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1.  Microarray-based detection of viruses causing vesicular or vesicular-like lesions in livestock animals 
Veterinary microbiology  2008;133(0):145-153.
Definitive diagnosis of vesicular or vesicular-like lesions in livestock animals presents challenges both for veterinary clinicians and diagnostic laboratories. It is often impossible to diagnose the causative disease agent on a clinical basis alone and difficult to collect ample vesicular epithelium samples. Due to restrictions of time and sample size, once laboratory tests have ruled out foot-and-mouth disease, vesicular stomatitis and swine vesicular disease a definitive diagnosis may remain elusive. With the ability to test a small quantity of sample for a large number of pathogens simultaneously, DNA microarrays represent a potential solution to this problem. This study describes the application of a long oligonucleotide microarray assay to the identification of viruses known to cause vesicular or vesicular-like lesions in livestock animals. Eighteen virus isolates from cell culture were successfully identified to genus level, including representatives of each foot-and-mouth disease virus serotype, two species of vesicular stomatitis virus, swine vesicular disease virus, vesicular exanthema of swine virus, bovine herpesvirus 1, orf virus, pseudocowpox virus, bluetongue virus serotype 1 and bovine viral diarrhoea virus 1. Vesicular stomatitis virus and vesicular exanthema of swine virus were also identified in vesicular epithelium samples, with varying levels of sensitivity. The results indicate that with further development this microarray assay could be a valuable tool for the diagnosis of vesicular and vesicular-like diseases.
doi:10.1016/j.vetmic.2008.05.030
PMCID: PMC4310687  PMID: 18621489
2.  Short Communication: New Recognition Of Enterovirus Infections In Bottlenose Dolphins (Tursiops Truncatus) 
Veterinary microbiology  2009;139(0):170-175.
An enterovirus was cultured from an erosive tongue lesion of a bottlenose dolphin (Tursiops truncatus). The morphology of virions on negative staining electron microscopy was consistent with those of enteroviruses. Analysis of 2613 bp of the polyprotein gene identified the isolate as a novel enterovirus strain, tentatively named bottlenose dolphin enterovirus (BDEV), that nests within the species Bovine enterovirus. Serologic evidence of exposure to enteroviruses was common in both free ranging and managed collection dolphins. Managed collection dolphins were more likely to have high antibody levels, although the highest levels were reported in free ranging populations. Associations between enterovirus antibody levels, and age, sex, complete blood counts, and clinical serum biochemistries were explored. Dolphins with higher antibody levels were more likely to be hyperproteinemic and hyperglobulinemic.
doi:10.1016/j.vetmic.2009.05.010
PMCID: PMC4310689  PMID: 19581059
3.  MOLECULAR CHARACTERIZATION OF SEVERE AND MILD CASES OF INFLUENZA A (H1N1) 2009 STRAIN FROM ARGENTINA 
Medicina  2010;70(6):518-523.
While worldwide pandemic influenza A(H1N1) pdm case fatality rate (CFR) was 0.4%, Argentina’s was 4.5%. A total of 34 strains from mild and severe cases were analyzed. A full genome sequencing was carried out on 26 of these, and a partial sequencing on the remaining eight. We observed no evidence that the high CFR can be attributed to direct virus changes. No evidence of re-assortment, mutations associated with resistance to antiviral drugs, or genetic drift that might contribute to virulence was observed. Although the mutation D225G associated with severity in the latest reports from the Ukraine and Norway is not observed among the Argentine strains, an amino acid change in the area (S206T) surrounding the HA receptor binding domain was observed, the same previously established worldwide.
PMCID: PMC4310694  PMID: 21163739
H1N1 pdm; influenza; Argentina
4.  Evaluation of the Potential Impact of Ebola Virus Genomic Drift on the Efficacy of Sequence-Based Candidate Therapeutics 
mBio  2015;6(1):e02227-14.
