Recombination as a possible major cause of genetic heterogeneity in Anticarsia gemmatalis nuclear polyhedrosis virus wild populations

Insecticidal Traits of Variants in a Genotypically Diverse Natural Isolate of Anticarsia Gemmatalis Multiple Nucleopolyhedrovirus (AgMNPV)

Outbreaks of Anticarsia gemmatalis (Hübner, 1818) (Lepidoptera: Erebidae), a major pest of soybean, can be controlled below economic thresholds with methods that do not involve the application of synthetic insecticides. Formulations based on natural isolates of the Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) (Baculoviridae: Alphabaculovirus) played a significant role in integrated pest management programs in the early 2000s, but a new generation of chemical insecticides and transgenic soybean have displaced AgMNPV-based products over the past decade. However, the marked genotypic variability present among and within alphabaculovirus isolates suggests that highly insecticidal genotypic variants can be isolated and used to reduce virus production costs or overcome isolate-dependent host resistance. This study aimed to select novel variants of AgMNPV with suitable insecticidal traits that could complement the existing AgMNPV active ingredients. Three distinct AgMNPV isolates were compared using their restriction endonuclease profile and in terms of their occlusion body (OB) pathogenicity. One isolate was selected (AgABB51) from which eighteen genotypic variants were plaque purified and characterized in terms of their insecticidal properties. The five most pathogenic variants varied in OB pathogenicity, although none of them was faster-killing or had higher OB production characteristics than the wild-type isolate. We conclude that the AgABB51 wild-type isolates appear to be genotypically structured for fast speed of kill and high OB production, both of which would favor horizontal transmission. Interactions among the component variants are likely to influence this insecticidal phenotype.

Mosaic genome evolution and phylogenetics of Chrysodeixis includens nucleopolyhedrovirus (ChinNPV) and virulence of seven new isolates from the Brazilian states of Minas Gerais and Mato Grosso

In a comparative analysis of genome sequences from isolates of the baculovirus Chrysodeixis includens nucleopolyhedrovirus (ChinNPV) from Brazil and Guatemala, we identified a subset of isolates possessing chimeric genomes. We identified six distinct phylogenetically incongruous regions (PIRs) dispersed in the genomes, of between 279 and 3345 bp in length. The individual PIRs possessed high sequence similarity among the affected ChinNPV isolates but varied in coverage in some instances. The donor for four of the PIRs implicated in horizontal gene transfer (HGT) was identified as Trichoplusia ni single nucleopolyhedrovirus (TnSNPV), an alphabaculovirus closely related to ChinNPV, or another unknown but closely related virus. BLAST searches of the other two PIRs returned only ChinNPV sequences, but HGT from an unknown donor baculovirus cannot be excluded. Although Chrysodeixis includens and Trichoplusia ni are frequently co-collected from soybean fields in Brazil, pathogenicity data suggest that natural coinfection of C. includens larvae with ChinNPV and TnSNPV is probably uncommon. Additionally, since the chimeric ChinNPV genomes with tracts of TnSNPV sequence were restricted to a single monophyletic lineage of closely related isolates, a model of progressive restoration of the native DNA sequence by recombination with ChinNPV possessing a fully or partially non-chimeric genome is reasonable. However, multiple independent HGT from TnSNPV to ChinNPV during the evolution of these isolates cannot be excluded. Mortality data suggest that the ChinNPV isolates with chimeric genomes are not significantly different in pathogenicity towards C. includens when compared to most other ChinNPV isolates. Exclusion of the PIRs prior to phylogenetic analysis had a large impact on the topology of part of the maximum-likelihood tree, revealing a homogenous clade of three isolates (IB, IC and ID) from Paraná state in Brazil collected in 2006, together with an isolate from Guatemala collected in 1972 (IA), comprising the lineage uniquely affected by HGT from TnSNPV. The other 10 Brazilian ChinNPV isolates from Paraná, Mato Grosso, and Minas Gerais states showed higher variability, where only three isolates from Paraná state formed a monophyletic group correlating with geographical origin.

Importance of the Host Phenotype on the Preservation of the Genetic Diversity in Codling Moth Granulovirus

To test the importance of the host genotype in maintaining virus genetic diversity, five experimental populations were constructed by mixing two Cydia pomonella granulovirus isolates, the Mexican isolate CpGV-M and the CpGV-R5, in ratios of 99% M + 1% R, 95% M + 5% R, 90% M + 10% R, 50% M + 50% R, and 10% M + 90% R. CpGV-M and CpGV-R5 differ in their ability to replicate in codling moth larvae carrying the type I resistance. This ability is associated with a genetic marker located in the virus pe38 gene. Six successive cycles of replication were carried out with each virus population on a fully-permissive codling moth colony (CpNPP), as well as on a host colony (R_GV) that carries the type I resistance, and thus blocks CpGV-M replication. The infectivity of offspring viruses was tested on both hosts. Replication on the CpNPP leads to virus lineages preserving the pe38 markers characteristic of both isolates, while replication on the R_GV colony drastically reduces the frequency of the CpGV-M pe38 marker. Virus progeny obtained after replication on CpNPP show consistently higher pathogenicity than that of progeny viruses obtained by replication on R_GV, independently of the host used for testing.

