Judith K Brown

PMID: 23340592;Abstract:

Recent advances in the ease with which the genomes of small circular single-stranded DNA viruses can be amplified, cloned, and sequenced have greatly accelerated the rate at which full genome sequences of mastreviruses (family Geminiviridae, genus Mastrevirus) are being deposited in public sequence databases. Although guidelines currently exist for species-level classification of newly determined, complete mastrevirus genome sequences, these are difficult to apply to large sequence datasets and are permissive enough that, effectively, a high degree of leeway exists for the proposal of new species and strains. The lack of a standardised and rigorous method for testing whether a new genome sequence deserves such a classification is resulting in increasing numbers of questionable mastrevirus species proposals. Importantly, the recommended sequence alignment and pairwise identity calculation protocols of the current guidelines could easily be modified to make the classification of newly determined mastrevirus genome sequences significantly more objective. Here, we propose modified versions of these protocols that should substantially minimise the degree of classification inconsistency that is permissible under the current system. To facilitate the objective application of these guidelines for mastrevirus species demarcation, we additionally present a user-friendly computer program, SDT (species demarcation tool), for calculating and graphically displaying pairwise genome identity scores. We apply SDT to the 939 full genome sequences of mastreviruses that were publically available in May 2012, and based on the distribution of pairwise identity scores yielded by our protocol, we propose mastrevirus species and strain demarcation thresholds of >78 % and >94 % identity, respectively. © 2013 Springer-Verlag Wien.

Legg, J.P., P. Sseruwagi, S, Boniface, G. Okao-Okuja, R. Shirima, S. Bigirimana, Gervais Gashaka, H.-W. Herrmann, S. Jeremiah, H. Obiero, I. Ndyetabula, W. Tata-Hangy, C. Masembe, and J. K. Brown. 2013. Spatio-temporal patterns of genetic change amongst cassava Bemisia tabaci whiteflies driving virus pandemics in East and Central Africa. Virus Res. doi.org/10.1016/j.virusres.2013.11.018.

Hameed, U., Ur-Rehman, Z., Herrmann, H.W., Haider, M.S. and Brown, J.K. 2014. First report of Okra enation leaf curl virus and associated Cotton leaf curl Multan betasatellite and Cotton leaf curl Multan alphasatellite infecting cotton in Pakistan: A new member of the cotton leaf curl disease complex. Plant Dis. 98:1447.

PMID: 18944765;Abstract:

A membrane feeding system and polymerase chain reaction (PCR) were used to track squash leaf curl virus (SLCV) DNA in whole whitefly body extracts and in saliva, honeydew, and hemolymph of its whitefly vector, Bemisia tabaci, and a whitefly nonvector, Trialeurodes vaporariorum. SLCV ingestion was monitored by PCR in whiteflies that were given acquisition access periods (AAPs) ranging from 0.5 to 96 h on virus-infected plants. SLCV detection by PCR in whole body extracts was considered reflective of virus ingestion. As whiteflies were given longer AAPs, the number of whiteflies that ingested SLCV increased. SLCV DNA was detected in honeydew of vector and nonvector whiteflies, indicating that virions, viral DNA, or both passed unimpeded through the digestive system. SLCV DNA was detected in saliva and hemolymph of B. tabaci, but not in these fractions from nonvector whiteflies, despite virus ingestion by both. Although vector and nonvector whiteflies both ingested SLCV, only in the vector, B. tabaci, did virus cross the gut barrier, enter the hemolymph, or pass into the salivary system. These results suggest that digestive epithelia of nonvector whiteflies did not permit SLCV passage from the gut to hemocoel, whereas virus effectively crossed the analogous gut barrier in vector whiteflies.

Naim, S., Brown, J.K., and Nibert, M.L. 2014. Diversification of penaeid shrimp infectious myonecrosis virus in Indonesia. Virus Res. 189: 97-105.