ABSTRACT 
Until recently, Ebola virus (EBOV) was a rarely encountered human pathogen that caused disease among small populations with extraordinarily high lethality. At the end of 2013, EBOV initiated an unprecedented disease outbreak in West Africa that is still ongoing and has already caused thousands of deaths. Recent studies revealed the genomic changes this particular EBOV variant undergoes over time during human-to-human transmission. Here we highlight the genomic changes that might negatively impact the efficacy of currently available EBOV sequence-based candidate therapeutics, such as small interfering RNAs (siRNAs), phosphorodiamidate morpholino oligomers (PMOs), and antibodies. Ten of the observed mutations modify the sequence of the binding sites of monoclonal antibody (MAb) 13F6, MAb 1H3, MAb 6D8, MAb 13C6, and siRNA EK-1, VP24, and VP35 targets and might influence the binding efficacy of the sequence-based therapeutics, suggesting that their efficacy should be reevaluated against the currently circulating strain.
doi:10.1128/mBio.02227-14
PMCID: PMC4313914  PMID: 25604787
5.  Gene duplication and phylogeography of North American members of the Hart Park serogroup of avian rhabdoviruses 
Virology  2013;448:10.1016/j.virol.2013.10.024.
Flanders virus (FLAV) and Hart Park virus (HPV) are rhabdoviruses that circulate in mosquito-bird cycles in the eastern and western United States, respectively, and constitute the only two North American representatives of the Hart Park serogroup. Previously, it was suggested that FLAV is unique among the rhabdoviruses in that it contains two pseudogenes located between the P and M genes, while the cognate sequence for HPV has been lacking. Herein, we demonstrate that FLAV and HPV do not contain pseudogenes in this region, but encode three small functional proteins designated as U1, U2, and U3 that apparently arose by gene duplication. To further investigate the U1-U2-U3 region, we conducted the first large-scale evolutionary analysis of a member of the Hart Park serogroup by analyzing over 100 spatially and temporally distinct FLAV isolates. Our phylogeographic analysis demonstrates that although FLAV appears to be slowly evolving, phylogenetically divergent lineages co-circulate sympatrically.
doi:10.1016/j.virol.2013.10.024
PMCID: PMC3873333  PMID: 24314659
Flanders virus; Hart Park virus; Hart Park serogroup; rhabdovirus; gene duplication; U1, U2, and U3 proteins; SH protein; coupled translation; bird-associated arbovirus
6.  Optimization of Antitumor Modulators of Pre-mRNA Splicing 
Journal of medicinal chemistry  2013;56(24):10033-10044.
The spliceosome regulates pre-mRNA splicing, which is a critical process in normal mammalian cells. Recently recurrent mutations in numerous spliceosomal proteins have been associated with a number of cancers. Previously natural product antitumor agents have been shown to interact with one of the proteins that is subject to recurrent mutations (SF3B1). We report the optimization of a class of tumor-selective spliceosome modulators, which demonstrate significant in vivo antitumor activity. This optimization culminated in the discovery of sudemycin D6, which shows potent cytotoxic activity in the melanoma line SK-MEL-2 (IC50= 39 nM) and other tumor lines, including: JeKo-1 (IC50= 26 nM), HeLa (IC50= 50 nM), and SK-N-AS (IC50= 81 nM). We also report improved processes for the synthesis of these compounds. Our work supports the idea that sudemycin D6 is worthy of further investigation as a novel preclinical anticancer agent with application in the treatment of numerous human cancers.
doi:10.1021/jm401370h
PMCID: PMC3932738  PMID: 24325474
7.  Reidentification of Ebola Virus E718 and ME as Ebola Virus/H.sapiens-tc/COD/1976/Yambuku-Ecran 
Genome Announcements  2014;2(6):e01178-14.
Ebola virus (EBOV) was discovered in 1976 around Yambuku, Zaire. A lack of nomenclature standards resulted in a variety of designations for each isolate, leading to confusion in the literature and databases. We sequenced the genome of isolate E718/ME/Ecran and unified the various designations under Ebola virus/H.sapiens-tc/COD/1976/Yambuku-Ecran.
doi:10.1128/genomeA.01178-14
PMCID: PMC4239354  PMID: 25414499
8.  Nomenclature- and Database-Compatible Names for the Two Ebola Virus Variants that Emerged in Guinea and the Democratic Republic of the Congo in 2014 
Viruses  2014;6(11):4760-4799.
