Vaccinia recombination 3 - Journal of Virology

JVI Accepts, published online ahead of print on 26 February 2014
J. Virol. doi:10.1128/JVI.00022-14
Copyright © 2014, American Society for Microbiology. All Rights Reserved.
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Title: Genome scale patterns of recombination between co-infecting vaccinia viruses
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Running Title: Vaccinia recombination
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Authors: Li Qin1, and David H. Evans1#
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Affiliation: 1Dept. of Medical Microbiology & Immunology and
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Li Ka Shing Institute of Virology
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6020H Katz Group Centre
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University of Alberta
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Edmonton, AB
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T6G 2H7 CANADA
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Word Counts:
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Abstract: 250 words
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Importance: 150 words
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Text (including above): 6,106 words
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#Corresponding author: Dept. of Medical Microbiology & Immunology, 6020 Katz
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Group Centre, University of Alberta, Edmonton, AB, T6G 2H7, CANADA. Phone (780)
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492-2308; FAX (780) 492-7521; E-mail [email protected]
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ABSTRACT
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Recombination plays a critical role in virus evolution. It helps avoid genetic decline and
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creates novel phenotypes. This promotes survival, and genome sequencing suggests that
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recombination
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Orthopoxviruses like variola virus. Recombination can also be used to map genes, but
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although recombinant poxviruses are easily produced in culture, classical attempts to map
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the vaccinia virus (VACV) genome this way, met with little success. We have sequenced
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recombinants formed when VACV TianTan and Dryvax strains are crossed under
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different conditions. These were a single round of growth in co-infected cells, five rounds
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of sequential passage, or using Leporipoxvirus-mediated DNA reactivation. Our studies
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showed that recombinants contain a patchwork of DNA, with the number of exchanges
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increasing with passage. Further passage also selected for TianTan DNA and correlated
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with increased plaque size. The recombinants produced through a single round of
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co-infection contain a disproportionate number of short conversion tracks (<1 kbp) and
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exhibited 1 exchange per 12 kbp, close to the ~1 per 8 kbp in the literature. One
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byproduct of this study was that rare mutations were also detected, VACV replication
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produces ~1×10-8 mutations per nucleotide copied per cycle of replication and ~1 large
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(21 kbp) deletion per 70 rounds of passage. Viruses produced using DNA reactivation
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appeared no different from recombinants produced using ordinary methods. An attractive
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feature of this approach is that, when combined with selection for a particular phenotype,
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it provides a way of mapping and dissecting more complex virus traits.
has
facilitated
the
evolution
of
human
pathogens
including
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IMPORTANCE
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When two closely related viruses co-infect the same cell, they can swap genetic
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information through a process called recombination. Recombination produces new
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viruses bearing different combinations of genes, and it plays an important role in virus
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evolution. Poxviruses are a family of viruses that includes variola (or smallpox) virus and
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although poxviruses are known to recombine, no one has previously mapped the patterns
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of DNAs exchanged between viruses. We co-infected cells with two different vaccinia
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poxviruses, isolated the progeny, and sequenced them.
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recombination is a very accurate process that assembles viruses containing DNA copied
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from both parents. In a single round of infection, DNA is swapped back and forth ~18
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times per genome to make recombinant viruses that are a mosaic of the two parental
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DNAs. This mixes many different genes in complex combinations and illustrates how
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recombination can produce viruses with greatly altered disease potential.
We show that poxvirus
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INTRODUCTION
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Recombination plays an essential role in DNA repair and, by creating new combinations
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of genetic traits, it averts the decline in fitness caused by the accumulation of mutations
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(”Muller’s ratchet”) while creating the genetic diversity that is the substrate for
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Darwinian selection. Bacteriophage were the first viruses shown to be subject to
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recombination (1) and the phenomenon was soon also detected in co-cultures of many
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other viruses including herpes simplex virus (2) and vaccinia virus (3). In the years
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immediately following, research showed that in vitro recombination could also produce
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hybrids between related poxviruses such as rabbit fibroma and myxoma viruses (4) and
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between variola virus and cowpox and rabbitpox viruses (5, 6). The subsequent discovery
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of another natural hybrid between rabbit fibroma and myxoma viruses, called malignant
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rabbit virus (7), suggested that poxviruses can also recombine in co-infected animals and
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the significance for human health is illustrated by the fact that variola minor virus may be
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a recombinant derived from more virulent West African and Asian variola major strains
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(8). We have recently published an analysis of some of the strain variants found in an old
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non-clonal smallpox vaccine, Dryvax, and detected one virus bearing a small region of
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sequence wherein the single nucleotide polymorphisms (SNPs) were more characteristic
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of horsepox than of vaccinia virus (VACV) (9). This may represent a sequence relic that
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has been retained in the absence of counter selection and the population bottlenecks
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caused by periodic plaque purification.
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Genetic crosses between viruses encoding different selectable markers were once
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also used to try and assemble recombination-based maps of VACV (10-12), although the
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method never proved very useful and was soon supplanted by marker rescue and DNA
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sequencing technologies. This was due to the limited distances over which linkage is
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retained relative to the spacing between many markers (<20 kbp over a 200 kbp genome)
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and the difficulty of reproducibly measuring recombinant frequencies (13). Further
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studies showed that homologous recombination can be used to genetically modify VACV
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(14, 15), that this is an accurate process (16, 17), and that these processes also operate in
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trans and can be detected using transfected DNAs (18). Poxviruses replicate in
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sequestered structures called factories (19), each of which derives from a single infecting
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particle, and it is presumed that recombinants can only form within these factories if
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different DNAs mix in the presence of the recombination machinery. VACV uses a
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single-strand annealing mechanism to produce recombinant molecules in a reaction
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catalyzed by the E9 viral DNA polymerase and I3 single-strand DNA binding protein (20,
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21) and, since both proteins primarily reside within virus factories, that is presumably
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where recombination also occurs. We have suggested that random variations in the timing
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and degree of mixing of virus factories within co-infected cells could explain why
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recombinant frequencies proved difficult to measure reproducibly (13). If two or more
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viruses infect any particular cell, but a portion of the factories don’t mix, such a process
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would decrease the yield of recombinants in a stochastic manner relative to the number of
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non-recombinant (i.e. fully parental) viruses produced by DNA replication.
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Although much has been learned concerning the mechanism of poxvirus
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recombination, questions remain regarding how these processes and physical constraints
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might affect the patterns of DNA exchange, and thus the overall genetic composition of
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the resulting pool of parental and recombinant viruses. How genetic linkage distances
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relate to the actual numbers of exchanges in recombinant viruses also remains to be
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established. In this study we have used the ~1400 SNPs that differentiate two strains of
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VACV, a Dryvax clone and a TianTan clone, as sequence tags that can be used to track
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the origins of the different DNA segments in recombinant progeny. Our study shows that
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VACV recombination reactions produce genomes exhibiting a “patchwork” of exchanges,
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some apparently derived from a succession of crossovers over the course of a single
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infection cycle. Interestingly, viruses produced using non-genetic reactivation methods
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(22), appear indistinguishable from recombinants produced in a more regular manner,
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showing that such viruses are likely subjected to similar replication and developmental
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pathways.
