Recombination Detection Program (RDP) is a program that applies a pairwise scanning approach to the detection of recombination amongst a group of aligned DNA sequences. The software runs under Windows95 and combines highly automated screening of large numbers of sequences with a highly interactive interface for examining the results of the analyses.

Virus-like particle-based vaccines for high-risk human papillomaviruses (HPVs) appear to have great promise; however, cell culture-derived vaccines will probably be very expensive. The optimization of expression of different codon-optimized versions of the HPV-16 L1 capsid protein gene in plants has been explored by means of transient expression from a novel suite of Agrobacterium tumefaciens binary expression vectors, which allow targeting of recombinant protein to the cytoplasm, endoplasmic reticulum (ER) or chloroplasts. A gene resynthesized to reflect human codon usage expresses better than the native gene, which expresses better than a plant-optimized gene. Moreover, chloroplast localization allows significantly higher levels of accumulation of L1 protein than does cytoplasmic localization, whilst ER retention was least successful. High levels of L1 (.17 % total soluble protein) could be produced via transient expression: the protein assembled into higher-order structures visible by electron microscopy, and a concentrated extract was highly immunogenic in mice after subcutaneous injection and elicited high-titre neutralizing antibodies. Transgenic tobacco plants expressing a human codon-optimized gene linked to a chloroplast-targeting signal expressed L1 at levels up to 11 % of the total soluble protein. These are the highest levels of HPV L1 expression reported for plants: these results, and the excellent immunogenicity of the product, significantly improve the prospects of making a conventional HPV vaccine by this means.

SummaryThe concept of using plants to produce high-value pharmaceuticals such as vaccines is 20 years old this year and is only now on the brink of realisation as an established technology. The original reliance on transgenic plants has largely given way to transient expression; proofs of concept for human and animal vaccines and of efficacy for animal vaccines have been established; several plant-produced vaccines have been through Phase I clinical trials in humans and more are scheduled; regulatory requirements are more clear than ever, and more facilities exist for manufacture of clinic-grade materials. The original concept of cheap edible vaccines has given way to a realisation that formulated products are required, which may well be injectable.The technology has proven its worth as a means of cheap, easily scalable production of materials: it now needs to find its niche in competition with established technologies. The realised achievements in the field as well as promising new developments will be reviewed, such as rapid-response vaccines for emerging viruses with pandemic potential and bioterror agents.

Maize streak virus (MSV; family Geminiviridae, genus Mastrevirus), the causal agent of maize streak disease, ranks amongst the most serious biological threats to food security in subSaharan Africa. Although five distinct MSV strains have been currently described, only one of these – MSV-A – causes severe disease in maize. Due primarily to their not being an obvious threat to agriculture, very little is known about the ‘grass-adapted’ MSV strains, MSV-B, -C, -D and -E. Since comparing the genetic diversities, geographical distributions and natural host ranges of MSV-A with the other MSV strains could provide valuable information on the epidemiology, evolution and emergence of MSV-A, we carried out a phylogeographical analysis of MSVs found in uncultivated indigenous African grasses. Amongst the 83 new MSV genomes presented here, we report the discovery of six new MSV strains (MSV-F to -K). The non-random recombination breakpoint distributions detectable with these and other available mastrevirus sequences partially mirror those seen in begomoviruses, implying that the forces shaping these breakpoint patterns have been largely conserved since the earliest geminivirus ancestors. We present evidence that the ancestor of all MSV-A variants was the recombinant progeny of ancestral MSV-B and MSV-G/-F variants. While it remains unknown whether recombination influenced the emergence of MSV-A in maize, our discovery that MSV-A variants may both move between and become established in different regions of Africa with greater ease, and infect more grass species than other MSV strains, goes some way towards explaining why MSV-A is such a successful maize pathogen.

Ageratum enation virus AEV Ageratum enation virus AJ437618 AEV Ageratum yellow vein China virus AYVCNV Ageratum yellow vein China virus -[Hn2] AJ495813 AYVCNV-[Hn2] Ageratum yellow vein Sri Lanka virus AYVSLV Ageratum yellow vein Sri Lanka virus AF314144 AYVSLV Ageratum yellow vein Taiwan virus AYVTV Ageratum yellow vein virus -[Taiwan] AF307861, AYVTV-[Tai] Ageratum yellow vein virus -[TaiwanPD] AF327902 AYVTV-[TaiPD] Ageratum yellow vein virus AYVV Ageratum yellow vein virus X74516 AYVV Bean calico mosaic virus BCaMV Bean calico mosaic virus AF110189, AF110190 BCaMV Bean dwarf mosaic virus BDMV Bean dwarf mosaic virus M88179, M88180 BDMV Bean golden mosaic virus BGMV (Bean golden mosaic virus -Brazil; BGMV-BR) Bean golden mosaic virus -[Brazil] M88686, M88687 BGMV-[BZ] Bean golden yellow mosaic virus BGYMV (Bean golden mosaic virus -Puerto Rico; BGMV-PR) Bean golden yellow mosaic virus [Dominican Republic] L01635, L01636 BGYMV-[DO] (Bean golden mosaic virus -Puerto Rico [Dominican Republic]; BGMV-PR[DO]) (Bean golden mosaic virus -Dominican Rep.; BGMV-DO) Bean golden yellow mosaic virus -[Guatemala] M91604, M91605 BGYMV-[GT] (continued) Species a Accession number AcronymCotton leaf curl Multan virus CLCuMV (Cotton leaf curl virus -Pakistan1; CLCuV-Pk1)