandemic poses a huge threat to human public health. Viral sequence data plays an important role in the scientific prevention and control of epidemics. A comprehensive virus database will be vital useful for virus data retrieval and deep analysis. To promote sharing of virus data, several virus databases and related analyzing tools have been created.ResultsTo facilitate virus research and promote the global sharing of virus data, we present here VirusDIP, a one-stop service platform for archive, integration, access, analysis of virus data. It accepts the submission of viral sequence data from all over the world and currently integrates data resources from the National GeneBank Database (CNGBdb), Global initiative on sharing all influenza data (GISAID), and National Center for Biotechnology Information (NCBI). Moreover, based on the comprehensive data resources, BLAST sequence alignment tool and multi-party security computing tools are deployed for multi-sequence alignment, phylogenetic tree building and global trusted sharing. VirusDIP is gradually establishing cooperation with more databases, and paving the way for the analysis of virus origin and evolution. All public data in VirusDIP are freely available for all researchers worldwide.Availabilityhttps://db.cngb.org/virus/[email protected]

scholarly journals Genome-Directed Isolation of the Key Nitrogen Fixer Leptospirillum ferrodiazotrophum sp. nov. from an Acidophilic Microbial Community

2005 ◽  
Vol 71 (10) ◽  
pp. 6319-6324 ◽  
Author(s):  
Gene W. Tyson ◽  
Ian Lo ◽  
Brett J. Baker ◽  
Eric E. Allen ◽  
Philip Hugenholtz ◽  
...  
Keyword(s):  
Mine Drainage ◽  
Sequence Data ◽  
Internal Transcribed Spacer Region ◽  
Free Living ◽  
Maximum Cell Density ◽  
Group Iii ◽  
A Genome ◽  
Low Diversity ◽  
Maximum Cell ◽  
Uncultured Microorganisms

ABSTRACT Analysis of assembled random shotgun sequence data from a low-diversity, subsurface acid mine drainage (AMD) biofilm revealed a single nif operon. This was found on a genome fragment belonging to a member of Leptospirillum group III, a lineage in the Nitrospirae phylum with no cultivated representatives. Based on the prediction that this organism is solely responsible for nitrogen fixation in the community, we pursued a selective isolation strategy to obtain the organism in pure culture. An AMD biofilm sample naturally abundant in Leptospirillum group III cells was homogenized, filtered, and serially diluted into a nitrogen-free liquid medium. The resulting culture in the terminal dilution grew autotrophically to a maximum cell density of ∼106 cells/ml, oxidizing ferrous iron as the sole energy source. 16S rRNA-internal transcribed spacer region clone library analysis confirmed that the isolate is a member of Leptospirillum group III and that the culture is axenic. We propose the name Leptospirillum ferrodiazotrophum sp. nov. for this iron-oxidizing, free-living diazotroph. This study highlights how environmental sequence data can provide insights for culturing previously uncultured microorganisms.

scholarly journals Factors mediating plastid dependency and the origins of parasitism in apicomplexans and their close relatives

2015 ◽  
Vol 112 (33) ◽  
pp. 10200-10207 ◽  
Author(s):  
Jan Janouškovec ◽  
Denis V. Tikhonenkov ◽  
Fabien Burki ◽  
Alexis T. Howe ◽  
Martin Kolísko ◽  
...  
Keyword(s):  
Plastid Genome ◽  
Sequence Data ◽  
Sister Group ◽  
Molecular Characteristics ◽  
Phylogenomic Analysis ◽  
Free Living ◽  
Plastid Genomes ◽  
Monophyletic Lineage ◽  
Causative Agents ◽  
Close Relatives

Apicomplexans are a major lineage of parasites, including causative agents of malaria and toxoplasmosis. How such highly adapted parasites evolved from free-living ancestors is poorly understood, particularly because they contain nonphotosynthetic plastids with which they have a complex metabolic dependency. Here, we examine the origin of apicomplexan parasitism by resolving the evolutionary distribution of several key characteristics in their closest free-living relatives, photosynthetic chromerids and predatory colpodellids. Using environmental sequence data, we describe the diversity of these apicomplexan-related lineages and select five species that represent this diversity for transcriptome sequencing. Phylogenomic analysis recovered a monophyletic lineage of chromerids and colpodellids as the sister group to apicomplexans, and a complex distribution of retention versus loss for photosynthesis, plastid genomes, and plastid organelles. Reconstructing the evolution of all plastid and cytosolic metabolic pathways related to apicomplexan plastid function revealed an ancient dependency on plastid isoprenoid biosynthesis, predating the divergence of apicomplexan and dinoflagellates. Similarly, plastid genome retention is strongly linked to the retention of two genes in the plastid genome, sufB and clpC, altogether suggesting a relatively simple model for plastid retention and loss. Lastly, we examine the broader distribution of a suite of molecular characteristics previously linked to the origins of apicomplexan parasitism and find that virtually all are present in their free-living relatives. The emergence of parasitism may not be driven by acquisition of novel components, but rather by loss and modification of the existing, conserved traits.

