A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses

Moser, Lindsey A.; Ramírez-Carvajal, Lisbeth; Puri, Vinita; Pauszek, Steven J.; Matthews, Krystal; Dilley, Kari A.; Mullan, Clancy; McGraw, Jennifer; Khayat, Michael M.; Beeri, Karen; Yee, Anthony; Dugan, Vivien G.; Heise, Mark T.; Frieman, Matthew B.; Rodrı́guez, Luis L.; Bernard, Kristen A.; Wentworth, David E.; Stockwell, Timothy B.; Shabman, Reed S.

doi:10.1128/msystems.00039-15

Cited by 32 publications

(25 citation statements)

References 43 publications

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“…At JCVI, sequence-independent single-primer amplification (SISPA) was performed on purified RNA as previously described (26,27). Barcoded SISPA products were pooled, and adaptors were ligated following the manufacturers' instructions (Illumina, San Diego, CA).…”

Section: Methodsmentioning

confidence: 99%

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Comprehensive Genome Scale Phylogenetic Study Provides New Insights on the Global Expansion of Chikungunya Virus

Chen

Puri

Fedorova

et al. 2016

J Virol

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Since the India and Indian Ocean outbreaks of 2005 and 2006, the global distribution of chikungunya virus (CHIKV) and the locations of epidemics have dramatically shifted. First, the Indian Ocean lineage (IOL) caused sustained epidemics in India and has radiated to many other countries. Second, the Asian lineage has caused frequent outbreaks in the Pacific islands and in 2013 was introduced into the Caribbean, followed by rapid spread to nearly all of the neotropics. Further, CHIKV epidemics, as well as exported cases, have been reported in central Africa after a long period of perceived silence. To understand these changes and to anticipate the future of the virus, the exact distribution, genetic diversity, transmission routes, and future epidemic potential of CHIKV require further assessment. To do so, we conducted the most comprehensive phylogenetic analysis to date, examined CHIKV evolution and transmission, and explored distinct genetic factors associated with the emergence of the East/Central/ South African (ECSA) lineage, the IOL, and the Asian lineage. Our results reveal contrasting evolutionary patterns among the lineages, with growing genetic diversities observed in each, and suggest that CHIKV will continue to be a major public health threat with the potential for further emergence and spread. IMPORTANCE Chikungunya fever is a reemerging infectious disease that is transmitted by

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Section: Methodsmentioning

confidence: 99%

“…Libraries were sequenced on the Illumina MiSeq (2-by 300-bp paired end [PE]). A combination of JCVI-and CLCbio-developed tools were used to process read data from all next-generation sequencing (NGS) runs (26,28).…”

Section: Methodsmentioning

confidence: 99%

Comprehensive Genome Scale Phylogenetic Study Provides New Insights on the Global Expansion of Chikungunya Virus

Chen

Puri

Fedorova

et al. 2016

J Virol

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“…Each sample was singly passaged in LFBK-αvβ6 cells in order to ensure sufficient virus for subsequent steps. Thirty-two samples were sequenced using a sequence-independent single primer amplification method using the Illumina MiSeq platform as previously described [46]. An additional twenty samples as well as the inoculum were sequenced on the Illumina NextSeq 500.…”