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METHODS
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Cells and viruses. Vaccinia virus strains DPP17 (GenBank JN654983), TP03 (GenBank
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KC207810), and TP05 (Genbank KC207811) were cloned from stocks of Dryvax
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(DPP17) and TianTan (TP03/05) viruses (9, 23). They were cultured on BSC-40 cells in
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modified Eagle’s medium (MEM, Gibco) supplemented with 5% fetal bovine serum, 1%
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nonessential amino acids, 1% L-glutamine, and 1% antibiotic at 37°Cin a 5%CO2
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atmosphere. Two types of recombinant virus stocks were prepared. The DTM viruses
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(Dryvax-TianTan mixture) were generated by co-infecting cells with DPP17 and TP05 at
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a multiplicity of infection (MOI) of 0.02 (each 0.01), culturing the cells for two days,
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harvesting the cell-virus mixture, and releasing the virus by freeze-thaw. A sample (10
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μL, 0.5% of the lysate, or ~0.02 PFU/cell) was then used to infect another fresh dish of
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cells and this was repeated for a total of five rounds of passage. Individual DTM viruses
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were then isolated using three rounds of cloning by limiting dilution as described (9). The
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DTH viruses (Dryvax-TianTan high MOI) were produced by co-infecting cells with
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DPP17 and TP05 at MOI=10 (each 5) for 24 hr, followed by three rounds of cloning.
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Plaque images were processed with ImageJ (24).
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Virus DNA reactivation. A third collection of recombinant VACV were prepared using
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DNA reactivation reactions as described previously (22). Briefly, BGMK cells were
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grown to near confluence in 60 mm dishes and infected with Shope fibroma virus (SFV,
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strain Kasza) at MOI=1 in PBS. After one hour at 37°C, the medium was replaced with
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MEM containing 10% fetal bovine serum, incubated for another hour, and the MEM
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replaced with Opti-MEM (Gibco). DPP17 and TP03 VACV DNAs were extracted from
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sucrose gradient-purified virions using phenol chloroform, mixed in 1:1 ratio, and the
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SFV-infected cells transfected with 5 μg of this DNA using Lipofectamine 2000 (Gibco).
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The cells were incubated for 4 hr, the Opti-MEM media was replaced with MEM
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containing 10% serum, and the cells cultured for another 3 days. The cells were then
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subjected to three rounds of freeze-thaw and 0.2 mL used to infect BSC-40 cells (which
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do not support SFV growth). The reactivated VACV were cloned using three rounds of
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limited dilution and recombinants were identified using the PCR and the primer pairs
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DVX-209F and DVX-226R plus DVX-004F and DVX-007R (Table 1). The 209F/226R
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primers should produce a 1.1 kbp amplicon in reactions containing DPP17 DNA whereas
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TP03 DNA does not serve as a substrate. The 004F/007R primer pair targets telomeric
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repeat sequences and should produce 665 bp and 1230 bp products in reactions
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containing TP03 and DPP17 DNAs, respectively. After cloning, the viruses were purified
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and sequenced as described. Four DTD clones (Dryvax-TianTan DNA reactivation) were
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sequenced.
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Virus sequencing and genomic analysis. Stocks of 16 DTM clones, 15 DTH, and 4
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DTD clones were prepared and purified over sucrose gradients. Viral DNAs were
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extracted and sequenced as described previously (9) using a Roche 454 GS Junior system.
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Roche GS De Novo Assembler software was used to deconvolute and assemble the raw
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sequencing data into contigs and nearly full-length genomes were generated using CLC
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Genomics Workbench 6. The average read redundancy was 15, which permitted the
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assembly and mapping of all of the recombinant junctions with confidence. Multiple
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sequence alignments were prepared using the program LAGAN (http://genome.lbl.gov)
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(25) and Base-by-Base software (26) was used to produce a visual summary of the whole
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genome alignments. The assembled sequence data have been assigned GenBank
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accession numbers KJ467582 to KJ467616, inclusive (Table S1).
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PCR and Southern blotting. Southern blotting was used to confirm the rearrangement
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detected in clone DTM28. Virus DNA was digested with NdeI (Fermentas) and size
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fractionated by electrophoresis on 0.7% agarose gels. The DNA was fragmented with
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0.2M HCl, denatured with 0.4M NaOH, transferred to a nylon membrane, and fixed with
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a UV cross-linker. Two primers (201F and 239R, Table 1) and the PCR were used to
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prepare a probe in a reaction containing biotin-16-dUTP (Roche, 1093070), which was
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subsequently hybridized to the prepared membrane and detected using IRDye
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800CW-coupled streptavidin (Li-Cor; 926-32230) and a Li-Cor imager. The DTM28 and
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DTM28Δ viruses were also differentiated using the PCR and 208F and 209R (Table 1)
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primers. This was done in combination with 201F and 239R in a PCR reaction containing
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all four primers.
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RESULTS and DISCUSSION
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Virus isolation and genome sequencing and assembly. We used three different methods
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to produce VACV recombinants. The first method was designed to explore the effects of
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repeated passage, at low MOI, on a seed mixture initially composed of just two different
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genetically tagged viruses. These viruses were originally cloned from stocks of Dryvax
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(DPP17) and TianTan (TP05) vaccines and differ in sequence by 1 SNP per ~140 bp.
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Compared to TP05, DPP17 also encodes a 6 kbp deletion near the right terminal inverted
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repeat boundary as well as ~150 other smaller insertions and deletions (indels) distributed
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across the two genomes (Figure 1). The TP05 strain forms plaques that are approximately
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twice the diameter of those formed by the DPP17 strain, which provided an opportunity
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to explore what effect a growth bias might have on the pattern of recombinants.