In 2014, Ebola virus (EBOV) was identified as the etiological agent of a large and still expanding outbreak of Ebola virus disease (EVD) in West Africa and a much more confined EVD outbreak in Middle Africa. Epidemiological and evolutionary analyses confirmed that all cases of both outbreaks are connected to a single introduction each of EBOV into human populations and that both outbreaks are not directly connected. Coding-complete genomic sequence analyses of isolates revealed that the two outbreaks were caused by two novel EBOV variants, and initial clinical observations suggest that neither of them should be considered strains. Here we present consensus decisions on naming for both variants (West Africa: “Makona”, Middle Africa: “Lomela”) and provide database-compatible full, shortened, and abbreviated names that are in line with recently established filovirus sub-species nomenclatures.
doi:10.3390/v6114760
PMCID: PMC4246247  PMID: 25421896
Ebola; Ebola virus; ebolavirus; filovirid; Filoviridae; filovirus; genome annotation; Lomela; Lokolia; Makona; mononegavirad; Mononegavirales; mononegavirus; virus classification; virus isolate; virus nomenclature; virus strain; virus taxonomy; virus variant
10.  Viral diversity and clonal evolution from unphased genomic data 
BMC Genomics  2014;15(Suppl 6):S17.
Background
Clonal expansion is a process in which a single organism reproduces asexually, giving rise to a diversifying population. It is pervasive in nature, from within-host pathogen evolution to emergent infectious disease outbreaks. Standard phylogenetic tools rely on full-length genomes of individual pathogens or population consensus sequences (phased genotypes).
Although high-throughput sequencing technologies are able to sample population diversity, the short sequence reads inherent to them preclude assessing whether two reads originate from the same clone (unphased genotypes). This obstacle severely limits the application of phylogenetic methods and investigation of within-host dynamics of acute infections using this rich data source.
Methods
We introduce two measures of diversity to study the evolution of clonal populations using unphased genomic data, which eliminate the need to construct full-length genomes. Our method follows a maximum likelihood approach to estimate evolutionary rates and times to the most recent common ancestor, based on a relaxed molecular clock model; independent of a growth model. Deviations from neutral evolution indicate the presence of selection and bottleneck events.
Results
We evaluated our methods in silico and then compared it against existing approaches with the well-characterized 2009 H1N1 influenza pandemic. We then applied our method to high-throughput genomic data from marburgvirus-infected non-human primates and inferred the time of infection and the intra-host evolutionary rate, and identified purifying selection in viral populations.
Conclusions
Our method has the power to make use of minor variants present in less than 1% of the population and capture genomic diversification within days of infection, making it an ideal tool for the study of acute RNA viral infection dynamics.
doi:10.1186/1471-2164-15-S6-S17
PMCID: PMC4240099  PMID: 25573168
Clonal evolution; Evolutionary dynamics; Viral genomic diversity; Marburgvirus
11.  Genome Sequences of Simian Hemorrhagic Fever Virus Variant NIH LVR42-0/M6941 Isolates (Arteriviridae: Arterivirus) 
Genome Announcements  2014;2(5):e00978-14.
Simian hemorrhagic fever virus (SHFV) variant NIH LVR42-0/M6941 is the only remaining SHFV in culture, and only a single genome sequence record exists in GenBank/RefSeq. We compared the genomic sequence of NIH LVR42-0/M6941 acquired from the ATCC in 2011 to NIH LVR42-0/M6941 genomes sequenced directly from nonhuman primates experimentally infected in 1989.
doi:10.1128/genomeA.00978-14
PMCID: PMC4192379  PMID: 25301647
12.  Transcriptome reconstruction and annotation of cynomolgus and African green monkey 
BMC Genomics  2014;15(1):846.
Background
Non-human primates (NHPs) and humans share major biological mechanisms, functions, and responses due to their close evolutionary relationship and, as such, provide ideal animal models to study human diseases. RNA expression in NHPs provides specific signatures that are informative of disease mechanisms and therapeutic modes of action. Unlike the human transcriptome, the transcriptomes of major NHP animal models are yet to be comprehensively annotated.
