Epidemiological Study of Begomoviruses in the North American Region

Abstract

Begomoviruses, belonging to the family Geminiviridae, are a large group of plant viruses having circular single stranded DNA genome. They are actively transmitted by whiteflies (Bemisia tabaci) insect vector which feeds on various plants resulting in transmission of Begomoviruses from one dicot plant to another. Begomoviruses have a huge economic impact as they infect a wide range of plants including not only crops and vegetables but also weeds and ornamental host plants. Among Begomovirus hosts, weeds and ornamental plants are the alternate hosts which serve as inoculum when the main hosts are not present. Moreover, the present classification system for Begomoviruses is ambiguous which creates anomalies like inclusion of one specie isolate being included in various other species creating ambiguity regarding their names. This study was focused on analyzing the Begomovirus species demarcation, host plants and geographical distribution in the region of North America. The FASTA and GenBank sequences of Begomoviruses in the North American countries were retrieved, and data was tabulated in sheets using the given parameters. MUSCLE alignment was performed, and Specie Demarcation Tool (SDT) was used to identify different species. Maximum Likelihood (ML) tree was generated using MegaX for phylogenetic analysis. The representative charts, graphs and maps were generated using Microsoft Excel in which details of parameters were tabulated. Begomoviruses had 307 species and around 5043 isolates in the world out of which North American countries were found to have 62 species and 543 isolates. 62 different Begomoviruses are hosted by different plant hosts including many crops, ornamental plants, medicinal plants, and weeds. The top 3 host plants sweet potato with 150 reports, Capsicum annuum with 98 reports, and tomato having 31 reports. However, 86 Begomovirus isolates have been isolated from unknown or unidentified plant sources. Sweet potato leaf curl virus (SPLCV) was found to be the most predominant specie of Begomoviruses in North America having 168 isolates infecting Convolvulaceae family plants and unknown plants. The second most significant and predominant Begomovirus specie was found to be Pepper Golden (PepGMV) having 67 isolates infecting Solanaceae and Cucurbitaceae families. The third most reported Begomovirus was Pepper huasteco yellow vein virus (PHYVV) having 49 isolates and infecting Solanaceae family plants. Sweet potato belongs to family Convolvulaceae and viruses infecting Convolvulaceae family plants are included in this specie. However, this was not the case for most of the viruses in this study in which one virus specie was infecting plants of multiple families. The top 3 Begomovirus 2 Abstract families infecting the most host plant families include Euphorbia mosaic virus (EuMV) infecting 6 plant families along with unknown plant families, Tobacco yellow crinckle virus (TbYCV) infecting 4 plant families along with unknown families, and Tobacco leaf curl Cuba virus (TbLCuCV) and Cabbage leaf curl virus (CabLCV) each infecting 3 plant families with CabLCV also infecting unknown plant families. Considering the results from the analyses on Begomovirus isolates of North American region, there were also some ambiguities including ambiguities in naming that included accessions submitted with incorrect names and ambiguities in classification in which isolate(s) of different viruses showed mixing according to the 91% species demarcation criteria. Therefore, there is a need to make a compendium with all the ambiguities along with their solutions and revise the 91% species demarcation criteria for Begomoviruses.