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For this first experiment, a 1:1 mixture of the two different VACV were used to
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infect BSC-40 cells at MOI=0.02, cultured 48 hr, and a portion (10 μL or ~0.02 PFU/cell)
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of the resulting progeny passaged again under the same conditions. This was repeated to
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produce a total of 5 rounds of replication. Each time the infection produced overlapping
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plaques that partly cleared the entire plate. We then plated out the diluted virus in 24-well
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plates, and identified 36 wells each containing just a single random plaque. These 36
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viruses were then cloned again, also by limiting dilution, and designated DTM
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(Dryvax-TianTan mixture) strains. Using this method minimized the risk of picking
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certain plaque types, since the only criteria we used to choose a clone was that the virus
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had to have been diluted to the point where it was the only plaque in a well, in the first
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round of selection. To avoid the problem of resequencing any non-recombinant parental
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stains, the PCR and three different primer pairs were used to determine the genetic origin
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of three different sites within each genome: within the terminal inverted repeats (primers
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004F/007R), in the central part of the genome (primers 107F/108R), and near the junction
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with the right terminal inverted repeat (213F/209F/226R) (Table 1). Fourteen clones were
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selected because at least one position was recombinant with respect to either of the other
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two sites. We also chose two additional viruses, which exhibited a parental arrangement
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of markers at these three sites, although these were subsequently determined to also be
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recombinants. These viruses were cloned two more times and 16 were sequenced. After
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sequencing and assembly, these DTM recombinants exhibited a patchy pattern of SNPs
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suggesting each virus was the product of approximately 30 exchanges over the course of
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virus replication.
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One expects that when viruses are passaged five times under these conditions, it
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should provide an opportunity for repeated rounds of replication and recombination. We
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also examined what the virus progeny would look like if they were permitted just a single
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round of infection, although it is expected that this would still involve multiple rounds of
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replication. To do this, we co-infected BSC-40 cells with DPP17 and TP05 viruses at
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MOI=10 (5 pfu/cell of each virus) and cultured the viruses for just 24 hr. These viruses
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were cloned and designated DTH strains (Dryvax-TianTan high MOI). After the first
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round of cloning, 43 viruses were randomly selected and the PCR was used to identify
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putative recombinants as described above. Thirteen hybrid viruses were cloned twice
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more, along with two additional viruses (DTH13 and DTH14) that exhibited a parental
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pattern of markers at the three positions tested by the PCR. DTH14 was subsequently
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identified as being identical to the TP05 parent virus, while DTH13 proved to be a
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recombinant. Ultimately, 15 DTH clones were sequenced and assembled as described
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before. These recombinants exhibited a mean of 18 exchanges per genome.
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We should note one caveat regarding these methods, in that single plaques isolated in
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the first round of purification were not always pure, and this provided some limited
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opportunity for additional rounds of replication and recombination. For example, when a
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plaque initially identified as recombinant DTM22 was cloned a second time, and the
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subsidiary plaques reanalyzed by PCR, it was realized that the two daughter plaques
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(DTM22.1 and DTM22.2) were not identical. However, they are clearly “sibs”, viruses
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sharing a common genetic origin as judged by a shared pattern of exchanges in the center
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of the two genomes (Figure 1). We also noted one case where a single apparently
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recombinant starting plaque resolved into two clearly unrelated recombinant clones upon
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replating (clones DTH10 and DTH10.2, Figure 1). For simplicity, our analysis has treated
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these particular clones as being the same as the other recombinants isolated in the study,
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although they may have experienced some additional limited opportunities to undergo
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recombination.
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Crossovers in DTM and DTH viruses. After assembly, the sequences were aligned with
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program LAGAN and the alignment corrected manually using Base-by-Base. Inspecting
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these sequences we could readily identify the origin of each SNP-tagged segment of
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DNA as belonging to either the DPP17 or TP05 parent (Figure 1). What was remarkable
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was the very low frequency of observed mutation even though numerous SNPs and
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smalls indels commonly differentiate clones isolated from a viral stock like Dryvax (9).
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No mutations were detected in any of the DTH clones, compared with the two parent
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viruses, and just two mutations in two of the DTM clones. One was a small deletion in
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DTM29 at alignment position 900, which removed two nucleotides (Figure 2, panel A)
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just 6 nt upstream of the ORF001 start codon. Although most small deletions are
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associated with repeats (9, 27), this event was not. It was located immediately adjacent to
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a SNP that differentiates DPP17 from TP05. We also discovered a point mutation in
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DTM27 at alignment position 70,493 (Figure 2, panel B). This causes a C-to-T transition
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mutation and an alanine-to-valine substitution in gene DVX_088 (RNA-helicase). A
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crude estimate of the VACV replicative error rate can be calculated from the following
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observations and assumptions. We note that there were only two independent mutations
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detected in 16 DTM viruses over the course of 5 rounds of infection, and there are
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~200,000 nt copied per genome per each round of infection. Each round of infection
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typically expands the VACV titer ~10,000-fold (i.e. between 214 and 215 doublings of the
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genome) and thus the error rate is very crudely estimated as 2÷[16×200,000×5×14.5] or
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~1×10-8 mutations per nucleotide copied per cycle of replication. Alternatively this is
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2÷[16×5×14.5] or ~1 mutation per 600 genomes per cycle of replication. By a similar
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method, the absence of any mutations detected amongst the 15 DTH clones over the
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course of a single round of infection suggests an error rate of <5×10-8. The VACV E9L
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gene encodes a typical B-family proofreading DNA polymerase of a type encoded by a
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variety of viruses and bacteriophage, and this error frequency resembles that reported for
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phage (28). Although some drug-resistant E9L alleles cause altered spontaneous mutation
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rates in vivo (29-31), for comparison purposes these cannot be converted into absolute
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mutation rates given the uncertainties in the size or number of genetic target(s). We could
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find no other reported absolute error rates for poxviruses in the literature.
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Beyond these two rare mutations, the remainder of the sequences in the recombinant
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genomes could be ascribed to having been inherited from one or the other of the two
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parent viruses. In total, 1399 SNPs (single nucleotide polymorphisms) can be used to
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differentiate DPP17 from TP05 and we used these SNPs to track the origins, and thus the
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sites of crossing over, in the hybrids. The relative abundance of these variant sites (1399
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scattered across ~200 kbp) allowed us to map the site(s) of crossing over with an average
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resolution of ~140 nt. In general, each hybrid virus encoded variable-length blocks of
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DNA derived from each of the two parent strains, and no uniquely conserved block (a
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hallmark of a highly selected patch of DNA) was detected in all of the viruses. The
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lengths of these blocks of recombined sequences varied, ranging in length from one to
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several hundred SNPs. We detected none of the large gene duplications that have been
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described by other authors (32, 33), but would not expect to do so given that these
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structures are stable only in the presence of strong selection pressure.
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To examine the pattern of crossing over in greater detail, we used “Base-by-Base”
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software to produce a table ascribing each of the 1399 SNPs detected in each hybrid as
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being of either DPP17 or TP05 origin (data not shown). This provided a tool for
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calculating the number of exchanges on the assumption that each time the pattern of
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SNPs changed from DPP17 to TP05 (or vice versa), that an exchange had occurred and
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was counted as one crossover. It is important to note that this is still an underestimate of
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the true physical recombination frequency, as any recombination between two parental
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genomes (e.g. DPP17×DPP17 or TP05×TP05), or recombination occurring over distances
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less than the distances between SNPs cannot be detected by this method. Figure 3 shows
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the results of this analysis. We had expected that viruses given more opportunities for
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recombination would exhibit a greater number of exchanges, and this was supported by
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these measurements. The number of crossovers in the DTM viruses ranged from 14 to 44
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(mean = 30±11 [SD]). In contrast, the numbers of crossovers in the DTH viruses ranged
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from 0 to 38 (mean = 18±11 [SD]), with one virus, DTH14, identical to the TP05 parents.