Results
In this manuscript, employing deep RNA sequencing of seven tissue samples, we characterize the transcriptomes of two commonly used NHP animal models: Cynomolgus macaque (Macaca fascicularis) and African green monkey (Chlorocebus aethiops). We present the Multi-Species Annotation (MSA) pipeline that leverages well-annotated primate species and annotates 99.8% of reconstructed transcripts. We elucidate tissue-specific expression profiles and report 13 experimentally validated novel transcripts in these NHP animal models.
Conclusion
We report comprehensively annotated transcriptomes of two non-human primates, which we have made publically available on a customized UCSC Genome Browser interface. The MSA pipeline is also freely available.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-846) contains supplementary material, which is available to authorized users.
doi:10.1186/1471-2164-15-846
PMCID: PMC4194418  PMID: 25277458
Cynomolgus macaque; Macaca fascicularis; African green monkey; Chlorocebus aethiops; RNA-seq; Transcriptome; Genomics; Annotation; Database
13.  Development and Evaluation of a Panel of Filovirus Sequence Capture Probes for Pathogen Detection by Next-Generation Sequencing 
PLoS ONE  2014;9(9):e107007.
A detailed understanding of the circulating pathogens in a particular geographic location aids in effectively utilizing targeted, rapid diagnostic assays, thus allowing for appropriate therapeutic and containment procedures. This is especially important in regions prevalent for highly pathogenic viruses co-circulating with other endemic pathogens such as the malaria parasite. The importance of biosurveillance is highlighted by the ongoing Ebola virus disease outbreak in West Africa. For example, a more comprehensive assessment of the regional pathogens could have identified the risk of a filovirus disease outbreak earlier and led to an improved diagnostic and response capacity in the region. In this context, being able to rapidly screen a single sample for multiple pathogens in a single tube reaction could improve both diagnostics as well as pathogen surveillance. Here, probes were designed to capture identifying filovirus sequence for the ebolaviruses Sudan, Ebola, Reston, Taï Forest, and Bundibugyo and the Marburg virus variants Musoke, Ci67, and Angola. These probes were combined into a single probe panel, and the captured filovirus sequence was successfully identified using the MiSeq next-generation sequencing platform. This panel was then used to identify the specific filovirus from nonhuman primates experimentally infected with Ebola virus as well as Bundibugyo virus in human sera samples from the Democratic Republic of the Congo, thus demonstrating the utility for pathogen detection using clinical samples. While not as sensitive and rapid as real-time PCR, this panel, along with incorporating additional sequence capture probe panels, could be used for broad pathogen screening and biosurveillance.
doi:10.1371/journal.pone.0107007
PMCID: PMC4160210  PMID: 25207553
14.  Advantages of tandem LC-MS for the rapid assessment of tissue-specific metabolic complexity using a pentafluorophenylpropyl stationary phase 
Journal of proteome research  2011;10(4):2104-2112.
In this study a UPLC-tandem (Waters Xevo TQ) MRM based MS method was developed for rapid, broad profiling of hydrophilic metabolites from biological samples, in either positive or negative ion modes without the need for an ion pairing reagent, using a reversed-phase pentafluorophenylpropyl (PFPP) column. The developed method was successfully applied to analyze various biological samples from C57BL/6 mice; including urine, duodenum, liver, plasma, kidney, heart, and skeletal muscle. As result, a total 112 of hydrophilic metabolites were detected within 8 min of running time to obtain a metabolite profile of the biological samples. The analysis of this number of hydrophilic metabolites is significantly faster than previous studies. Classification separation for metabolites from different tissues was globally analyzed by PCA, PLS-DA and HCA biostatistical methods. Overall, most of the hydrophilic metabolites were found to have a “fingerprint” characteristic of tissue dependency. In general, a higher level of most metabolites was found in urine, duodenum and kidney. Altogether, these results suggest that this method has potential application for targeted metabolomic analyzes of hydrophilic metabolites in a wide ranges of biological samples.