The Pangenome of the Anticarsia gemmatalis Multiple Nucleopolyhedrovirus (AgMNPV)

The alphabaculovirus Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) is the world's most successful viral bioinsecticide. Through the 1980s and 1990s, this virus was extensively used for biological control of populations of Anticarsia gemmatalis (Velvetbean caterpillar) in soybean crops. During this period, genetic studies identified several variable loci in the AgMNPV; however, most of them were not characterized at the sequence level. In this study we report a full genome comparison among 17 wild-type isolates of AgMNPV. We found the pangenome of this virus to contain at least 167 hypothetical genes, 151 of which are shared by all genomes. The gene bro-a that might be involved in host specificity and carrying transporter is absent in some genomes, and new hypothetical genes were observed. Among these genes there is a unique rnf12-like gene, probably implicated in ubiquitination. Events of gene fission and fusion are common, as four genes have been observed as single or split open reading frames. Gains and losses of genomic fragments (from 20 to 900 bp) are observed within tandem repeats, such as in eight direct repeats and four homologous regions. Most AgMNPV genes present low nucleotide diversity, and variable genes are mainly located in a locus known to evolve through homologous recombination. The evolution of AgMNPV is mainly driven by small indels, substitutions, gain and loss of nucleotide stretches or entire coding sequences. These variations may cause relevant phenotypic alterations, which probably affect the infectivity of AgMNPV. This work provides novel information on genomic evolution of the AgMNPV in particular and of baculoviruses in general.

The effect of inoculum dose on the genetic diversity detected within Helicoverpa armigera nucleopolyhedrovirus populations

Environmental and infection variables may affect the genetic diversity of baculovirus populations. In this study, Helicoverpa armigera nucleopolyhedrovirus (HearNPV) was used as a model system for studying the effects of a key infection variable, inoculum dose, on the genetic diversity within nucleopolyhedrovirus populations. Diversity and equitability indices were calculated from DNA polymerase-specific denaturing gradient gel electrophoresis profiles obtained from individual H. armigera neonate larvae inoculated with either an LD5 or LD95 of HearNPV. Although the genetic diversity detected in larvae treated with an LD95 was not statistically different from the diversity detected in the HearNPV inoculum samples, there was a statistically significant difference in the genetic diversity detected in the LD5-inoculated larvae compared with the genetic diversity detected in the HearNPV samples used for the inoculations. The study suggests that inoculum dose needs to be considered carefully in experiments that evaluate HearNPV genetic diversity or in studies where differences in genetic diversity may have phenotypic consequences.

Genotypic variation among Douglas-fir tussock moth nucleopolyhedrovirus (OpNPV) isolates in the western United States

Periodic outbreaks of the Douglas-fir tussock moth (Orgyia pseudotsugata) in forests of western North America generally end with a sudden collapse due primarily to an epizootic caused by a nucleopolyhedrovirus (NPV) that occurs naturally within O. pseudotsugata populations. We genotypically characterized NPV populations from Washington State, Oregon, Idaho, New Mexico and California for the first time. Of 159 infected tussock moth samples, restriction fragment length polymorphism (RFLP) analysis showed that 125 (78.6%) contained single nucleopolyhedrovirus (OpSNPV), 28 (17.6%) contained multiple nucleopolyhedrovirus (OpMNPV), and six (3.8%) contained both OpSNPV and OpMNPV. In comparison, our previous studies in the southern interior of British Columbia showed that all 298 samples examined were infected with OpMNPV, and none were infected with OpSNPV. More than half of the Washington OpSNPV samples shared the same genotype, but most OpSNPV genotypes were rare or unique: across the five states, 31 of the 43 different OpSNPV genotypes were each only found in a single sample. In contrast, only four different OpMNPV genotypes were found, and 29 of the 34 OpMNPV samples shared the same genotype, designated genotype AA. This strain of OpMNPV has been developed, registered and used in both Canada and the United States to control outbreaks of the Douglas-fir tussock moth. It is also the most common genotype in southern British Columbia. The estimated degree of genetic divergence ranged from 0% to 4.19% for the various OpSNPV genotypes and from 0% to 3.16% for the OpMNPV genotypes (based on number of shared bands). This is the first description of the genotypic diversity in a population of OpSNPV, and the first genotypic characterization of NPVs infecting O. pseudotsugata in the USA.

High levels of genetic diversity in Spodoptera exempta NPV from Tanzania

The African armyworm, Spodoptera exempta, is a major pest in sub-Saharan Africa. A nucleopolyhedrovirus (NPV) is often recorded in later population outbreaks and can cause very high levels of mortality. Research has been addressing whether this NPV can be developed into a strategic biological control agent. As part of this study, the variation in natural populations of NPV is being studied. An isolate of S. exempta NPV was cloned in vivo and found to contain at least 17 genetically-distinct genotypes. These genotypes varied in size from approximately 115 to 153 kb.

Stability of a Spodoptera frugiperda nucleopolyhedrovirus deletion recombinant during serial passage in insects

The stabilities of the Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV) complete genome bacmid (Sfbac) and a deletion recombinant (Sf29null) in which the Sf29 gene was replaced by a kanamycin resistance cassette were determined during sequential rounds of per os infection in insect larvae. The Sf29 gene is a viral factor that determines the number of virions in occlusion bodies (OBs). The Sf29null bacmid virus was able to recover the Sf29 gene during passage. After the third passage (P3) of Sf29null bacmid OBs, the population was observed to reach an equilibrium involving a mixture of those with a kanamycin resistance cassette and those with the Sf29 gene. The biological activity of Sf29null bacmid OBs at P3 was similar to that of Sfbac OBs. The recovered gene in the Sf29null virus was 98 to 100% homologous to the Sf29 genes of different SfMNPV genotypes. Reverse transcription-PCR analysis of uninoculated S. frugiperda larvae confirmed the expression of the SfMNPV ie-0 and Sf29 genes, indicating that the insect colony harbors a covert SfMNPV infection. Additionally, the nonessential bacterial artificial chromosome vector was spontaneously deleted from both viral genomes upon passage in insects.

