Mixed Infections of Four Viruses, the Incidence and Phylogenetic Relationships of Sweet Potato Chlorotic Fleck Virus (Betaflexiviridae) Isolates in Wild Species and Sweetpotatoes in Uganda and Evidence of Distinct Isolates in East Africa

Abstract

Viruses infecting wild flora may have a significant negative impact on nearby crops, and vice-versa. Only limited information is available on wild species able to host economically important viruses that infect sweetpotatoes (Ipomoea batatas). In this study, Sweet potato chlorotic fleck virus (SPCFV; Carlavirus, Betaflexiviridae) and Sweet potato chlorotic stunt virus (SPCSV; Crinivirus, Closteroviridae) were surveyed in wild plants of family Convolvulaceae (genera Astripomoea, Ipomoea, Hewittia and Lepistemon) in Uganda. Plants belonging to 26 wild species, including annuals, biannuals and perennials from four agro-ecological zones, were observed for virus-like symptoms in 2004 and 2007 and sampled for virus testing. SPCFV was detected in 84 (2.9%) of 2864 plants tested from 17 species. SPCSV was detected in 66 (5.4%) of the 1224 plants from 12 species sampled in 2007. Some SPCSV-infected plants were also infected with Sweet potato feathery mottle virus (SPFMV; Potyvirus, Potyviridae; 1.3%), Sweet potato mild mottle virus (SPMMV; Ipomovirus, Potyviridae; 0.5%) or both (0.4%), but none of these three viruses were detected in SPCFV-infected plants. Co-infection of SPFMV with SPMMV was detected in 1.2% of plants sampled. Virus-like symptoms were observed in 367 wild plants (12.8%), of which 42 plants (11.4%) were negative for the viruses tested. Almost all (92.4%) the 419 sweetpotato plants sampled from fields close to the tested wild plants displayed virus-like symptoms, and 87.1% were infected with one or more of the four viruses. Phylogenetic and evolutionary analyses of the 3'-proximal genomic region of SPCFV, including the silencing suppressor (NaBP)- and coat protein (CP)-coding regions implicated strong purifying selection on the CP and NaBP, and that the SPCFV strains from East Africa are distinguishable from those from other continents. However, the strains from wild species and sweetpotato were indistinguishable, suggesting reciprocal movement of SPCFV between wild and cultivated Convolvulaceae plants in the field.

Fig 1. Map of Uganda showing the districts surveyed for wild Convolvulaceae species and viruses in Uganda.

Fig 2. Examples of wild species of Convolvulaceae in their natural habitats in Uganda, and some virus-like symptoms.

(A) Ipomoea wightii and (B) I. acuminata (in the background) trailing into sweet potato field (foreground) in the Mbarara and Mukono districts, respectively. Wild vegetation in these districts is dominated by tall shrubs. (C) I. sinensis (dotted circle) in close proximity to sweetpotato field (edge inside solid circle) in the Soroti district, which is dominated by short grassland vegetation (background). (D) I. sinensis (white asterisks) growing as weeds in a sweetpotato field in the Katakwi district. (E) Sweetpotato plant (white o) mixed with plants of I. wightii (white asterisks) in the Mukono district. (F-J) Examples of virus-like symptoms. (F) Leaf chlorosis in H. sublobata. (G) Chlorotic spots on a leaf of I. tenuirostris. (H, I) Mild (H) and severe (I) purpling in old leaves of I. sinensis. (J) Mild chlorotic spots on a leaf of I. acuminata. Plants in F, G and J tested positive for SPCFV; plants in H and I tested positive for SPCSV.

Fig 3. Phylogenetic analysis of SPCFV based on the CP and NaBP nucleotide sequences.

Nine SPCFV isolates from wild plant species (▲) or sweetpotatoes (●) in this study are compared with 29 and 23 isolates, respectively, from previous studies. (A, B) Sequences for CP (A) and NaBP (B) were analyzed. Sequences cluster according to the geographical origin of the virus isolates, i.e., East Africa (SPCFV-EA) or Asia (SPCFV-Asian1 and SPCFV-Asian2). The geographical origins are unknown for isolates Le-97-598_EU375905, TN399_EU375909 and 007VIIMS_EU375897. Numbers at branches represent bootstrap values of 1000 replicates. Only bootstrap values of ≥50% are shown. Scale indicates nucleotide substitutions per site according to Tamura [69].