doi:10.1021/pr1011119
PMCID: PMC4158837  PMID: 21322650
metabolomics; metabolic networks; metabolic complexity; hydrophilic metabolites; LC/MS; MRM; reversed-phase HPLC; C57BL/6 mice
15.  Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names 
Kuhn, Jens H. | Andersen, Kristian G. | Bào, Yīmíng | Bavari, Sina | Becker, Stephan | Bennett, Richard S. | Bergman, Nicholas H. | Blinkova, Olga | Bradfute, Steven | Brister, J. Rodney | Bukreyev, Alexander | Chandran, Kartik | Chepurnov, Alexander A. | Davey, Robert A. | Dietzgen, Ralf G. | Doggett, Norman A. | Dolnik, Olga | Dye, John M. | Enterlein, Sven | Fenimore, Paul W. | Formenty, Pierre | Freiberg, Alexander N. | Garry, Robert F. | Garza, Nicole L. | Gire, Stephen K. | Gonzalez, Jean-Paul | Griffiths, Anthony | Happi, Christian T. | Hensley, Lisa E. | Herbert, Andrew S. | Hevey, Michael C. | Hoenen, Thomas | Honko, Anna N. | Ignatyev, Georgy M. | Jahrling, Peter B. | Johnson, Joshua C. | Johnson, Karl M. | Kindrachuk, Jason | Klenk, Hans-Dieter | Kobinger, Gary | Kochel, Tadeusz J. | Lackemeyer, Matthew G. | Lackner, Daniel F. | Leroy, Eric M. | Lever, Mark S. | Mühlberger, Elke | Netesov, Sergey V. | Olinger, Gene G. | Omilabu, Sunday A. | Palacios, Gustavo | Panchal, Rekha G. | Park, Daniel J. | Patterson, Jean L. | Paweska, Janusz T. | Peters, Clarence J. | Pettitt, James | Pitt, Louise | Radoshitzky, Sheli R. | Ryabchikova, Elena I. | Saphire, Erica Ollmann | Sabeti, Pardis C. | Sealfon, Rachel | Shestopalov, Aleksandr M. | Smither, Sophie J. | Sullivan, Nancy J. | Swanepoel, Robert | Takada, Ayato | Towner, Jonathan S. | van der Groen, Guido | Volchkov, Viktor E. | Volchkova, Valentina A. | Wahl-Jensen, Victoria | Warren, Travis K. | Warfield, Kelly L. | Weidmann, Manfred | Nichol, Stuart T.
Viruses  2014;6(9):3663-3682.
Sequence determination of complete or coding-complete genomes of viruses is becoming common practice for supporting the work of epidemiologists, ecologists, virologists, and taxonomists. Sequencing duration and costs are rapidly decreasing, sequencing hardware is under modification for use by non-experts, and software is constantly being improved to simplify sequence data management and analysis. Thus, analysis of virus disease outbreaks on the molecular level is now feasible, including characterization of the evolution of individual virus populations in single patients over time. The increasing accumulation of sequencing data creates a management problem for the curators of commonly used sequence databases and an entry retrieval problem for end users. Therefore, utilizing the data to their fullest potential will require setting nomenclature and annotation standards for virus isolates and associated genomic sequences. The National Center for Biotechnology Information’s (NCBI’s) RefSeq is a non-redundant, curated database for reference (or type) nucleotide sequence records that supplies source data to numerous other databases. Building on recently proposed templates for filovirus variant naming [ ()////-], we report consensus decisions from a majority of past and currently active filovirus experts on the eight filovirus type variants and isolates to be represented in RefSeq, their final designations, and their associated sequences.
doi:10.3390/v6093663
PMCID: PMC4189044  PMID: 25256396
Bundibugyo virus; cDNA clone; cuevavirus; Ebola; Ebola virus; ebolavirus; filovirid; Filoviridae; filovirus; genome annotation; ICTV; International Committee on Taxonomy of Viruses; Lloviu virus; Marburg virus; marburgvirus; mononegavirad; Mononegavirales; mononegavirus; Ravn virus; RefSeq; Reston virus; reverse genetics; Sudan virus; Taï Forest virus; virus classification; virus isolate; virus nomenclature; virus strain; virus taxonomy; virus variant
16.  Draft Genome Assembly of Acinetobacter baumannii ATCC 19606 
Genome Announcements  2014;2(4):e00832-14.