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In a previous publication (13) we conducted a meta-analysis of all of the published
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VACV genetic recombination data and attempted to correlate these data with the known
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physical map of the virus. From these studies we derived an estimate that half-maximal
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recombination was detected in a single round of infection (akin to the method used to
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produce the DTH viruses), when the distance between VACV markers was ~8 kbp.
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Although this number is difficult to estimate with precision due to a number of
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experimental factors (13), from our measurements of the conversion track lengths (see
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below) we calculated that the DTH viruses exhibited a mean of about 1 physical
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crossover per 12 kbp, a number compatible with the ~8 kbp deduced from the older
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genetic literature. Historically, classical genetic crosses never proved a useful tool for
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mapping VACV genomes, due to a combination of experimental noise and short linkage
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distances relative to the distances between most VACV markers. When one considers that
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our estimate of 1 crossover per 12 kbp is associated with a standard deviation of 19 kbp
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(i.e. 12±19 kbp), the source of this problem is clearly apparent.
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Average length of the conversion tracts. Besides measuring the numbers of exchanges
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suffered by each of the recombinant viruses, we also examined the lengths of the DNA
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segments exchanged between viruses (i.e. the conversion track length) in the DTH group.
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To do this, the calculation assumed that the start and end of each exchange lay midway
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between the SNPs flanking the two sites of exchange. The resolution of the method varies
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depending upon the local SNP density, but with an average of 1 SNP per 140 bp we could
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detect exchanges ranging in size from 55 to 92,000 bp. An interesting feature of VACV
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recombination is illustrated by this analysis, which showed that there were relatively
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more short conversion tracks than long ones (Figure 4). Thus while the mean length of a
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conversion track was 12 kbp, the median was only 2.6 kbp. The abundance of short
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conversion tracks would help favor intragenic recombination events, which can be
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detected between markers spaced only 54 bp apart (34). We should note that this estimate
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of the recombination frequency is lower than has been previously reported. For example
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we detected a loss of linkage at distances exceeding 350 bp in one study (35). However,
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this earlier experiment measured the yield of recombinants when DNA was transfected
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into Shope fibroma virus-infected cells, and it is possible that the non-specific DNA
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replication that is seen under these circumstances (36) also exposes transfected DNAs to
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higher levels of recombination than is normally experienced by viruses.
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Crossing over is not the only process that could produce this abundance of short
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exchanges. Poxvirus replication and recombination reactions also produce hybrid (or
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heteroduplex) DNA (37). Such molecules would contain mismatched bases wherever the
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sequences differ and if a subset of mismatches were subjected to mismatch-specific and
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directionally biased short patch DNA repair prior to further replication, it could create the
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appearance of closely linked crossovers. However, our data provide no evidence that
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mismatch repair is producing artifactual exchanges. If any repair bias existed, it would
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most probably occur at sites where the hybrid DNA contained G·T mismatches, since G·T
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mismatches are generally repaired to G·C basepairs in cells by a pathway employing a
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thymine DNA glycolylase (38). A G·T mismatch would be formed (along with a
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reciprocal A·C mismatch) at sites where substitution mutations differentiate the two
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viruses. Such substitutions (i.e. GÆA, AÆG, CÆT, or TÆC) comprise 72% of the SNP
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markers in these crosses. If one makes the simplifying assumption that A·C mismatches
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are just replicated and not repaired, and that all G·T mismatches are converted to G·C
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prior to replication, then these single marker exchanges should be biased 2:1 in favour of
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forming (or retaining) a G or C. We detected 51 single exchanges at sites containing base
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substitutions (82% of all single exchanges), in the DTM and DTH viruses. Of these, 29
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retained a G or C, and 22 retained an A or T, which is not significantly different from a
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1:1 split (Ȥ2=0.96, P=0.33). Although we cannot disprove the hypothesis that biased
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mismatched repair created some of the short conversion tracts, the simplest explanation
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for these data is that poxvirus recombination reactions produce an abundance of short
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conversion tracks through a process formally akin to crossing over.
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Biased genetic origins in progeny viruses. An interesting difference between the
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TianTan and Dryvax clones used in this study is that TP05 forms plaques twice the size
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of DPP17 plaques on BSC40 cells. We wondered how this phenotype might segregate
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amongst the recombinants deriving from either the DTH or DTM crosses. We used the
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SNPs to determine what fraction of each genome derived from TP05 or DPP17, and
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plated all of the cloned viruses on BSC-40 cells, at the same time, to determine the
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average plaque size. The DTH viruses, passaged just once, showed no particular
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compositional bias, comprising about equal portions (50±27%) of each of the parental
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viruses (Figure 5A). In contrast the DTM hybrids bear a diminished (19±11%) fraction of
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the genome derived from DPP17 SNPs (Figure 5A). Oddly, there seems to be a simple
368
linear relationship between plaque size and the proportion of the genome derived from
369
each parent strain, with larger plaque sizes associated with a greater proportion of
370
TP05-derived DNA (Figure 5B). These data suggest that the TP05-derived DNA may
371
confer a selective growth advantage in multiple rounds of culture (i.e. DTM viruses), but
372
one round of growth (i.e. DTH viruses) provides insufficient time or selective pressure to
373
bias the composition of the recombinants.
Qin et al.
Vaccinia virus recombination
Page 15 of 31
374
What would produce this effect is not clear. Plaque size is likely determined by many
375
different genetic factors, and there are many differences in the gene composition of the
376
two parent strains. For example DPP17 contains a large deletion in the right TIR
377
compared to TP05 and this deletion bears a number of different genes (Table 2). However,
378
this deletion is not completely responsible for plaque variation since DPP25, containing
379
all the genes in this region, forms plaques only slightly larger than DPP17 (9). We
380
subsequently annotated all of the hybrid genomes using GATU (39) and evaluated the
381
differences (Table 3). There are many mutant genes segregating in complex ways
382
between the different viruses including mutant forms of I4L (40), F3L (41), E5R (42),
383
M1L, A51R, and C23L, but no obvious distribution patterns could be discerned by
384
inspection beyond the fact that the more presumably functional genes the virus encoded
385
(Table 3, grey cells), the better it grew. The non-transcribed telomeric repeats in VAC
386
telomeres cannot be assembled into contiguous sequences, due to the redundancies in the
387
repeats, but some of the fragments of junction sequences differ enough in TianTan and
388
Dryvax to deduce the origins of the telomeres. This analysis detected a trend suggesting
389
that viruses bearing TP05-like telomeres also form larger plaques. However, all that
390
could really be concluded from this analysis is that TianTan-derived sequences generally
391
contribute greater advantage in culture than does Dryvax DNA.