Characterization of short-lived intermediates produced during replication of baculovirus DNA

In this report the short-lived DNA replication intermediates produced in both uninfected and Autographa californica multiple nucleopolyhedrovirus (AcMNPV) infected Spodoptera frugiperda cells were characterized. The methods used included pulse-labeling of DNA in permiabilized cells, treatment of nascent DNA with Mung bean nuclease, and electrophoresis in neutral and alkaline agarose gels. In contrast to uninfected cells that produced a population of small DNA fragments of about 200bp, a population of heterogeneous fragments of up to 5kb with an average size of 1-2kb derived randomly from the virus genome was identified as the short-lived intermediates produced during AcMNPV replication. The intermediates likely include Okazaki fragments derived from the lagging strands in viral replication forks as well as fragments produced during the recombination-dependent replication.

Structural divergence among genomes of closely related baculoviruses and its implications for baculovirus evolution

Baculoviruses are members of a large, well-characterized family of dsDNA viruses that have been identified from insects of the orders Lepidoptera, Hymenoptera, and Diptera. Baculovirus genomes from different virus species generally exhibit a considerable degree of structural diversity. However, some sequenced baculovirus genomes from closely related viruses are structurally very similar and share overall nucleotide sequence identities in excess of 95%. This review focuses on the comparative analysis of partial and complete nucleotide sequences from two groups of closely related baculoviruses with broad host ranges: (a) group I multiple nucleopolyhedroviruses (MNPVs) from a cluster including Autographa californica (Ac)MNPV, Rachiplusia ou (Ro)MNPV, and Plutella xylostella (Plxy)MNPV; and (b) granuloviruses (GVs) from a cluster including Xestia c-nigrum (Xecn)GV and Helicoverpa armigera (Hear)GV. Even though the individual viruses in these clusters share high nucleotide sequence identities, a significant degree of genomic rearrangement (in the form of insertions, deletions, and homologous recombination resulting in allelic replacement) is evident from alignments of their genomes. These observations suggest an important role for recombination in the early evolution and biological characteristics of baculoviruses of these two groups.

Isolation and characterization of plaque-purified strains of Malacosoma disstria Nucleopolyhedrovirus

Seven plaque-purified genotypic variants or strains, derived from a previously described field isolate of the Malacosoma disstria Nucleopolyhedrovirus (MadiNPV) from Alberta populations of forest tent caterpillar, were characterized based on distinctive restriction endonuclease fragment patterns. Two strains, MadiNPV-pp3 and MadiNPV-pp11, were selected for further characterization, as they represented strains producing high and low budded virus (BV) titres, respectively, in the M. disstria cell line UA-Md203. Analysis of restriction endonuclease fragment profiles indicated the genomes differed significantly in size, 133.8 +/- 2.4 kb for MadiNPV-pp3 and 118.1 +/- 3.5 kb for MadiNPV-pp11. These strains were characterized based on their BV production in three different cell lines derived from M. disstria haemocytes. Compared with MadiNPV-pp11, MadiNPV-pp3 produced two- to three-fold more BVs in UA-Md203 and 210 other cell lines; however, BV production was only marginally higher for MadiNPV-pp3 in the UA-Md221 cell line. Similarly, the yield of polyhedral inclusion bodies was significantly higher for MadiNPV-pp3 in UA-Md203 and 210 cell lines than for MadiNPV-pp11 but not in the UA-Md221 cell line. This data, although derived from a limited number of cell lines, suggested MadiNPV-pp3 may have a broader tissue tropism than MadiNPV-pp11.

Application of the PCR-RFLP method for the rapid differentiation of Spodoptera exigua nucleopolyhedrovirus genotypes

Quality control during mass production of Spodoptera exigua multiple nucleopolyhedrovirus (SeMNPV), and studies on environmental fate following the use of this virus as a biological pesticide, would be facilitated by a rapid method for the detection and identification of isolates. A molecular biology tool was developed that combined the polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) to differentiate SeMNPV isolates. Oligonucleotide primers were designed to amplify five variable SeMNPV genomic regions (V01, V02, V03, V04, V05). Four wild-type SeMNPV strains isolated from the United States (US2) and Spain (SP1, SP2, and SP3), and a laboratory cloned genotype (US1A), were analyzed with 36 different primer-endonuclease combinations. BglII digestion of the variable region 1 (V01) amplicon was the only combination that differentiated each of the five virus isolates tested, although genetic heterogeneity limited the discriminatory power of the technique. Six novel SeMNPV isolates originating from greenhouse soils in southern Spain were successfully identified using this method. As judged by sequence analysis, the V01 region, which comprises the homologous region 1 (hr1), is the most variable genomic region among the genotypes present in the Spanish isolates. This method constitutes a useful tool for processing large number of environmental samples and could be used to address environmental biosafety concerns.

