Analyses of seven new whole genome sequences of cassava brown streak viruses in Mozambique reveals two distinct clades: evidence for new species

Cassava brown streak disease (CBSD) caused by Cassava brown streak virus (CBSV) and Uganda cassava brown streak virus (UCBSV) is a major constraint to cassava production in Mozambique. Full genome sequences of CBSD-associated virus isolates contribute to the understanding of genetic diversity and the development of new diagnostic primers that can be used for early detection of the viruses for sustainable disease management. This study determined seven new whole CBSV genomes from total RNA isolated from cassava leaves with CBSD symptoms collected from Nampula and Zambezia in Mozambique. Phylogenetic analyses of the new genomes with published CBSV and UCBSV sequences in GenBank grouped the CBSV isolates from Mozambique into two distinct clades together with CBSV isolates from Tanzania. Clade 1 and 2 isolates shared low nucleotide (79.1-80.4%) and amino acid (86.5-88.2%) sequence identity. Further, comparisons within the seven new CBSV isolates, and between them and the single published complete CBSV sequence (CBSV_MO_83_FN434436) from Mozambique, revealed nucleotide sequence identities of 79.3-100% and 79.3-98%, respectively, and amino acid identities of 86.7-100% and 86.7-98.8%. In addition, using RDP4, a recombination analysis comprising all CBSV and UCBSV genome sequences from GenBank detect 11 recombination events. Using several comprehensive evolutionary models and statistical programs, it was confirmed that CBSV and UCBSV are distinct virus species, with an additional probable new species (clade 2).

Lanai: A small, fast growing tomato variety is an excellent model system for studying geminiviruses

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Florida Lanai is a tomato variety suitable for virus-host interaction studies.

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Florida-Lanai was infected by geminiviruses delivered by different methods.

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Florida-Lanai shows distinct measurable symptoms for different geminiviruses.

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Florida-Lanai has a small size, rapid growth and is easy to maintain.

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Florida-Lanai is an excellent choice for comparing geminivirus infections.

Geminiviruses are devastating single-stranded DNA viruses that infect a wide variety of crops in tropical and subtropical areas of the world. Tomato, which is a host for more than 100 geminiviruses, is one of the most affected crops. Developing plant models to study geminivirus-host interaction is important for the design of virus management strategies. In this study, “Florida Lanai” tomato was broadly characterized using three begomoviruses (Tomato yellow leaf curl virus, TYLCV; Tomato mottle virus, ToMoV; Tomato golden mosaic virus, TGMV) and a curtovirus (Beet curly top virus, BCTV). Infection rates of 100% were achieved by agroinoculation of TYLCV, ToMoV or BCTV. Mechanical inoculation of ToMoV or TGMV using a microsprayer as well as whitefly transmission of TYLCV or ToMoV also resulted in 100% infection frequencies. Symptoms appeared as early as four days post inoculation when agroinoculation or bombardment was used. Symptoms were distinct for each virus and a range of features, including plant height, flower number, fruit number, fruit weight and ploidy, was characterized. Due to its small size, rapid growth, ease of characterization and maintenance, and distinct responses to different geminiviruses, “Florida Lanai” is an excellent choice for comparing geminivirus infection in a common host.

Cassava brown streak disease in Rwanda, the associated viruses and disease phenotypes

Cassava brown streak disease (CBSD) was first observed on cassava (Manihot esculenta) in Rwanda in 2009. In 2014 eight major cassava-growing districts in the country were surveyed to determine the distribution and variability of symptom phenotypes associated with CBSD, and the genetic diversity of cassava brown streak viruses. Distribution of the CBSD symptom phenotypes and their combinations varied greatly between districts, cultivars and their associated viruses. The symptoms on leaf alone recorded the highest (32.2%) incidence, followed by roots (25.7%), leaf + stem (20.3%), leaf + root (10.4%), leaf + stem + root (5.2%), stem + root (3.7%), and stem (2.5%) symptoms. Analysis by RT-PCR showed that single infections of Ugandan cassava brown streak virus (UCBSV) were most common (74.2% of total infections) and associated with all the seven phenotypes studied. Single infections of Cassava brown streak virus (CBSV) were predominant (15.3% of total infections) in CBSD-affected plants showing symptoms on stems alone. Mixed infections (CBSV + UCBSV) comprised 10.5% of total infections and predominated in the combinations of leaf + stem + root phenotypes. Phylogenetic analysis and the estimates of evolutionary divergence, using partial sequences (210 nt) of the coat protein gene, revealed that in Rwanda there is one type of CBSV and an indication of diverse UCBSV. This study is the first to report the occurrence and distribution of both CBSV and UCBSV based on molecular techniques in Rwanda.