392
393
Large deletions formed through illegitimate recombination. Poxviruses are also
394
known to suffer deletion mutations during passage. The most extreme example is
395
probably modified vaccinia virus Ankara (MVA), which accumulated six large deletions,
396
and many smaller ones, when it was passaged >570 times in chicken embryo fibroblasts
397
(43). Over the course of these experiments we did detect one such large deletion mutation
398
when we sequenced clone DTM28. The deletion spans 21 kbp and encompasses genes
399
DVX_201 to 239 (Figure 6). In the initial assembly, we found 11 sequence reads that
Qin et al.
Vaccinia virus recombination
Page 16 of 31
400
started in gene DVX_201 and terminated in gene DVX_239 (Figure 6a), along with
401
sequence reads derived from all of the intervening genes. The deletion spans the right
402
TIR boundary, but amongst the reads were some from the unique genes DVX_202-209
403
suggesting we had sequenced a stock of virus containing the DTM28 parent contaminated
404
by a virus bearing the deletion (DTM28Δ). To confirm this interpretation of the data we
405
prepared primers 201F and 239R (which are located 21 kbp apart in genes DVX_201 and
406
DVX_239, respectively; Figure 6b) and used the PCR to detect the novel 1.2 kbp
407
amplicon that was predicted to be formed in this process (Figure 6c). We also tested
408
DNAs extracted from the virus stocks that had been archived during the process of
409
passaging these viruses 5 times, before cloning, as well as DTM27, another independent
410
clone that was purified in parallel. Only the purified DTM28 stock contained a virus
411
bearing the deletion (Figure 6c) suggesting that DTM28Δ arose during the expansion of
412
the stock. Finally we used the 1.2 kbp amplicon to probe a Southern blot of NdeI-cut
413
virus DNA, and showed that the DTM28 stock contains viruses contributing a 6.7kbp
414
band characteristic of the deletion-containing fragment as well as a 5.4 kbp band, which
415
derives from the two 5.4 kbp NdeI fragments that encode the boundaries of the deletion
416
(Figure 6d). We subsequently sub-cloned this stock and separately isolated the two
417
viruses, confirming the viability of DTM28Δ and the fact that none of the deleted genes
418
are essential (Figure 6e) in cell culture.
419
The DNA surrounding the vaccinia virus right TIR boundary is a well-established
420
hotspot for large deletion mutations (23). The mechanism is probably the same as that
421
which drives the formation of small deletion mutations, stating with the misalignment of
422
regions containing imperfect repeats (9, 27). If one aligns the reads spanning the junction
423
boundary between DVX_201 and DVX_239, one sees several small blocks of homology
424
(Figure 6a, boxed) that could have stabilized the first step in an illegitimate
425
recombination reaction. It is difficult to establish an exact rate by which such mutations
Qin et al.
Vaccinia virus recombination
Page 17 of 31
426
arise, but this stock was plaque purified three times, following bulk up and only one virus
427
in 16 DTM viruses passaged in parallel suffered a deletion of this type. This creates a rate
428
of ~0.06/4 passages or 1 deletion per 70 passages. The six large deletions introduced into
429
MVA over 570 passages are thus quite consistent with this estimate although, of course,
430
the selection pressures are very different in the two experiments.
431
432
Recombination in SFV-reactivated vaccinia viruses. A third small collection of
433
recombinant viruses was also produced using Shope fibroma virus mediated DNA
434
reactivation assays and DNAs extracted from DPP17 and TianTan strain TP03 (22). [We
435
used TP03, instead of the TP05 used for the preceding experiments, to test whether
436
viruses could also be produced encoding all three of the large TP03 and DP17 telomeric
437
deletions.] This method relies upon a replicating helper virus (SFV) to rescue or
438
“reactivate” fragments of transfected virus DNA (VACV). The SFV is subsequently
439
eliminated by passage on a cell line that supports only VACV growth. Figure 7 shows the
440
maps of the viruses that were recovered by this method. There were just four viruses
441
obtained and two (DTD03 and DTD11) are so similar that they are probably “sibs”
442
sharing a mostly common history. These viruses were too few in number, and the passage
443
history too complicated, to derive much in the way of statistics about recombination
444
patterns, but the pattern of exchanges generally resembled the lesser numbers and longer
445
conversion tracks seen in the DTH viruses. The method did also produce clones bearing
446
the three large telomeric deletions (DTD03 and DTD18, Figure 7), which left the virus
447
with TIRs just 7.3 kbp long. An important caveat is that the DTD viruses were recovered
448
from cells that had been transfected for a few hours and then incubated for three days, so
449
whether the recombinants were produced during the reactivation stage or during
450
subsequent rounds of re-infection and replication is difficult to deduce.
Qin et al.
Vaccinia virus recombination
Page 18 of 31
451
Overall, there were no strikingly unique features of these reactivated viruses that
452
would differentiate them from any other type of recombinant poxvirus. Perhaps the most
453
important conclusion that could be drawn from this brief study is that this process is very
454
accurate (no mutant viruses were recovered) and no Shope fibroma virus DNA sequences
455
were detected in any of the reactivated VACV. The two most similar genes in SFV and
456
VACV are S068R and J6R, respectively (44), which share only 73% nucleotide sequence
457
identity with no blocks of perfect alignment >17 nt. There is even less similarity between
458
VACV and fowlpox virus, another virus that has also been used to reactivate
459
Orthopoxviruses (45). This is probably insufficient sequence similarity to support
460
frequent recombination between the helper and reactivated viruses. Additionally VACV
461
hybrids may well be rare and difficult to isolate in the absence of selection, if not simply
462
inviable. Such data support the long-standing suspicion that using a heterologous helper
463
virus, like SFV or fowlpox virus, to reactivate Orthopoxviruses can be done without
464
mutation and does not produce hybrid strains.
465
466
Conclusions. Next generation DNA sequencing technologies are greatly improving our
467
understanding of the genome structures and genes encoded by large DNA viruses. Here
468
we show that these methods can also be used to characterize the structures of
469
recombinant poxviruses. These studies show that recombinant VACV are not surprisingly
470
composed of a patchwork of DNA fragments derived from the parent viruses. The
471
numbers of exchanges varies depending upon the passage history, but if one uses
472
methods like those classically used to produce VACV recombinants (a high multiplicity
473
of infection [10] and one day of co-culture), one detects about 1 physical crossover per 12
474
kbp in the DTH viruses, a number only slightly higher than the ~8 kbp we have estimated
475
from a review of the older genetic literature. However, there is a lot of noise observed in
Qin et al.