Genotypic and phenotypic diversity of a baculovirus population within an individual insect host

It is becoming increasingly apparent that many pathogen populations, including those of insects, show high levels of genotypic variation. Baculoviruses are known to be highly variable, with isolates collected from the same species in different geographical locations frequently showing genetic variation and differences in their biology. More recent studies at smaller scales have also shown that virus DNA profiles from individual larvae can show polymorphisms within and between populations of the same species. Here, we investigate the genotypic and phenotypic variation of an insect baculovirus infection within a single insect host. Twenty four genotypically distinct nucleopolyhedrovirus (NPV) variants were isolated from an individual pine beauty moth, Panolis flammea, caterpillar by in vivo cloning techniques. No variant appeared to be dominant in the population. The PaflNPV variants have been mapped using three restriction endonucleases and shown to contain three hypervariable regions containing insertions of 70-750 bp. Comparison of seven of these variants in an alternative host, Mamestra brassicae, demonstrated that the variants differed significantly in both pathogenicity and speed of kill. The generation and maintenance of pathogen heterogeneity are discussed.

Physical and partial genetic map of Spodoptera frugiperda nucleopolyhedrovirus (SfMNPV) genome

A Nicaraguan isolate of Spodoptera frugiperda multicapsid nucleopolyhedrovirus (SfMNPV) is undergoing field trials for control of this pest in the Americas. This isolate is composed of multiple genotypes, some of which are deletion mutants. Identification of the genetic changes in deleted genotypes cannot be accomplished without the construction of a detailed physical map. In the present study, combinations of restriction endonuclease analysis and Southern blot analysis was performed. This map was refined by sequencing the termini of cloned restriction fragments. The SfMNPV genome was estimated to be 129.3 kb, 8 kb larger than the previously characterized Sf-2 variant from the United States, due to a deletion between 14.8 and 21.0 m.u. in the physical map described in this study. A total of 27.92 kb were sequenced, which represented 21.5% of the whole genome and included 38 ORFs. Comparison with other sequenced baculoviruses revealed that SfMNPV displayed the highest sequence identity (66%) and gene arrangement (78%) with Spodoptera exigua MNPV, sharing 36 putative ORFs. In addition, the genome organization was similar to that of SeMNPV, with minor differences. Phylogenetic analysis confirmed the close relatedness between SeMNPV and SfMNPV, suggesting they evolved from a common ancestor.

Complete comparative genomic analysis of two field isolates of Mamestra configurata nucleopolyhedrovirus-A

A second genotype of Mamestra configurata nucleopolyhedrovirus-A (MacoNPV-A), variant 90/4 (v90/4), was identified due to its altered restriction endonuclease profile and reduced virulence for the host insect, M. configurata, relative to the archetypal genotype, MacoNPV-A variant 90/2 (v90/2). To investigate the genetic differences between these two variants, the genome of v90/4 was sequenced completely. The MacoNPV-A v90/4 genome is 153 656 bp in size, 1404 bp smaller than the v90/2 genome. Sequence alignment showed that there was 99·5 % nucleotide sequence identity between the genomes of v90/4 and v90/2. However, the v90/4 genome has 521 point mutations and numerous deletions and insertions when compared to the genome of v90/2. Gene content and organization in the genome of v90/4 is identical to that in v90/2, except for an additional bro gene that is found in the v90/2 genome. The region between hr1 and orf31 shows the greatest divergence between the two genomes. This region contains three bro genes, which are among the most variable baculovirus genes. These results, together with other published data, suggest that bro genes may influence baculovirus genome diversity and may be involved in recombination between baculovirus genomes. Many ambiguous residues found in the v90/4 sequence also reveal the presence of 214 sequence polymorphisms. Sequence analysis of cloned HindIII fragments of the original MacoNPV field isolate that the 90/4 variant was derived from indicates that v90/4 is an authentic variant and may represent approximately 25 % of the genotypes in the field isolate. These results provide evidence of extensive sequence variation among the individual genomes comprising a natural baculovirus outbreak in a continuous host population.

The deletion of the pif gene improves the biosafety of the baculovirus-based technologies

Our goal was to improve the biosafety of baculovirus-based technologies by deleting the pif (per os infectivity factor) gene from baculovirus expression vectors. Such a deletion would block transmission in nature without disturbing protein production. A pif deletion mutant of Autographa californica multiplecapsid nucleopolyhedrovirus (AcMNPV) was constructed and its infectivity to two host species was tested by oral or intrahemocoelic inoculation. Virus replication after oral inoculation was monitored using PCR. Oral inoculations with a mixture of the wild type and the pif deletion viruses were carried out. The pif deletion blocked oral infection but it did not hamper infectivity in cell culture. The blockage took place early after inoculation and could not be overcome by mixed inoculations with the wild type. The cat gene was inserted under the control of the polyhedrin promoter in the deletion mutant and the wild type CAT yield was measured in Spodoptera frugiperda insect cells (Sf9) infected with either recombinant. The pif deletion did not hamper CAT production. This deletion significantly improved CAT yields early in the infection. Hence, expression vectors lacking pif may produce higher quality protein. The pif deletion is a simple measure that dramatically reduces the chances of virus spread or gene transfer in nature.

