Adrian Gibbs

Sixteen groups of plant viruses.

Abstract Sixteen groups of plant viruses are described. The type members and main characteristics of each group are listed. The extension of this system to other plant viruses is discussed, and it is recommended that only well studied viruses should be grouped. Names are proposed for twelve of the groups: bromovirus, carlavirus, caulimovirus, comovirus, cucumovirus, nepovirus, potexvirus, potyvirus, tobamovirus, tobravirus, tombusvirus, and tymovirus. We suggest that the value of these names should be tested by using them for an experimental period.

Potyviruses and the Digital Revolution

The potyviruses are one of the two most speciose taxa of plant viruses. Our expanded knowledge of the breadth and depth of their diversity and its origins has depended greatly on the use of computing and the Internet in biological research and is reviewed here. We report a fully supported phylogeny based on gene sequence data for approximately half the named species. The phylogeny shows that the genus probably originated from a virus of monocotyledonous plants and that it first diverged approximately 7250 years ago in Southwest Eurasia or North Africa. The use of computer programs to better understand the structure and evolutionary trajectory of potyvirus populations is illustrated. The review concludes with recommendations for improving potyvirus nomenclature and the databasing of potyvirus information.

Two viruses from adult honey bees (Apis mellifera Linnaeus)

Two viruses were isolated from honey bees. When fed to, sprayed on, or injected into healthy bees either virus made the bees become trembly within a few days, but whereas bees infected with one virus died quickly (acute “paralysis”), bees infected with the other survived for several days after first showing symptoms (chronic “paralysis”). Purified preparations of acute bee paralysis virus (ABPV) contained isometric particles about 28 mμ in diameter, whereas those of chronic bee paralysis virus (CBPV) contained particles of irregular shape about 27 × 45 mμ. Both viruses occurred in apparently healthy bees, but only CBPV particles were numerous in diseased bees from colonies naturally affected with the disease called “bee paralysis.” On inoculation to healthy bees the symptoms caused by CBPV resembled those of the naturally occurring disease more than did those caused by ABPV.

On the evolution and molecular epidemiology of the potyvirus Papaya ringspot virus

The potyvirus Papaya ringspot virus (PRSV) is found throughout the tropics and subtropics. Its P biotype is a devastating pathogen of papaya crops and its W biotype of cucurbits. PRSV-P is thought to arise by mutation from PRSV-W. However, the relative impact of mutation and movement on the structure of PRSV populations is not well characterized. To investigate this, we have determined the coat protein sequences of isolates of both biotypes of PRSV from Vietnam (50), Thailand (13), India (1) and the Philippines (1), and analysed them together with 28 PRSV sequences already published, so that we can better understand the molecular epidemiology and evolution of PRSV. In Thailand, variation was greater among PRSV-W isolates (mean nucleotide divergence 7.6%) than PRSV-P isolates (mean 2.6%), but in Vietnamese populations the P and W biotypes were more but similarly diverse. Phylogenetic analyses of PRSV also involving its closest known relative, Moroccan watermelon mosaic virus, indicate that PRSV may have originated in Asia, particularly in the Indian subcontinent, as PRSV populations there are most diverse and hence have probably been present longest. Our analyses show that mutation, together with local and long-distance movement, contributes to population variation, and also confirms an earlier conclusion that populations of the PRSV-P biotype have evolved on several occasions from PRSV-W populations.

Sacbrood virus of the larval honey bee (Apis mellifera linnaeus)

Extracts of honey bee larvae suffering from sacbrood contained many isometric particles that were about 28 mμ in diameter. When the extracts or purified preparations of the particles were put into the food of healthy larvae, these developed sacbrood. The particles, which were not found in comparable extracts of healthy larvae, resemble those of acute bee paralysis virus, but cross infection and serological tests failed to show any relationship between the two viruses. Isolates of sacbrood virus from Europe and North America appear to be identical.

Plant virus classification.

Publisher Summary In any new and active branch of research, such as the study of plant viruses, various ways of interpreting and classifying information are tried before underlying patterns are revealed, and a stable and useful classification can be made. In this chapter, most of the named plant viruses and their possible or known relationships are discussed. Some viruses seem quite distinct and do not appear closely related by their properties to any other viruses, whereas others fall into well-defined groups, such as the potato virus Y group, which already contains more than two dozen viruses. The chapter provides information about viruses transmitted by mites (eriophyidae, acarina), viruses transmitted by white fly (aleyrodidae, hemiptera), viruses transmitted by aphids (aphididae, hemiptera), viruses transmitted by leafhoppers (auchenorrhyncha, hemiptera), viruses transmitted by mealybugs (coccidae, hemiptera), viruses transmitted by flea beetles (coleoptera, insecta), viruses transmitted by fungi (chytridiales and plasmodiophorales), viruses transmitted by mirid, piesmid, or tingid bugs (gymnocerata hemiptera), viruses transmitted by nematodes (nematoda), viruses transmitted by psyllas (psyllidae, hemiptera), viruses transmitted by thrips (thysanoptera), and viruses with no known vectors. A classification was computed for about 140 viruses using several of their properties. The viruses chosen were some of those whose particles have been identified by electron microscopy.