Vaccinia virus recombination
Page 19 of 31
476
this number (12±19 kbp), perhaps explaining why accurate classical recombination maps
477
were never produced for VACV.
478
Interestingly the lengths of the recombinant patches (i.e. the conversion tracts) are
479
heavily biased towards shorter sizes, something that would favour intragenic
480
recombination. What mechanism would produce such an effect is difficult to identify,
481
although we have previously used genetic methods to show that VACV replication and
482
recombination are intimately linked processes (18, 46), probably because the VACV E9
483
DNA polymerase exhibits properties characteristic of a recombinase both in vitro (21)
484
and in vivo (20). Thus recombination may just be an indirect by-product of virus
485
replication, conceivably associated with the DNA polymerase-catalyzed repair of broken
486
replication structures. Regardless of the mechanism, this process could have interesting
487
genetic consequences for virus evolution, as it would create a lot of diversity within
488
recombinant genes, not just diverse combinations of different genes. This becomes of
489
critical importance when one considers the challenge posed to viruses by rapidly evolving
490
responses to biological features like immunodominant epitopes. Short conversion tracks
491
offer a selective advantage for a virus, as they provide a mechanism for rearranging and
492
eliminating peptide epitopes while still retaining gene function.
493
These studies also show how sequencing could be used to characterize more complex
494
virus traits than those regulated by single genes. Continued passage of the DTM viruses
495
selected for viruses bearing greater proportions of the TianTan genome and this was
496
correlated in some, still unclear, manner to plaque size. By producing recombinants,
497
applying a selection strategy (perhaps in an iterative manner), and then sequencing clones
498
bearing the desired traits, it should be possible to map genes that collectively regulate the
499
phenotype of interest. This is not a novel approach of course; related methods have been
500
used for decades to map complex genetic traits in many different organisms. However,
501
the widespread availability of next generation sequencing technologies creates a tool that
Qin et al.
Vaccinia virus recombination
Page 20 of 31
502
could easily be used by many more laboratories studying gene families and gene
503
interactions in large DNA viruses.
504
Acknowledgements. We thank Dr. Wendy Magee and Mr. Rob Maranchuk for their
505
technical supports with the Roche 454 Junior sequencer. This work was supported by
506
operating grants from the Canadian Institutes for Health Research and the Alberta Cancer
507
Foundation and by an infrastructure award from the Canada Foundation for Innovation.
Qin et al.
Vaccinia virus recombination
Page 21 of 31
508
FIGURE LEGENDS
509
510
Figure 1. Patterns of DNA exchange in recombinant vaccinia viruses. The genome
511
sequences of DTM (panel A) and DTH (panel B) recombinant clones were aligned
512
against the parent genomes DPP17 and TP05 using the program “LAGAN”, and edited
513
using the program “Base-by-Base”. TP05 was used as the reference strain and any
514
differences between a given virus and TP05 are colour coded to indicate insertion,
515
substitution, and deletion mutations derived from strain DPP17 (inset at bottom). Thus
516
the blank regions represented fragments derived from TP05.
517
518
Figure 2. Rare mutations associated with replication and recombination. Panel A
519
shows a deletion mutation in DTM29, immediately adjacent to a G-to-T SNP found at
520
alignment position 70493. Panel B shows a C-to-T substitution detected only in clone
521
DTM27 at position 900.
522
523
Figure 3. Numbers of exchanges in DTM and DTH clones. Each of the hybrid viruses
524
was first aligned against strains TP05 and DPP17. Then, the program “Base-by-Base”
525
was used to determine where each cross-over was located relative to the 1399 SNPs that
526
differentiate the two strains, along with the number of such exchanges. The viruses
527
passaged five times (DTM) exhibited more exchanges per genome than the viruses
528
passed just once (DTH). That is 30±11 versus 18±11 exchanges/genome, respectively.
529
530
Figure 4. Length of the DNA segments exchanged in DTH clones. The lengths of all
531
the conversion tracks were measured in all 14 genomes using midpoints defined by the
532
four SNPs flanking the two bounding sites of exchange. The numbers of events, of a
533
given exchange length, were then determined by assignment to 200 bp bins. A
Qin et al.
Vaccinia virus recombination
Page 22 of 31
534
semi-logarithm of the bin size (i.e. exchange length) is presented because the values
535
differ so greatly in scale across the different genomes. VACV recombination appears to
536
be associated with a disproportionate number of very short exchanges. Because there is
537
approximately one SNP per 140 bp, greater resolution than ~200 bp is not achievable.
538
539
Figure 5. Biased selection for sequences associated with the TianTan parent. The
540
percent of DNA derived from each of the parental viruses was determined from the
541
fraction of SNPs derived from each parent. Panel A shows how the composition varied in
542
viruses passaged just once (DTH hybrids) or five times (DTM hybrids) prior to cloning.
543
Passage appeared to select for SNPs linked to the TP05 TianTan parent, as the percentage
544
of Dryvax DNA decreased from 50±27% to 19±11% with continued passage. Panel B
545
illustrates how the plaque size is related to the genetic origins of the hybrid. The viruses
546
forming smaller plaques, more closely resemble the DPP17 parent. To measure the
547
plaque size, each of the cloned hybrids was plated on BSC-40 cells (in parallel), cultured
548
for two days, stained with crystal violet, scanned, and the plaque area determined using
549
ImageJ(24). Twenty randomly selected plaques were measured for each virus.
550
551
Figure 6. Illegitimate recombination detected during the cloning and sequencing of
552
hybrid DTM28. During the sequencing of DTM28, 11 reads were detected linking gene
553
DVX_201 to gene DVX_239. Panel A shows an alignment of these reads to sequences
554
within the two genes, which are normally spaced 21 kbp apart. We have also identified
555
sequence identities (circles), short patches of homology (boxed) and a simple repeat
556
(underlined) common to sequences flanking the fusion site. The sequence in these reads
557
transitions cleanly from one gene to the next, with no evidence of any unrelated
558
additional sequences having been added in the process. Panel B showed a way to form
559
this deletion. Illegitimate recombination between identical parents (DTM28) excised
Qin et al.
Vaccinia virus recombination
Page 23 of 31
560
21kbp and created the virus we subsequently called DTM28Δ. Panel C shows the results
561
of a PCR analysis using primers targeting sites flanking the fusion site. These are located
562
too far apart in the parent viruses (e.g. DTM27) to amplify 21 kpb of intervening
563
sequence. The DTM28Δ virus was probably formed during the expansion of the clone
564
prior to sequencing, as it is not detected in intermediary viruses during the course of
565
passages. Panel D shows a Southern blot of NdeI-digested virus DNA showing that the
566
sequenced virus stock contained two viruses. These are the DTM28 hybrid (indicated by
567
a 5.4 kbp fragment common to both parent strains), and the DTM28Δ
568
(indicated by a 6.7 kbp fragment containing the fusion junction). Panel E shows the
569
DTM28Δ is independently viable. Six randomly selected viruses were separately plaque
570
purified from the sequenced stock and the PCR was used to detect sequences found only
571
in the deleted region in DTM28 (primers 208F+209R) or only capable of being amplified
572
if the intervening sequences are deleted (primers 201F+239R).