scholarly journals Possible Early Vertical Transmission of COVID-19 from an Infected Pregnant Female to Her Neonate: A Case Report

2020 ◽  
Author(s):  
Tapas Bandyopadhyay ◽  
Abhinav Sharma ◽  
Pratima Kumari ◽  
Arti Maria ◽  
Rahul Choudhary
Keyword(s):  
Public Health ◽  
Vertical Transmission ◽  
Antibody Test ◽  
Public Health Emergency ◽  
Pregnant Female ◽  
Rare Entity ◽  
Rt Pcr ◽  
Igg Antibody ◽  
Mode Of Transmission ◽  
Reported Data

Abstract Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-19) has emerged as a public health emergency in recent times. The reported data on the mode of transmission of coronavirus disease 2019 (COVID-19) are largely through contact, droplet, airborne and fomite transmission methods with vertical transmission being a rare entity. We hereby report a case of a probable vertical transmission of SARS-CoV-19 from an infected pregnant female to her neonate. The transmission has been confirmed by a positive RT-PCR at 16 h of life along with a positive IgG antibody test for SARS-CoV-19 in the baby and after excluding the possible environmental contamination of the sample. The baby was asymptomatic during the course of hospital stay and was discharged from the facility on Day 9 of life.

scholarly journals Deep Sequencing of a Dimethylsulfoniopropionate-Degrading Gene (dmdA) by Using PCR Primer Pairs Designed on the Basis of Marine Metagenomic Data

2009 ◽  
Vol 76 (2) ◽  
pp. 609-617 ◽  
Author(s):  
Vanessa A. Varaljay ◽  
Erinn C. Howard ◽  
Shulei Sun ◽  
Mary Ann Moran
Keyword(s):  
Sequence Data ◽  
Gene Clusters ◽  
Amino Acid Identity ◽  
Metagenomic Data ◽  
Data Sets ◽  
Free Living ◽  
Metagenomic Sequence ◽  
Primer Sets ◽  
Design And Testing ◽  
Pcr Primer

ABSTRACT In silico design and testing of environmental primer pairs with metagenomic data are beneficial for capturing a greater proportion of the natural sequence heterogeneity in microbial functional genes, as well as for understanding limitations of existing primer sets that were designed from more restricted sequence data. PCR primer pairs targeting 10 environmental clades and subclades of the dimethylsulfoniopropionate (DMSP) demethylase protein, DmdA, were designed using an iterative bioinformatic approach that took advantage of thousands of dmdA sequences captured in marine metagenomic data sets. Using the bioinformatically optimized primers, dmdA genes were amplified from composite free-living coastal bacterioplankton DNA (from 38 samples over 5 years and two locations) and sequenced using 454 technology. An average of 6,400 amplicons per primer pair represented more than 700 clusters of environmental dmdA sequences across all primers, with clusters defined conservatively at >90% nucleotide sequence identity (∼95% amino acid identity). Degenerate and inosine-based primers did not perform better than specific primer pairs in determining dmdA richness and sometimes captured a lower degree of richness of sequences from the same DNA sample. A comparison of dmdA sequences in free-living versus particle-associated bacteria in southeastern U.S. coastal waters showed that sequence richness in some dmdA subgroups differed significantly between size fractions, though most gene clusters were shared (52 to 91%) and most sequences were affiliated with the shared clusters (∼90%). The availability of metagenomic sequence data has significantly enhanced the design of quantitative PCR primer pairs for this key functional gene, providing robust access to the capabilities and activities of DMSP demethylating bacteria in situ.

scholarly journals Transmission models for the fish pathogen Ichthyophonus: synthesis of field observations and empirical studies

2019 ◽  
Vol 76 (4) ◽  
pp. 636-642 ◽  
Author(s):  
Richard M. Kocan
Keyword(s):  
Empirical Studies ◽  
Large Fish ◽  
Fish Pathogen ◽  
Free Living ◽  
Saltwater Fish ◽  
Mode Of Transmission ◽  
Infected Prey ◽  
Transmission Models ◽  
Inshore Migration