Genetic structure of a Spodoptera frugiperda nucleopolyhedrovirus population: high prevalence of deletion genotypes

A Nicaraguan field isolate (SfNIC) of Spodoptera frugiperda nucleopolyhedrovirus was purified by plaque assay on Sf9 cells. Nine distinct genotypes, A to I, were identified by their restriction endonuclease profiles. Variant SfNIC-B was selected as the standard because its restriction profile corresponded to that of the wild-type isolate. Physical maps were generated for each of the variants. The differences between variants and the SfNIC-B standard were confined to the region between map units 9 and 32.5. This region included PstI-G, PstI-F, PstI-L, PstI-K and EcoRI-L fragments. Eight genotypes presented a deletion in their genome compared with SfNIC-B. Occlusion body-derived virions of SfNIC-C, -D and -G accounted for 41% of plaque-purified clones. These variants were not infectious per os but retained infectivity by injection into S. frugiperda larvae. Median 50% lethal concentration values for the other cloned genotypes were significantly higher than that of the wild type. The variants also differed in their speed of kill. Noninfectious variants SfNIC-C and -D lacked the pif and pif-2 genes. Infectivity was restored to these variants by plasmid rescue with a plasmid comprising both pif and pif-2. Transcription of an SfNIC-G gene was detected by reverse transcription-PCR in insects, but no fatal disease developed. Transcription was not detected in SfNIC-C or -D-inoculated larvae. We conclude that the SfNIC population presents high levels of genetic diversity, localized to a 17-kb region containing pif and pif-2, and that interactions among complete and deleted genotypic variants will likely influence the capacity of this virus to control insect pests.

Virus entry or the primary infection cycle are not the principal determinants of host specificity of Spodoptera spp. nucleopolyhedroviruses

The multicapsid nucleopolyhedroviruses (NPVs) of Spodoptera exigua (SeMNPV), Spodoptera frugiperda (SfMNPV), and Spodoptera littoralis (SpliNPV) are genetically similar (78 % similarity) but differ in their degree of host specificity. Infection by each of the three NPVs in these three Spodoptera host species was determined by oral inoculation of larvae with occlusion bodies (OBs) or intrahaemocoelic injection with occlusion derived virions (ODVs). RT-PCR analysis of total RNA from inoculated insects, targeted at immediate early (ie-0), early (egt, DNA polymerase), late (chitinase) and very late genes (polyhedrin), indicated that each of the NPVs initiated an infection in all three host species tested. SpliMNPV produced a fatal NPV disease in both heterologous hosts, S. frugiperda and S. exigua, by oral inoculation or injection. SfMNPV was lethal to heterologous hosts, S. exigua and S. littoralis, but infected larvae did not melt and disintegrate, and progeny OBs were not observed. SeMNPV was able to replicate in heterologous hosts and all genes required for replication were present in the genome, as the virus primary infection cycle was observed. However, gene expression was significantly lower in heterologous hosts. SeMNPV pathogenesis in S. frugiperda and S. littoralis was blocked at the haemocoel transmission stage and very nearly cleared. SeMNPV mixtures with SpliMNPV or SfMNPV did not extend the host range of SeMNPV; in all cases, only the homologous virus was observed to proliferate. It is concluded that entry and the primary virus infection cycle are not the only, or the major determinants, for SeMNPV infection of heterologous Spodoptera species.

Genetically variable nucleopolyhedroviruses isolated from spatially separate populations of the winter moth Operophtera brumata (Lepidoptera: Geometridae) in Orkney

Here we report a lepidopteran system in which a pathogen is both abundant and genotypically variable. Geographically separate populations of winter moth (Operophtera brumata L.) were sampled in heather habitats on the Orkney Isles to investigate the prevalence of a pathogen, O. brumata Nucleopolyhedrovirus (OpbuNPV), within the natural system. Virus was recorded in 11 of the 13 winter moth populations sampled, with two populations suffering mortality due to virus at levels of 50%. The virus genome from 200 single insect isolations was investigated for variation using restriction endonuclease digests. Twenty-six variants of OpbuNPV were detected using SalI. The polyhedrin gene of the virus was partially sequenced, allowing the relationship between the 26 variants to be portrayed as a cladogram. The phylogenetic relationship between OpbuNPV and other known baculovirus polyhedrin gene sequences was also established. The discovery of virus at such high prevalence is discussed with reference to occurrence and genetic variation of pathogens in other lepidopteran host populations. This study shows encouraging results for further studies into the role of pathogens in the regulation of host insect populations.

Specificity of the Endonuclease Activity of the Baculovirus Alkaline Nuclease for Single-stranded DNA

The Autographa californica multiple nucleocapsid nucleopolyhedrovirus (AcMNPV) alkaline nuclease (AN) likely participates in the maturation of virus genomes and in DNA recombination. AcMNPV AN was expressed in a recombinant baculovirus as a His -tagged fusion and obtained in pure form (*AN) or as a (6)complex with the baculoviral single-stranded DNA-binding protein LEF-3 (*AN/L3). Both AN preparations possessed potent 5' --> 3'-exonuclease and weak endonuclease activities. Mutant *AN(S146A)/L3 with a change from serine to alanine at position 146 in a conservative motif was impaired in both activities. This proved that the endonuclease is an intrinsic activity of baculovirus AN. The AN endonuclease showed specificity for single-stranded DNA and converted supercoiled plasmid DNA (replicative form I, RFI) into the open circular form (RFII) by a single strand break. Plasmid DNA relaxed with topoisomerase I was resistant to *AN/L3 indicating that the partially single-stranded regions in negatively supercoiled molecules served as targets for the endonuclease. Unwinding the supercoiled DNA with ethidium bromide also made DNA resistant to AN/L3. In reactions with nicked circular DNA (RFII), AN and AN/L3 hydrolyzed exonucleolytically the broken strand or cut endonucleolytically the intact strand at the position opposite the nick (gap). When LEF-3 was added to the assay, the balance between the exonucleolytic and endonucleolytic modes of hydrolysis shifted in favor of the exonuclease. The data suggest that the AN endonuclease may digest the intermediates in replication and recombination at positions of structural irregularities in DNA duplexes, whereas LEF-3 may further regulate processing of the intermediates by AN via the endonuclease and exonuclease pathways.