573
574
Figure 7. Patterns of DNA exchange in recombinant vaccinia viruses produced using
575
Leporipoxvirus-mediated reactivation reactions. The genome sequences of the DTD
576
recombinant clones were aligned against the parent genomes DPP17 and TP03 using the
577
program “LAGAN”, and edited using the program “Base-by-Base”. Because this
578
experiment used TP03 DNA, and TP05 was always used as the reference strain in all of
579
our analyses (Figure 1), the telomeric deletion mutations that differentiate TP05 from
580
TP03 show up as additional red blocks in the TP03 alignment.
581
Qin et al.
Vaccinia virus recombination
Page 24 of 31
582
TABLES
583
584
Table 1. PCR primers used in this study
585
Amplicon size (bp)
DPP17
TP05
1120
-
-
653
1230
665
225
260
712
712
Primer ID
Primer (5’-to-3’)
DVX-209F
CGAAGAAGATGATGGGGAC
DVX-226R
ATAAGAGGAAAGAGGACAC
DVX-213F
CGTTGGATGGATTCGATA
DVX-226R
ATAAGAGGAAAGAGGACAC
DVX-004F
GCAGTAGGCTAGTATCTT
DVX-007R
TACCGGCATCATAAACAC
DVX-107F
AACTGGAGTAGAGATAGC
DVX-108R
CCGAGAATATAGCTGTCC
201F
AATATGATGGTGATGAGCGA
239R
TATTGCGAGATGTGAAGG
208F
TTTCTTCTCTTCTCCCTTTC
209R
ATTCTATCCCGTACCTCT
586
Qin et al.
Vaccinia virus recombination
Page 25 of 31
587
Table 2. Gene differences in the right TIR deletion: TP05 versus DPP17.
588
Gene/virus
Gene (or feature)
Nucleotide length (bp)
Copenhagen
Dryvax
DPP17
TP05
IL-1-β-receptor
Cop-B16R
DVX_209
1002
981
Unknown
Cop-B17L
DVX_210
-
1023
Ankyrin motifs
Cop-B18R
DVX_211
-
1725
IFN-α/β-receptor
Cop-B19R
DVX_212
-
1056
Ankyrin motifs
Cop-B20R
DVX_213
-
1794
589
Qin et al.
Vaccinia virus recombination
Page 26 of 31
590
Table 3. Gene complement in parent and hybrid viruses
Virus
DPP17
DTH13
DTH22
DTH36
DTH21
DTH31
DTH08
DTH34
DTM29
DTH06
DTH27
DTH10.2
DTH41
DTM03
DTM10
DTH30
DTH28
DTM32
DTM28
DTM27
DTH10
DTM30
DTM11
DTM22.2
DTM09
DTM33
DTM22.1
DTM06
DTM04
DTM19
DTH14
DTM08
TP05
Qin et al.
Plaque
area
100%
101
103
108
111
112
115
118
124
126
131
137
137
140
141
144
146
150
156
158
160
162
168
175
176
178
179
181
186
188
199
204
206
Telo
mere
D1
D
D
D
T2
T
D
D
T
D
T
D
T
D
D
D
T
D
D
T
T
T
T
D
D
T
T
T
T
T
T
T
T
right
TIR
-3
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
F4L
C23L
M1L
F3L
E5R
A51R
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+4
+
+
+
+
+
+
+
+
+
+
+
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Vaccinia virus recombination
Page 27 of 31
591
1. D=DPP17-like telomere repeats; 2. T=TP05-like telomere repeats; 3. Gene or genes
592
are truncated or deleted; 4. Gene appears intact (gray shading).
593
REFERENCES CITED
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
Hershey AD, Rotman R. 1948. Linkage Among Genes Controlling Inhibition of
Lysis in a Bacterial Virus. Proc Natl Acad Sci U S A 34:89-96.
Wildy P. 1955. Recombination with herpes simplex virus. J Gen Microbiol
13:346-360.
Fenner F, Comben BM. 1958. [Genetic studies with mammalian poxviruses. I.
Demonstration of recombination between two strains of vaccina virus]. Virology
5:530-548.
Woodroofe GM, Fenner F. 1960. Genetic studies with mammalian poxviruses.
IV. Hybridization between several different poxviruses. Virology 12:272-282.
Bedson HS, Dumbell KR. 1964. Hybrids Derived from the Viruses of Variola
Major and Cowpox. The Journal of hygiene 62:147-158.
Bedson HS, Dumbell KR. 1964. Hybrids Derived from the Viruses of Alastrim
and Rabbit Pox. The Journal of hygiene 62:141-146.
Strayer DS, Skaletsky E, Cabirac GF, Sharp PA, Corbeil LB, Sell S, Leibowitz
JL. 1983. Malignant rabbit fibroma virus causes secondary immunosuppression in
rabbits. J Immunol 130:399-404.
Esposito JJ, Sammons SA, Frace AM, Osborne JD, Olsen-Rasmussen M,
Zhang M, Govil D, Damon IK, Kline R, Laker M, Li Y, Smith GL, Meyer H,
Leduc JW, Wohlhueter RM. 2006. Genome sequence diversity and clues to the
evolution of variola (smallpox) virus. Science 313:807-812.
Qin L, Upton C, Hazes B, Evans DH. 2011. Genomic analysis of the vaccinia
virus strain variants found in Dryvax vaccine. J Virol 85:13049-13060.
Ensinger MJ, Rovinsky M. 1983. Marker rescue of temperature-sensitive
mutations of vaccinia virus WR: correlation of genetic and physical maps. J Virol
48:419-428.
Ensinger MJ. 1982. Isolation and genetic characterization of
temperature-sensitive mutants of vaccinia virus WR. J Virol 43:778-790.
Condit RC, Motyczka A, Spizz G. 1983. Isolation, characterization, and physical
mapping of temperature-sensitive mutants of vaccinia virus. Virology
128:429-443.
Lin YC, Evans DH. 2010. Vaccinia virus particles mix inefficiently, and in a way
that would restrict viral recombination, in coinfected cells. J Virol 84:2432-2443.
Qin et al.
Vaccinia virus recombination
Page 28 of 31
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
14.
15.
16.
17.
18.
19.
20.
21.
22.
23.
24.
25.
26.
27.
28.
Panicali D, Paoletti E. 1982. Construction of poxviruses as cloning vectors:
insertion of the thymidine kinase gene from herpes simplex virus into the DNA of
infectious vaccinia virus. Proc Natl Acad Sci U S A 79:4927-4931.