Empirical studies have demonstrated that Ichthyophonus is transmitted among piscivores via consumption of infected prey; however, this unidirectional mode of transmission from small to large fish cannot sustain Ichthyophonus within a population. To circumvent this problem, Ichthyophonus evolved an infective waterborne cell that has been shown to infect both fresh- and saltwater fish. Successful transmission of Ichthyophonus via a waterborne stage is linked to the proximity of infected and susceptible individuals, a condition met when the two groups occupy the same habitat. It is posited that this occurs during annual inshore migrations when herring (Clupea spp.) enter areas occupied by infected demersal predators. A plausible transmission scenario is that during inshore excursions, planktivores are exposed to infective waterborne cells shed by demersal piscivores. Once planktivores are infected, the parasite is recycled when consumed by predators. This model is supported by reports of ichthyophoniasis increasing in herring populations at the time of inshore migration. The possible role of an intermediate host for Ichthyophonus, as well as evidence for a free-living stage in its life cycle, is presented.

scholarly journals The Comprehensive Antibiotic Resistance Database

2013 ◽  
Vol 57 (7) ◽  
pp. 3348-3357 ◽  
Author(s):  
Andrew G. McArthur ◽  
Nicholas Waglechner ◽  
Fazmin Nizam ◽  
Austin Yan ◽  
Marisa A. Azad ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Sequence Data ◽  
Antibiotic Resistance Genes ◽  
Research Database ◽  
Free Living ◽  
Bacterial Populations ◽  
Bioinformatic Tools ◽  
Antibiotic Drug ◽  
Genetics And Genomics ◽  
Living Organisms

ABSTRACTThe field of antibiotic drug discovery and the monitoring of new antibiotic resistance elements have yet to fully exploit the power of the genome revolution. Despite the fact that the first genomes sequenced of free living organisms were those of bacteria, there have been few specialized bioinformatic tools developed to mine the growing amount of genomic data associated with pathogens. In particular, there are few tools to study the genetics and genomics of antibiotic resistance and how it impacts bacterial populations, ecology, and the clinic. We have initiated development of such tools in the form of the Comprehensive Antibiotic Research Database (CARD;http://arpcard.mcmaster.ca). The CARD integrates disparate molecular and sequence data, provides a unique organizing principle in the form of the Antibiotic Resistance Ontology (ARO), and can quickly identify putative antibiotic resistance genes in new unannotated genome sequences. This unique platform provides an informatic tool that bridges antibiotic resistance concerns in health care, agriculture, and the environment.

scholarly journals Diversity and distribution of Blastocystis sp. subtypes in non-human primates

Parasitology ◽  
2013 ◽  
Vol 140 (8) ◽  
pp. 966-971 ◽  
Author(s):  
MOHAMMED A. ALFELLANI ◽  
ALISON S. JACOB ◽  
NATALI ORTIZ PEREA ◽  
ROSINA C. KRECEK ◽  
DERYA TANER-MULLA ◽  
...  
Keyword(s):  
Host Specificity ◽  
New World ◽  
Sequence Data ◽  
Ssu Rdna ◽  
Restricted Range ◽  
Free Living ◽  
Allele Distribution ◽  
Rdna Sequence Data ◽  
Blastocystis Sp ◽  
Geographical Association

SUMMARYBlastocystis SSU-rDNA sequence data from 317 captive and free-living non-human primates (NHPs) representing 30 genera of apes, Old and New World (OW and NW) monkeys and prosimians were analysed to investigate subtype (ST) and allele distribution among hosts. Excluding 20 mixed ST infections, 27% of the sequences belonged to ST1, 22% to ST2, 34% to ST3, 1% to ST4, 4% to ST5, 11% to ST8, <1% to ST13 and 1% to ST15. The study confirmed cryptic host specificity of ST1 and ST3; conversely, considerable overlap in ST2 alleles exists among humans and NHPs. Subtype distribution in humans and NHPs differs mainly in that ST4 is rarely reported in NHPs while ST5 and ST8 are both unusual in humans. This may be due to host specificity and/or the apparent geographically restricted range of some subtypes. While the distribution of ST1, ST2 and ST3 was independent of NHP group or geographical association, ST5 was seen only in apes and OW monkeys and ST8 primarily in arboreal NHPs and only in species native to Asia or South America.

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