High-frequency homologous recombination between baculoviruses involves DNA replication

We determined the frequency of DNA recombination between Bombyx mori nucleopolyhedroviruses (BmNPVs) and between BmNPV and the closely related Autographa californica NPV (AcMNPV) in BmN cells, Sf-21 cells, and larvae of Heliothis virescens. The BmN cells were coinfected with two BmNPVs, one with a mutation at the polyhedrin gene (polh) locus and a second carrying a lacZ gene marker cassette. Eleven different BmNPV mutants carrying the lacZ gene marker at various distances (1.4 to 61.7 kb) from polh were used for the coinfections. The Sf-21 cells and larvae of H. virescens were coinfected with wild-type AcMNPV and 1 of the 11 lacZ-marked BmNPV mutants. In BmN cells, high-frequency recombination was detected as early as 15 h postcoinfection but not at 12 h postcoinfection. At 18 h postcoinfection, the mean frequency of recombination ranged between 20.0 and 35.4% when the polh and lacZ marker genes were separated by at least 9.7 kb. When these marker genes were separated by only 1.4 kb, the mean frequency of recombination was 2.7%. In BmN cells, the mean recombination frequency between two BmNPVs increased only marginally when the multiplicity of infection of each virus was increased 10-fold. In Sf-21 cells and the larvae of H. virescens, the recombination frequency between BmNPV and AcMNPV was </=1.0%. AcMNPV DNA replication occurred normally after the coinfection of Sf-21 cells. BmNPV DNA replication, however, was not detected, indicating that normal DNA replication by both viruses is required for high-frequency recombination.

The gp64 locus of Anticarsia gemmatalis multicapsid nucleopolyhedrovirus contains a 3′ repair exonuclease homologue and lacks v-cath and ChiA genes

Anticarsia gemmatalis multicapsid nucleopolyhedrovirus (AgMNPV) is one of the most successful biological insecticides. In this study, we cloned and sequenced a 12.5 kbp BamHI-D restriction endonuclease fragment of the AgMNPV isolate 2D genome that includes the gp64 gene. We compared this highly conserved region with that of other baculoviruses. AgMNPV contained two genes, p22.2 and v-trex, in common with Choristoneura fumiferana MNPV (CfMNPV) that were not present in other baculoviruses. The v-trex gene has homology to a eukaryotic 3' repair exonuclease and appears to have been acquired from an invertebrate host. The v-trex gene product has the potential to be involved in virus recombination or UV-light tolerance. Multigene phylogenetic analysis suggested that AgMNPV is most closely related to Orgyia pseudotsugata MNPV (OpMNPV). AgMNPV differed from other group I NPVs in that ChiA and v-cath gene homologues were missing from the region downstream of the gp64 gene. Proteinase assays and genetic probes suggest the v-cath gene is absent from AgMNPV.

Defective or effective? Mutualistic interactions between virus genotypes

Defective viruses lack genes essential for survival but they can co-infect with complete virus genotypes and use gene products from the complete genotype for their replication and transmission. As such, they are detrimental to the fitness of complete genotypes. Here, we describe a mutualistic interaction between genotypes of an insect baculovirus (nucleopolyhedrovirus of Spodoptera frugiperda (Lepidoptera)) that increases the pathogenicity of the viral population. Mixtures of a complete genotype able to be transmitted orally and a deletion mutant unable to be transmitted orally resulted in a phenotype of increased pathogenicity. Because the infectiousness of mixed genotype infections was greater than that of single genotype infections, we predict that the transmissibility of mixed genotype occlusion bodies will be greater than that of any of their single genotype components. Such interactions will be subject to frequency-dependent selection and will influence the impact of these viruses on insect population dynamics and their efficacy as biological insecticides.

Hierarchical spatial structure of genetically variable nucleopolyhedroviruses infecting cyclic populations of western tent caterpillars

The cyclic population dynamics of western tent caterpillars, Malacosoma californicum pluviale, are associated with epizootics of a nucleopolyhedrovirus, McplNPV. Given the dynamic fluctuations in host abundance and levels of viral infection, host resistance and virus virulence might be expected to change during different phases of the cycle. As a first step in determining if McplNPV virulence and population structure change with host density, we used restriction fragment length polymorphism (RFLP) analysis to examine the genetic diversity of McplNPV infecting western tent caterpillar populations at different spatial scales. Thirteen dominant genetic variants were identified in 39 virus isolates (individual larvae) collected from field populations during one year of low host density, and another distinct variant was discovered among nine additional isolates in two subsequent years of declining host density. The distribution of these genetic variants was not random and indicated that the McplNPV population was structured at several spatial levels. A high proportion of the variation could be explained by family grouping, which suggested that isolates collected within a family were more likely to be the same than isolates compared among populations. Additionally, virus variants from within populations (sites) were more likely to be the same than isolates collected from tent caterpillar populations on different islands. This may indicate that there is limited mixing of virus among tent caterpillar families and populations when host population density is low. Thus there is potential for the virus to become locally adapted to western tent caterpillar populations in different sites. However, no dominant genotype was observed at any site. Whether and how selection acts on the genetically diverse nucleopolyhedrovirus populations as host density changes will be investigated over the next cycle of tent caterpillar populations.

