Comprehensive Surveys of Bean common mosaic virus and Bean common mosaic necrosis virus and Molecular Evidence for Occurrence of Other Phaseolus vulgaris Viruses in Tanzania

Abstract

Virus diseases are among the main biotic factors constraining common bean (Phaseolus vulgaris L.) production in Tanzania. Disease management requires information on types, distribution, incidence, and genetic variation of the causal viruses, which is currently limited. Thus, a countrywide comprehensive survey was conducted. Use of a next-generation sequencing technique enabled simultaneous detection of 15 viruses belonging to 11 genera. De novo assembly resulted in many contigs, including complete or nearly complete sequences of Bean common mosaic virus (BCMV), Bean common mosaic necrosis virus (BCMNV), and Southern bean mosaic virus (SBMV). Some viruses (for example, SBMV and Tomato leaf curl Uganda virus-related begomovirus) were detected for the first time in common bean in Tanzania. Visually assessed virus-like disease incidence ranged from 0 to 98% but reverse-transcription polymerase chain reaction-based incidence of BCMV and BCMNV (7,756 samples) was mostly less than 40%. The Sanger-based nucleotide sequences encoding coat proteins of BCMV and BCMNV isolates were 90.2 to 100% and 97.1 to 100% identical to each other, respectively. Phylogenetic analysis showed that BCMV isolates were more diverse than BCMNV isolates. The information generated in this study will contribute to the development of molecular diagnostic tools and strategies for management of virus diseases nationally and internationally. [Formula: see text] Copyright © 2018 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

Fig. 1

Locations surveyed for common bean viral diseases in Tanzania. Lake zone: A, Kagera Region (Ngara, Biharamulo, Muleba, Missenyi, and Karagwe Districts) and B, Mara Region (Tarime District). Western zone: C, Kigoma Region (Kasulu and Kibondo Districts). Northern zone: D, Arusha Region (Karatu and Arumeru Districts), E, Kilimanjaro Region (Siha and Hai Districts), and F, Tanga Region (Lushoto District). Eastern zone: G, Morogoro Region (Morogoro Rural, Mvomero, and Gairo Districts). Southern highlands zone: H, Rukwa Region (Nkasi District), I, Mbeya and Songwe Regions (Mbozi, Mbeya Rural Districts), J, Njombe Region (Njombe Rural and Wanging’ombe Districts), and K, Ruvuma Region (Namtumbo and Mbinga Districts).

Fig. 2

Some symptoms observed on common bean plants in fields during 2015 to 2017. A, Vein clearing in plants infected with Southern bean mosaic virus (Kasulu District in the western zone). B, Yellow mottling (Missenyi District in Lake zone). C and D, Mosaic and leaf curl (Missenyi District in Lake zone). E, mosaic (Karatu District in northern zone). F, Mosaic and stunted growth (northern zone). G and H, leaf necrosis (Kilimanjaro Region in northern zone). I, Mosaic and severe leaf deformation (Mvomero District in eastern zone).

Fig. 3

Phylogenetic tree generated using the coat protein nucleotide sequences (620 nucleotides) of Bean common mosaic virus (BCMV) and Bean common mosaic necrosis virus (BCMNV) isolates. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. Numbers at branches represent bootstrap values of 1,000 replicates, of which only values of >60% are shown. Isolate names are shown along with the accession numbers assigned to their sequences in this study (nonbold text) and in previous studies (bold text).