Acinetobacter baumannii is an emerging nosocomial pathogen, and therefore high-quality genome assemblies for this organism are needed to aid in detection, diagnostic, and treatment technologies. Here we present the improved draft assembly of A. baumannii ATCC 19606 in two scaffolds. This 3,953,621-bp genome contains 3,750 coding regions and has a 39.1% G+C content.
doi:10.1128/genomeA.00832-14
PMCID: PMC4153487  PMID: 25146140
17.  Israeli Acute Paralysis Virus: Epidemiology, Pathogenesis and Implications for Honey Bee Health 
PLoS Pathogens  2014;10(7):e1004261.
Israeli acute paralysis virus (IAPV) is a widespread RNA virus of honey bees that has been linked with colony losses. Here we describe the transmission, prevalence, and genetic traits of this virus, along with host transcriptional responses to infections. Further, we present RNAi-based strategies for limiting an important mechanism used by IAPV to subvert host defenses. Our study shows that IAPV is established as a persistent infection in honey bee populations, likely enabled by both horizontal and vertical transmission pathways. The phenotypic differences in pathology among different strains of IAPV found globally may be due to high levels of standing genetic variation. Microarray profiles of host responses to IAPV infection revealed that mitochondrial function is the most significantly affected biological process, suggesting that viral infection causes significant disturbance in energy-related host processes. The expression of genes involved in immune pathways in adult bees indicates that IAPV infection triggers active immune responses. The evidence that silencing an IAPV-encoded putative suppressor of RNAi reduces IAPV replication suggests a functional assignment for a particular genomic region of IAPV and closely related viruses from the Family Dicistroviridae, and indicates a novel therapeutic strategy for limiting multiple honey bee viruses simultaneously and reducing colony losses due to viral diseases. We believe that the knowledge and insights gained from this study will provide a new platform for continuing studies of the IAPV–host interactions and have positive implications for disease management that will lead to mitigation of escalating honey bee colony losses worldwide.
Author Summary
The mysterious outbreak of honey bee Colony Collapse Disorder (CCD) in the US in 2006–2007 has attracted massive media attention and created great concerns over the effects of various risk factors on bee health. Understanding the factors that are linked to the honey bee colony declines may provide insights for managing similar incidents in the future. We conducted this study to elucidate traits of a key honey bee virus, Israeli acute paralysis virus. We then developed an innovative strategy to control virus levels. The knowledge and insights gained from this study will have positive implications for bee disease management, helping to mitigate worldwide colony losses.
doi:10.1371/journal.ppat.1004261
PMCID: PMC4117608  PMID: 25079600
18.  Diagnostics and Discovery in Viral Hemorrhagic Fevers 
The rate of discovery of new microbes and of new associations of microbes with health and disease is accelerating. Many factors contribute to this phenomenon including those that favor the true emergence of new pathogens as well as new technologies and paradigms that enable their detection and characterization. This chapter reviews recent progress in the field of pathogen surveillance and discovery with a focus on viral hemorrhagic fevers.
doi:10.1111/j.1749-6632.2009.05056.x
PMCID: PMC4109264  PMID: 19751404
19.  Evaluation of two molecular methods for the detection of Yellow fever virus genome 
Journal of virological methods  2011;174(0):29-34.