Characterization of pif, a gene required for the per os infectivity of Spodoptera littoralis nucleopolyhedrovirus

During plaque purification of Spodoptera littoralis nucleopolyhedrovirus in S. littoralis Sl52 cell culture, a deletion mutant virus was isolated. Analysis of the biological properties of this mutant virus revealed an absence of per os infectivity of the occluded virus. Infectivity by injection of the non-occluded (budded) virus is not different between the wild-type and the deleted virus. Restriction analysis of the mutant virus genome revealed a 4.5 kb deletion within the NotI D fragment. The observed phenotype was mapped to the deleted region by rescue experiments. The deletion was characterized and the equivalent DNA fragment on the wild-type virus was sequenced. By co-transfecting the DNA of the deleted virus with plasmids derived from the wild-type virus, it was possible to determine that ORF 7 in this fragment is responsible for the observed phenotype. ORF 7, called pif (per os infectivity factor), is homologous to ORF 119 of Autographa californica nucleopolyhedrovirus. Similar ORFs are present in all sequenced baculoviruses. The product of this gene is an occlusion body-derived virion structural protein required only for the first steps of larva infection, as viruses being produced in cells expressing the gene but not containing it in their genomes are able to produce successful infections.

Genetic requirements for homologous recombination in Autographa californica nucleopolyhedrovirus

It is known that baculovirus infection promotes high-frequency recombination between its genomes and plasmid DNA during the construction of recombinant viruses for foreign gene expression. However, little is known about the viral genes necessary to promote homologous recombination (HR). We developed an assay to identify viral genes that are necessary to stimulate HR. In this assay, we used two plasmids containing extensive sequence homology that yielded a visible and quantifiable phenotype if HR occurred. The plasmids contained the green fluorescent protein gene (gfp) that was mutated at either the N or the C terminus and a viral origin of DNA replication. When the plasmids containing these mutant gfp genes were transfected into insect cells alone or together, few green fluorescent protein (GFP)-positive cells were observed, confirming that the host cell machinery alone was not able to promote high levels of HR. However, if viral DNA or viral genes involved in DNA replication were cotransfected into cells along with the mutant gfp-containing plasmids, a dramatic increase in GFP-positive cells was observed. The viral genes ie-1, ie-2, lef-7, and p35 were found to be important for efficient HR in the presence of all other DNA replication genes. However, ie-1 and ie-2 were sufficient to promote HR in the absence of other viral genes. Recombination substrates lacking a viral origin of replication had similar genetic requirements for recombination but were less dependent on ie-1. Interestingly, even though HR was stimulated by the presence of a viral origin of DNA replication, virally stimulated HR could proceed in the presence of the DNA synthesis inhibitor aphidicolin.

The genome sequence and evolution of baculoviruses

Comparative analysis of the complete genome sequences of 13 baculoviruses revealed a core set of 30 genes, 20 of which have known functions. Phylogenetic analyses of these 30 genes yielded a tree with 4 major groups: the genus Granulovirus (GVs), the group I and II lepidopteran nucleopolyhedroviruses (NPVs), and the dipteran NPV, CuniNPV. These major divisions within the family Baculoviridae were also supported by phylogenies based on gene content and gene order. Gene content mapping has revealed the patterns of gene acquisitions and losses that have taken place during baculovirus evolution, and it has highlighted the fluid nature of baculovirus genomes. The identification of shared protein phylogenetic profiles provided evidence for two putative DNA repair systems and for viral proteins specific for infection of lymantrid hosts. Examination of gene order conservation revealed a core gene cluster of four genes, helicase, lef-5, ac96, and 38K(ac98), whose relative positions are conserved in all baculovirus genomes.

Use of whole genome sequence data to infer baculovirus phylogeny

Several phylogenetic methods based on whole genome sequence data were evaluated using data from nine complete baculovirus genomes. The utility of three independent character sets was assessed. The first data set comprised the sequences of the 63 genes common to these viruses. The second set of characters was based on gene order, and phylogenies were inferred using both breakpoint distance analysis and a novel method developed here, termed neighbor pair analysis. The third set recorded gene content by scoring gene presence or absence in each genome. All three data sets yielded phylogenies supporting the separation of the Nucleopolyhedrovirus (NPV) and Granulovirus (GV) genera, the division of the NPVs into groups I and II, and species relationships within group I NPVs. Generation of phylogenies based on the combined sequences of all 63 shared genes proved to be the most effective approach to resolving the relationships among the group II NPVs and the GVs. The history of gene acquisitions and losses that have accompanied baculovirus diversification was visualized by mapping the gene content data onto the phylogenetic tree. This analysis highlighted the fluid nature of baculovirus genomes, with evidence of frequent genome rearrangements and multiple gene content changes during their evolution. Of more than 416 genes identified in the genomes analyzed, only 63 are present in all nine genomes, and 200 genes are found only in a single genome. Despite this fluidity, the whole genome-based methods we describe are sufficiently powerful to recover the underlying phylogeny of the viruses.

