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.

Figure 1.

Maximum-likelihood tree of a 488-base alignment of partial coat protein sequences of New World isolates of tomato yellow leaf curl virus with three non-North American isolates, constructed with a Tamura–Nei (TrN) model of nucleotide substitution. Branches with greater than or equal to 75% bootstrap support are labelled. Taxon labels are as previously published (Duffy & Holmes 2007) or labelled according to convention (Fauquet et al. 2008) and given with its GenBank accession number.

Figure 2.

Maximum-likelihood tree of a 513-base alignment of coat protein sequences (the 513-base ORF on DNA-3) of banana bunchy top virus, constructed with a TrN substitution model including the fraction of invariant sites (I) and substitution rate heterogeneity among sites (Γ). Branches with greater than or equal to 75% bootstrap support are labelled. Taxon labels are GenBank accession numbers preceded by two-letter country codes: AU, Australia; BI, Burundi; CM, Cameroon; CN, China; EG, Egypt; FJ, Fiji; ID, Indonesia; IN, India; JP, Japan; MM, Myanmar; PH, Philippines; PK, Pakistan; TW, Taiwan; VN, Vietnam. Isolates from Hainan, China are shown in black, other locations are shown in grey.

Figure 3.

Maximum-likelihood tree of a 309-base alignment of partial heat shock protein 70 sequences of tomato chlorosis virus, constructed with a transversional (TVM) model of nucleotide substitution. Branches with greater than or equal to 50% bootstrap support are labelled. Taxon labels are GenBank accession numbers preceded by two-letter country codes: BR, Brazil; CU, Cuba; ES, Spain; FR, France; GR, Greece; IT, Italy; LB, Lebanon; MX, Mexico; MU, Mauritius; PT, Portugal; RE, Reunion Island; TR, Turkey; YT, Mayotte.