Section: Methodsmentioning

confidence: 99%

The evolution of a super-swarm of foot-and-mouth disease virus in cattle

Arzt

Fish

Pauszek

et al. 2019

Preprint

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23 Foot-and-mouth disease (FMD) is a highly contagious viral disease that severely impacts global 24 food security and is one of the greatest constraints on international trade of animal products.25 Extensive viral population diversity and rapid, continuous mutation of circulating FMD viruses 26 (FMDVs) pose significant obstacles to the control and ultimate eradication of this important 27 transboundary pathogen. The current study investigated mechanisms contributing to within-host 28 evolution of FMDV in a natural host species (cattle). Specifically, vaccinated and non-29 vaccinated cattle were infected with FMDV under controlled, experimental conditions and 30 subsequently sampled for up to 35 days to monitor viral genomic changes as related to phases of 31 disease and experimental cohorts. Consensus-level genomic changes across the entire FMDV 32 coding region were characterized through three previously defined stages of infection: early, 33 transitional, and persistent. The overall conclusion was that viral evolution occurred via a 34 combination of two mechanisms: emergence of full-genomic minority haplotypes from within 35 the inoculum super-swarm, and concurrent continuous point mutations. Phylogenetic analysis 36 indicated that individuals were infected with multiple distinct haplogroups that were pre-existent 37 within the ancestral inoculum used to infect all animals. Multiple shifts of dominant viral 38 haplotype took place during the early and transitional phases of infection, whereas few shifts 39 occurred during persistent infection. These insights into FMDV population dynamics have 40 important implications for virus sampling methodology and molecular epidemiology. 41 42 43 3 44 Introduction 45Foot-and-mouth disease (FMD) is a highly contagious viral disease that affects wild and 46 domestic even-toed ruminants [1, 2]. FMD is a major global concern for livestock owners and 47 managers, and the disease has substantial impact on regulation of international trade in animal 48 products [3]. The classical signs of disease include oral and pedal vesicles and erosions, often 49 associated with lameness, pyrexia, and obtundation [2, 4]. The causative agent, FMD virus 50 (FMDV) is extremely contagious and disseminates rapidly amongst susceptible animals. 51 Although the disease is rarely fatal, FMD-endemic regions incur substantial economic burdens 52 associated with production losses and disease control [5]. Sporadic outbreaks in countries that 53 are normally free from FMD result in costly mediations including culling of large numbers of 54 animals and animal movement restrictions, as well as massive economic losses due to 55 implications on trade in animal products. 56 FMDV (family: Picornaviridae, genus: Aphthovirus) is a single-stranded RNA virus which 57 exists in 7 defined serotypes; O, A, C, Asia-1, and Southern African Territories (SAT) 1-3. The 58 FMDV genome encodes a total of 12 mature proteins translated from a single polyprotein coding 59 region approximately 7 kilobases in length. The structu...

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“…Total RNA from cells at rest was enriched for messenger RNA with oligo dT dynabeads (Invitrogen, Carlsbad CA). Total RNA from mock-infected and Zika-infected samples were subjected to SISPA multiplex library construction [53] and sequenced by Illumina NextSeq 1x150 bp sequencing.…”

Section: Methodsmentioning

confidence: 99%

“…Quantitative PCR confirmed Zika RNA was abundant in the Zika-infected samples vs. the mock-infected samples. A single multiplex sequencing library was prepared by the low-cost SISPA method [53]. Unpaired Illumina RNA sequencing reads were filtered by mapping to C6/36; see Table S17.…”

Section: Demonstration Of Subtraction Database For Viral Assaysmentioning

confidence: 99%

Analysis of theAedes albopictusC6/36 genome provides insight into cell line adaptations toin vitroviral propagation

Miller

Koren

Dilley

et al. 2017

Preprint

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BackgroundThe 50-year old Aedes albopictus C6/36 cell line is a resource for the detection, amplification, and analysis of mosquito-borne viruses including Zika, dengue, and chikungunya. The cell line is derived from an unknown number of larvae from an unspecified strain of Aedes albopictus mosquitoes. Toward improved utility of the cell line for research in virus transmission, we present an annotated assembly of the C6/36 genome.ResultsThe C6/36 genome assembly has the largest contig N50 (3.3 Mbp) of any mosquito assembly, presents the sequences of both haplotypes for most of the diploid genome, reveals independent null mutations in both alleles of the Dicer locus, and indicates a male-specific genome. Gene annotation was computed with publicly available mosquito transcript sequences. Gene expression data from cell line RNA sequence identified enrichment of growth-related pathways and conspicuous deficiency in aquaporins and inward rectifier K+ channels. As a test of utility, RNA sequence data from Zika-infected cells was mapped to the C6/36 genome and transcriptome assemblies. Host subtraction reduced the data set by 89%, enabling faster characterization of non-host reads.ConclusionsThe C6/36 genome sequence and annotation should enable additional uses of the cell line to study arbovirus vector interactions and interventions aimed at restricting the spread of human disease.

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A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses

Cited by 32 publications

References 43 publications

Comprehensive Genome Scale Phylogenetic Study Provides New Insights on the Global Expansion of Chikungunya Virus

Comprehensive Genome Scale Phylogenetic Study Provides New Insights on the Global Expansion of Chikungunya Virus

The evolution of a super-swarm of foot-and-mouth disease virus in cattle

Analysis of theAedes albopictusC6/36 genome provides insight into cell line adaptations toin vitroviral propagation

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