Time--the emerging dimension of plant virus studies.

Recent research has revealed that some plant viruses, like many animal viruses, have measurably evolving populations. Most of these viruses have single-stranded positive-sense RNA genomes, but a few have single-stranded DNA genomes. The studies show that extant populations of these viral species are only decades to centuries old. The genera in which they are placed have diverged since agriculture was invented and spread around the world during the Holocene period. We suggest that this is not mere coincidence but evidence that the conditions generated by agriculture during this era have favoured particular viruses. There is also evidence, albeit less certain, that some plant viruses, including a few shown to have measurably evolving populations, have much more ancient origins. We discuss the possible reasons for this clear discordance between short- and long-term evolutionary rate estimates and how it might result from a large timescale dependence of the evolutionary rates. We also discuss briefly why it is useful to know the rates of evolution of plant viruses.

PAPAYA RINGSPOT POTYVIRUS : ISOLATE VARIABILITY AND THE ORIGIN OF PRSV TYPE P (AUSTRALIA)

We have sequenced the coat protein gene of nine isolates of papaya ringspot virus (PRSV) including six Australian and three Asian isolates and compared these with four previously reported sequences of PRSV. There was up to 12% sequence variation between isolates at the nucleotide level. However, there was no significant difference between the sequences obtained from Australian isolates irrespective of whether they were PRSV type P (cucurbit or papaya infecting) or PRSV type W (cucurbit infecting) and these isolates were more closely related to one another than to any other isolate. These results imply that PRSV-P, first recorded in Australia in 1991, arose locally from PRSV-W (first recorded in Australia in 1978) rather than being introduced. Further, there was no consistent sequence difference between PRSV-P and PRSV-W isolates that would obviously account for their host range difference.

The phylogeny of Turnip mosaic virus ; comparisons of 38 genomic sequences reveal a Eurasian origin and a recent emergence in east Asia

The genomes of a representative world‐wide collection of 32 Turnip mosaic virus (TuMV) isolates were sequenced and these, together with six previously reported sequences, were analysed. At least one‐fifth of the sequences were recombinant. In phylogenetic analyses, using genomic sequences of Japanese yam mosaic virus as an outgroup, the TuMV sequences that did not show clear recombination formed a monophyletic group with four well‐supported lineages. These groupings correlated with differences in pathogenicity and provenance; the sister group to all others was of Eurasian B‐strain isolates from nonbrassicas, and probably represents the ancestral TuMV population, and the most recently ‘emerged’ branch of the population was probably that of the BR‐strain isolates found only in east Asia. Eight isolates, all from east Asia, were clear recombinants, probably the progeny of recent recombination events, whereas a similar number, from other parts of the world, were seemingly older recombinants. This difference indicates that the presence of clear recombinants in a subpopulation may be a molecular signature of a recent ‘emergence’.

Comparison of a dengue-2 virus and its candidate vaccine derivative: sequence relationships with the flaviviruses and other viruses.

Abstract A comparison of the sequence of the dengue-2 16681 virus with that of the candidate vaccine strain (16681-PDK53) derived from it identified 53 of the 10,723 nucleotides which differed between the strains. Nucleotide changes occurred in genes coding for all virion and nonvirion proteins, and in the 5′ and 3′ untranslated regions. Twenty-seven of the nucleotide changes resulted in amino acid alterations. The greatest amino acid sequence differences in the virion proteins occurred in prM (2.20%; 2 91 amino acids) followed by the M protein (1.33%; 1 75 amino acids), the C protein (0.88%; 1 114 amino acid), and the E protein (0.61%; 3 495 amino acids). Differences in the amino acid sequence of nonvirion proteins ranged from 1.51% ( 6 398 amino acids) in NS4 to 0.33% ( 3 900 amino acids) in NS5. The encoded protein sequences of 16681-PDK53 were also compared with the published sequences of other flaviviruses to obtain a detailed classification of 17 flaviviruses using the neighbor-joining tree method. The analyses of the sequence data produced dendrograms which supported the traditional groupings based on serological evidence, and they suggested that the flaviviruses have evolved by divergent mutational change and there was no evidence of genetic recombination between members of the group. Comparisons of the sequences of the flavivirus polymerase and helicase-like proteins (NS5 and NS3, respectively) with those from other viruses yielded a classification of the flaviviruses indicating that the primary division of the flaviviruses was between those transmitted by mosquitoes and those transmitted by ticks.