Four genotypic variants of a Spodoptera exigua Nucleopolyhedrovirus (Se-SP2) are distinguishable by a hypervariable genomic region

Four genotypes named SP2A, SP2B, SP2C and SP2D were obtained in vivo by infecting S. exigua larvae with limiting dilutions of the Spanish field isolate Spodoptera exigua Nucleopolyhedrovirus (Se-SP2) of SeMNPV. The cloning of variants SP2A, SP2B and SP2C took 1, 6, and 3 passages, respectively, before the DNA profiles showed all bands in equimolar concentrations, and they remained constant for at least six further passages indicating the stability of their genotypes. The SP2D variant isolation took over ten passages and it was genetically less stable. Physical maps of their genomes were constructed for the restriction enzymes BamHI, BglII, PstI, and XbaI. The region between 8-10 m.u. was highly variable and characteristic of each cloned genotype and, hence, can be used as RFLP markers for all four genotypic variants. This region, included in the PstI-MB fragment, was cloned and sequenced showing that all the Se-SP2 variants contained a homologous region (hr) with a variable number of 98 bp sequences tandemly repeated, which were used to distinguish genotypic variants from each other. The biological activity of the genotypic variants SP2A, SP2B, and SP2C when compared in terms of LD50 and LT50, were not significantly different. However, the SP2D genotypic variant was found to be significantly less infective (higher LD50). The emergence of new genotypes in the Se-SP2 field populations is discussed.

Assessment of the application of baculoviruses for control of Lepidoptera

Baculoviruses, among other insect viruses, are regarded as safe and selective bioinsecticides, restricted to invertebrates. They have been used worldwide against many insect pests, mainly Lepidoptera. Their application as microbial pesticides, however, has not met their potential to control pests in crops, forests, and pastures, with the exception of the nuclear polyhedrosis virus of the soybean caterpillar (Anticarsia gemmatalis), which is used on approximately 1 million ha annually in Brazil. Problems that have limited expansion of baculovirus use include narrow host range, slow killing speed, technical and economical difficulties for in vitro commercial production, timing of application based on frequent host population monitoring, variability of field efficacy due to climatic conditions, and farmers' attitudes toward pest control, which have been based on application of fast-killing chemical insecticides. Farmer education regarding use of biological insecticides and their characteristics is considered one of the major actions necessary for increased use of baculoviruses. Strategies to counteract some of the limitations of baculoviruses, especially their slow killing activity, have been investigated and are promising. These include the use of chemical or biological substances added to virus formulations and genetic engineering of the viruses themselves to express insect toxins or hormones. Such strategies can enhance viral activity and increase speed of kill as well as reduce larval feeding activity. The use of baculoviruses against Lepidoptera is reviewed, with the utilization of the nuclear polyhedrosis virus of A. gemmatalis in Brazil serving as a case-study.

Naturally occurring deletion mutants are parasitic genotypes in a wild-type nucleopolyhedrovirus population of spodoptera exigua

A wild-type nucleopolyhedrovirus (NPV) isolate from Spodoptera exigua from Florida (Se-US2) is a variant of the SeMNPV type strain since it has a unique DNA profile but is closely related to other known geographical isolates of SeMNPV. It consists of several genotypic variants, of which seven were identified in a Se-US2 virus stock by a modification of the in vivo cloning method developed by Smith and Crook (Virology 166:240-244, 1988). The US2A variant was the most prevalent genotype, and it was designated the prototype Se-US2 variant, while four of the variants (US2B, US2D, US2F, and US2H) were found at low frequency. US2C and US2E were also very abundant, and their diagnostic bands were easily observed in wild-type isolate restriction endonuclease patterns. The analysis of each variant, compared to the prototype US2A, showed that US2B and US2H presented minor differences, while US2D and US2F contained slightly larger insertions or deletions. Variants US2C and US2E contained major deletions of 21.1 and 14 kb, respectively, mapping at the same genomic region (between 14.5 and 30.2 map units [m.u.] and between 12.8 and 23 m.u., respectively). This is the first report of such deletion mutants in a natural baculovirus population. Variants US2A, US2B, US2D, US2F, and US2H were isolated as pure genotypes, but we failed to clone US2C and US2E in vivo. When these two variants appeared without apparent contamination with any other variant, they lost their pathogenicity for Spodoptera exigua larvae. A further biological characterization showed evidence that these two naturally occurring deletion mutants act as parasitic genotypes in the virus population. Bioassay data also demonstrated that pure US2A is significantly more pathogenic against second-instar S. exigua larvae than the wild-type isolate. The need for precise genotypic characterization of a baculovirus prior to its development as a bioinsecticide is discussed.

A variable region of Anticarsia gemmatalis nuclear polyhedrosis virus contains tandemly repeated DNA sequences

A variable region (PstI-T fragment) of two genotypic variants of the Anticarsia gemmatalis multiple nucleocapsid nuclear polyhedrosis virus (AgMNPV) was sequenced and compared. This region, which is known to have deletions and duplications in AgMNPV variants, was shown to be formed of units of a 127 bp tandemly repeated sequence containing two 30 bp imperfect palindromes. Southern blot experiments showed that the PstI-T fragment contained one of the four homologous regions mapped interspersed in the AgMNPV genome. The comparison of the nucleotide sequences of the two variants, AgMNPV-2D and AgMNPV-D7, showed that the difference between these two variants in one of these regions (hr4) was caused by the addition or elimination of 381 bp corresponding exactly to three of the 127 bp repeated sequences. An analysis of the sequence showed homology to the homologous regions (hr) of other baculoviruses. The sequence upstream of the repetitive region contained a sequence homologous to the N-terminal portion of the Autographa californica MNPV and Choristoneura fumiferana MNPV p74 gene.