Yellow fever virus (YFV), a member of the family Flaviviridae, genus Flavivirus is endemic to tropical areas of Africa and South America and is among the arboviruses that pose a threat to public health. Recent outbreaks in Brazil, Bolivia, and Paraguay and the observation that vectors capable of transmitting YFV are presenting in urban areas underscore the urgency of improving surveillance and diagnostic methods. Two novel methods (RT-hemi-nested-PCR and SYBR®Green qRT-PCR) for efficient detection of YFV strains circulating in South America have been developed. The methods were validated using samples obtained from golden hamsters infected experimentally with wild-type YFV strains as well as human serum and tissue samples with acute disease.
doi:10.1016/j.jviromet.2011.02.025
PMCID: PMC4109279  PMID: 21419803
Yellow fever virus; molecular diagnostic; RT-hemi-nested-PCR; SYBR®Green qRT-PCR
20.  Microbe Hunting in Laboratory Animal Research 
Recent advances in nucleic acid diagnostic technologies have revolutionized microbiology by facilitating rapid, sensitive pathogen surveillance and differential diagnosis of infectious diseases. With the expansion and dissemination of genomic sequencing technology scientists are discovering new microbes at an accelerating pace. In this article we review recent progress in the field of pathogen surveillance and discovery with a specific focus on applications in the field of laboratory animal research. We discuss the challenges in proving a causal relationship between the presence of a candidate organism and disease. We also discuss the strengths and limitations of various assay platforms and describe a staged strategy for viral diagnostics. To illustrate the complexity of pursuing pathogen discovery research, we include examples from our own work that are intended to provide insights into the process that led to the selection of particular strategies.
PMCID: PMC4107416  PMID: 21131725
high-throughput sequencing; MassTag; microbe; molecular assay; pathogen discovery; pathogen surveillance; polymerase chain reaction (PCR)
21.  Standards for Sequencing Viral Genomes in the Era of High-Throughput Sequencing 
mBio  2014;5(3):e01360-14.
ABSTRACT
Thanks to high-throughput sequencing technologies, genome sequencing has become a common component in nearly all aspects of viral research; thus, we are experiencing an explosion in both the number of available genome sequences and the number of institutions producing such data. However, there are currently no common standards used to convey the quality, and therefore utility, of these various genome sequences. Here, we propose five “standard” categories that encompass all stages of viral genome finishing, and we define them using simple criteria that are agnostic to the technology used for sequencing. We also provide genome finishing recommendations for various downstream applications, keeping in mind the cost-benefit trade-offs associated with different levels of finishing. Our goal is to define a common vocabulary that will allow comparison of genome quality across different research groups, sequencing platforms, and assembly techniques.
doi:10.1128/mBio.01360-14
PMCID: PMC4068259  PMID: 24939889
22.  VIRUS NOMENCLATURE BELOW THE SPECIES LEVEL: A STANDARDIZED NOMENCLATURE FOR LABORATORY ANIMAL-ADAPTED STRAINS AND VARIANTS OF VIRUSES ASSIGNED TO THE FAMILY FILOVIRIDAE 
Archives of virology  2013;158(6):1425-1432.
The International Committee on Taxonomy of Viruses (ICTV) organizes the classification of viruses into taxa, but is not responsible for the nomenclature for taxa members. International experts groups, such as the ICTV Study Groups, recommend the classification and naming of viruses and their strains, variants, and isolates. The ICTV Filoviridae Study Group has recently introduced an updated classification and nomenclature for filoviruses. Subsequently, and together with numerous other filovirus experts, a consistent nomenclature for their natural genetic variants and isolates was developed that aims at simplifying the retrieval of sequence data from electronic databases. This is a first important step toward a viral genome annotation standard as sought by the US National Center for Biotechnology Information (NCBI). Here, this work is extended to include filoviruses obtained in the laboratory by artificial selection through passage in laboratory hosts. The previously developed template for natural filovirus genetic variant naming ( ///-) is retained, but it is proposed to adapt the type of information added to each field for laboratory animal-adapted variants. For instance, the full-length designation of an Ebola virus Mayinga variant adapted at the State Research Center for Virology and Biotechnology “Vector” to cause disease in guinea pigs after seven passages would be akin to “Ebola virus VECTOR/C.porcellus-lab/COD/1976/Mayinga-GPA-P7”. As was proposed for the names of natural filovirus variants, we suggest using the full-length designation in databases, as well as in the method section of publications. Shortened designations (such as “EBOV VECTOR/C.por/COD/76/May-GPA-P7”) and abbreviations (such as “EBOV/May-GPA-P7”) could be used in the remainder of the text depending on how critical it is to convey information contained in the full-length name. “EBOV” would suffice if only one EBOV strain/variant/isolate is addressed.
