98% identical, 100% wrong: per cent nucleotide identity can lead plant virus epidemiology astray

Abstract

Short-form publications such as Plant Disease reports serve essential functions: the rapid dissemination of information on the geography of established plant pathogens, incidence and symptomology of pathogens in new hosts, and the discovery of novel pathogens. Many of these sentinel publications include viral sequence data, but most use that information only to confirm the virus' species. When researchers use the standard technique of per cent nucleotide identity to determine that the new sequence is closely related to another sequence, potentially erroneous conclusions can be drawn from the results. Multiple introductions of the same pathogen into a country are being ignored because researchers know fast-evolving plant viruses can accumulate substantial sequence divergence over time, even from a single introduction. An increased use of phylogenetic methods in short-form publications could speed our understanding of these cryptic second introductions and aid in control of epidemics.

Low Genetic Diversity Suggests a Single Introduction and Recent Spread of Tomato chlorosis virus in Brazil

“…), which suggests divergent evolutionary relationships among ToCV isolates found throughout the world. ToCV isolates from the New World were found to cluster in distinct monophyletic branches composing lineages II, III and IV corroborating the hypothesis of Duffy and Seah () for multiple introductions of ToCV into New World (Fig. ).…”

“…To this end, genetic diversity and phylogenetic analyses may be carried out. These analyses will permit us to test the hypothesis proposed by Duffy and Seah (), for which ToCV might have been introduced multiple times in the New World. At that time they had available partial nucleotide sequence of the heat shock protein (HSP70) homologue gene for only one Brazilian isolate of the virus, they did not make any definitive statements about the origin and introduction of ToCV into Brazil.…”

Rymovirus: a cautionary tale

“…The use of PI estimates as a surrogate for distinguishing the natural groups, or more specifically phylogenetic groups, of potyviruses by Shulka and Ward [11] was expanded by Adams et al [2], but subsequently questioned by Duffy and Seah [3], who highlighted the problem that "When researchers use the standard technique of per cent nucleotide identity to determine that the new sequence is closely related to another sequence, potentially erroneous conclusions can be drawn from the results. "…”

“…A tree calculated from the same sequences by the neighborjoining method in ClustalX [7] was topologically the same as the ML tree with the sequences again forming monophyletic clusters with 100% bootstrap support (1000 replicates). Thus phylogenetic methods distinguish the three potyvirid genera, whereas PI analyses do not as they have problems with closely related clusters, just as they have with outliers [3]. Recently the Code of the International Committee on Taxonomy of Viruses (ICTV; https://talk.ictvonline.org/ information/w/ictv-information/383/ictv-code) updated its Rule 3.20, to define species as "a monophyletic group of viruses whose properties can be distinguished from those of other species by multiple criteria.…”

New experimental and theoretical approaches towards the understanding of the emergence of viral infections

“…Duffy & Seah (2010) question the definition of 'new' and 'emergent' plant viruses by distinguishing single and multiple introductions of the same pathogen into a country based on looking at the percentages of sequence identity. In her article, Roossinck (2010) calls our attention to the existence of persistent plant viruses (i.e.…”