Mackett M, Smith GL, Moss B. 1982. Vaccinia virus: a selectable eukaryotic
cloning and expression vector. Proc Natl Acad Sci U S A 79:7415-7419.
Ball LA. 1987. High-frequency homologous recombination in vaccinia virus
DNA. J Virol 61:1788-1795.
Ball LA. 1995. Fidelity of homologous recombination in vaccinia virus DNA.
Virology 209:688-691.
Evans DH, Stuart D, McFadden G. 1988. High levels of genetic recombination
among cotransfected plasmid DNAs in poxvirus-infected mammalian cells. J
Virol 62:367-375.
Condit RC. 2007. Vaccinia, Inc.--probing the functional substructure of poxviral
replication factories. Cell Host Microbe 2:205-207.
Gammon DB, Evans DH. 2009. The 3'-to-5' exonuclease activity of vaccinia
virus DNA polymerase is essential and plays a role in promoting virus genetic
recombination. J Virol 83:4236-4250.
Willer DO, Yao XD, Mann MJ, Evans DH. 2000. In vitro concatemer formation
catalyzed by vaccinia virus DNA polymerase. Virology 278:562-569.
Yao XD, Evans DH. 2003. High-frequency genetic recombination and
reactivation of orthopoxviruses from DNA fragments transfected into
leporipoxvirus-infected cells. J Virol 77:7281-7290.
Qin L, Liang M, Evans DH. 2013. Genomic analysis of vaccinia virus strain
TianTan provides new insights into the evolution and evolutionary relationships
between Orthopoxviruses. Virology 442:59-66.
Abramoff MD, Magalhaes, P.J., Ram, S.J. 2004. Image Processing with
ImageJ. Biophotonics International 11:36-42.
Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, Green ED, Sidow A,
Batzoglou S. 2003. LAGAN and Multi-LAGAN: efficient tools for large-scale
multiple alignment of genomic DNA. Genome Res 13:721-731.
Brodie R, Smith AJ, Roper RL, Tcherepanov V, Upton C. 2004.
Base-By-Base: single nucleotide-level analysis of whole viral genome alignments.
BMC Bioinformatics 5:96.
Coulson D, Upton C. 2011. Characterization of indels in poxvirus genomes.
Virus Genes 42:171-177.
Goodman MF, Fygenson KD. 1998. DNA polymerase fidelity: from genetics
toward a biochemical understanding. Genetics 148:1475-1482.
Qin et al.
Vaccinia virus recombination
Page 29 of 31
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
29.
30.
31.
32.
33.
34.
35.
36.
37.
38.
39.
40.
Taddie JA, Traktman P. 1991. Genetic characterization of the vaccinia virus
DNA polymerase: identification of point mutations conferring altered drug
sensitivities and reduced fidelity. J Virol 65:869-879.
Taddie JA, Traktman P. 1993. Genetic characterization of the vaccinia virus
DNA polymerase: cytosine arabinoside resistance requires a variable lesion
conferring phosphonoacetate resistance in conjunction with an invariant mutation
localized to the 3'-5' exonuclease domain. J Virol 67:4323-4336.
Andrei G, Gammon DB, Fiten P, De Clercq E, Opdenakker G, Snoeck R,
Evans DH. 2006. Cidofovir resistance in vaccinia virus is linked to diminished
virulence in mice. J Virol 80:9391-9401.
Slabaugh MB, Roseman NA, Mathews CK. 1989. Amplification of the
ribonucleotide reductase small subunit gene: analysis of novel joints and the
mechanism of gene duplication in vaccinia virus. Nucleic Acids Res
17:7073-7088.
Elde NC, Child SJ, Eickbush MT, Kitzman JO, Rogers KS, Shendure J,
Geballe AP, Malik HS. 2012. Poxviruses deploy genomic accordions to adapt
rapidly against host antiviral defenses. Cell 150:831-841.
Fathi Z, Dyster LM, Seto J, Condit RC, Niles EG. 1991. Intragenic and
intergenic recombination between temperature-sensitive mutants of vaccinia
virus. J Gen Virol 72 ( Pt 11):2733-2737.
Parks RJ, Evans DH. 1991. Effect of marker distance and orientation on
recombinant formation in poxvirus-infected cells. J Virol 65:1263-1272.
DeLange AM, McFadden G. 1986. Sequence-nonspecific replication of
transfected plasmid DNA in poxvirus- infected cells. Proc Natl Acad Sci U S A
83:614-618.
Fisher C, Parks RJ, Lauzon ML, Evans DH. 1991. Heteroduplex DNA
formation is associated with replication and recombination in poxvirus-infected
cells. Genetics 129:7-18.
Maiti A, Drohat AC. 2011. Dependence of substrate binding and catalysis on pH,
ionic strength, and temperature for thymine DNA glycosylase: Insights into
recognition and processing of G.T mispairs. DNA Repair (Amst) 10:545-553.
Tcherepanov V, Ehlers A, Upton C. 2006. Genome Annotation Transfer Utility
(GATU): rapid annotation of viral genomes using a closely related reference
genome. BMC Genomics 7:150.
Gammon DB, Gowrishankar B, Duraffour S, Andrei G, Upton C, Evans DH.
2010. Vaccinia virus-encoded ribonucleotide reductase subunits are differentially
required for replication and pathogenesis. PLoS Pathog 6:e1000984.
Qin et al.
Vaccinia virus recombination
Page 30 of 31
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
41.
42.
43.
44.
45.
46.
Froggatt GC, Smith GL, Beard PM. 2007. Vaccinia virus gene F3L encodes an
intracellular protein that affects the innate immune response. J Gen Virol
88:1917-1921.
Murcia-Nicolas A, Bolbach G, Blais JC, Beaud G. 1999. Identification by mass
spectroscopy of three major early proteins associated with virosomes in vaccinia
virus-infected cells. Virus Res 59:1-12.
Antoine G, Scheiflinger F, Dorner F, Falkner FG. 1998. The complete genomic
sequence of the modified vaccinia Ankara strain: comparison with other
orthopoxviruses. Virology 244:365-396.
Willer DO, McFadden G, Evans DH. 1999. The complete genome sequence of
shope (rabbit) fibroma virus. Virology 264:319-343.
Scheiflinger F, Dorner F, Falkner FG. 1992. Construction of chimeric vaccinia
viruses by molecular cloning and packaging. Proc Natl Acad Sci U S A
89:9977-9981.
Willer DO, Mann MJ, Zhang W, Evans DH. 1999. Vaccinia virus DNA
polymerase promotes DNA pairing and strand-transfer reactions. Virology
257:511-523.
Qin et al.
Vaccinia virus recombination
Page 31 of 31

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