doi:10.1007/s00705-012-1594-2
PMCID: PMC3669655  PMID: 23358612
cuevavirus; Ebola; Ebola virus; ebolavirus; filovirid; Filoviridae; filovirus; genome annotation; ICTV; International Committee on Taxonomy of Viruses; Lloviu virus; Marburg virus; marburgvirus; mononegavirad; Mononegavirales; mononegavirus; virus classification; virus isolate; virus nomenclature; virus strain; virus taxonomy; virus variant
23.  E2F1 plays a direct role in Rb stabilization and p53-independent tumor suppression 
Cell cycle (Georgetown, Tex.)  2008;7(12):1776-1781.
To better understand the role of E2F1 in tumor formation, we analyzed spontaneous tumorigenesis in p53−/−E2F1+/+ and p53−/−E2F1−/− mice. We show that the combined loss of p53 and E2F1 leads to an increased incidence of sarcomas and carcinomas compared to the loss of p53 alone. E2F1-deficient tumors show wide chromosomal variation, indicative of genomic instability. Consistent with this, p53−/−E2F1−/− primary fibroblasts have a reduced capacity to maintain genomic stability when exposed to S-phase inhibitors or genotoxic drugs. A major mechanism of E2F1’s contribution to genomic integrity lies in mediating stabilization and engagement of the Rb protein.
PMCID: PMC4012429  PMID: 18583939
Rb protein; p53; G2M checkpoint; DNA replication
24.  Air Travel Is Associated with Intracontinental Spread of Dengue Virus Serotypes 1–3 in Brazil 
Dengue virus and its four serotypes (DENV-1 to DENV-4) infect 390 million people and are implicated in at least 25,000 deaths annually, with the largest disease burden in tropical and subtropical regions. We investigated the spatial dynamics of DENV-1, DENV-2 and DENV-3 in Brazil by applying a statistical framework to complete genome sequences. For all three serotypes, we estimated that the introduction of new lineages occurred within 7 to 10-year intervals. New lineages were most likely to be imported from the Caribbean region to the North and Northeast regions of Brazil, and then to disperse at a rate of approximately 0.5 km/day. Joint statistical analysis of evolutionary, epidemiological and ecological data indicates that aerial transportation of humans and/or vector mosquitoes, rather than Aedes aegypti infestation rates or geographical distances, determine dengue virus spread in Brazil.
Author Summary
Dengue virus serotypes are associated with millions of infections and thousands of deaths globally each year, primarily in tropical and subtropical regions. We investigated the spatial dynamics of DENV (serotypes 1–3) in Brazil by applying a statistical framework to complete genome sequences. Co-circulation of distinct genotypes, lineage extinction and replacement and multiple viral introduction events were found for all three serotypes. New lineages were typically introduced from the Caribbean into Northern Brazil and dispersed thereafter at a rate of ≈0.5 km/year. Our analysis indicates that aerial transportation is a more important determinant of viral dispersal than Aedes aegypti infestation rates or geographical distance.
doi:10.1371/journal.pntd.0002769
PMCID: PMC3990485  PMID: 24743730
25.  Characterization of the Salehabad virus species complex of the genus Phlebovirus (Bunyaviridae) 
The Journal of General Virology  2013;94(Pt 4):837-842.
Genomic and antigenic characterization of the Salehabad virus, a species of the genus Phlebovirus, and four other unclassified phleboviruses (Arbia, Adria, Arumowot and Odrenisrou) demonstrate a serological and genetic relation to one another and are distinct from the eight other recognized species within the genus Phlebovirus. We propose to incorporate these four unclassified viruses as part of the Salehabad species complex within the genus. The known geographical distribution for the members of this species group includes southern Europe, Central Asia and Africa.
doi:10.1099/vir.0.048850-0
PMCID: PMC3709685  PMID: 23239568

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