Phylogenetic characterization of East African cassava mosaic begomovirus (Geminiviridae) isolated from Manihot carthaginensis subsp. glaziovii (Müll.Arg.) Allem., from a non-cassava growing region in Tanzania

Manihot carthaginensis subsp. glaziovii (Müll.Arg.) Allem., a wild relative of cassava, native to Brazil, is one of the popular agroforestry trees used for hedges and/or boundary plants surrounding homesteads and farms and also harbours cassava mosaic begomoviruses (CMBs) and cassava brown streak ipomoviruses. Sequences of the DNA-A component of East African cassava mosaic virus (EACMV) isolates from M. carthaginensis subsp. glaziovii (Müll.Arg.) Allem., collected from non-cassava growing areas of Tanzania were characterized. Thirteen full length DNA-A sequences were analysed together with 15 already reported EACMV sequences and six CMB species reference genomes. The results show 96 to 100% nucleotide sequence identity with EACMV isolates from Kenya. Phylogenetic analysis revealed that EACMV isolates from M. carthaginensis subsp. glaziovii (Müll.Arg.) Allem, belong to a single cassava mosaic begomovirus species. The EACMV monophyletic clade is distinct from all other CMB species. The presence of Cassava infecting begomoviruses in wild cassava relative growing from traditionally non cassava growing region serve as inoculum sources for cassava-infecting begomoviruses and therefore their eradication is key in the sustainable management of CMBs, especially in the non-cassava growing areas.

A single-tube duplex and multiplex PCR for simultaneous detection of four cassava mosaic begomovirus species in cassava plants

A single-tube duplex and multiplex PCR was developed for the simultaneous detection of African cassava mosaic virus (ACMV), East African cassava mosaic Cameroon virus (EACMCV), East African cassava mosaic Malawi virus (EACMMV) and East African cassava mosaic Zanzibar virus (EACMZV), four cassava mosaic begomoviruses (CMBs) affecting cassava in sub-Saharan Africa. Co-occurrence of the CMBs in cassava synergistically enhances disease symptoms and complicates their detection and diagnostics. Four primer pairs were designed to target DNA-A component sequences of cassava begomoviruses in a single tube PCR amplification using DNA extracted from dry-stored cassava leaves. Duplex and multiplex PCR enabled the simultaneous detection and differentiation of the four CMBs, namely ACMV (940bp), EACMCV (435bp), EACMMV (504bp) and EACMZV (260bp) in single and mixed infections, and sequencing results confirmed virus identities according to the respective published sequences of begomovirus species. In addition, we report here a modified Dellapotra et al. (1983) protocol, which was used to extract DNA from dry and fresh cassava leaves with comparable results. Using the duplex and multiplex techniques, time was saved and amount of reagents used were reduced, which translated into reduced cost of the diagnostics. This tool can be used by cassava breeders screening for disease resistance; scientists doing virus diagnostic studies; phytosanitary officers checking movement of diseased planting materials, and seed certification and multipliers for virus indexing.

First Report of Sweetpotato symptomless virus 1 and Sweetpotato virus A in Sweetpotatoes in Tanzania

Sweetpotato (Ipomea batatas L.) is grown widely from tropical to temperate regions and is an important food security crop in tropical countries. In Africa, sweetpotato is infected by RNA viruses of many taxa (4), but DNA viruses, such as the genus Begomovirus (family Geminiviridae), infecting sweetpotatoes in the Americas have been reported only in Kenya (3). A caulimo-like DNA virus (family Caulimoviridae) has been detected in sweetpotatoes in Uganda (1). Recently, two novel badnaviruses (genus Badnavirus, family Caulimoviridae) and a new mastrevirus (genus Mastrevirus, family Geminiviridae) were discovered in a local sweetpotato cultivar maintained in a germplasm collection in Peru (2) but were not reported elsewhere. This study examined the possible existence of these novel viruses in landrace sweetpotato varieties grown in Tanzania. Nine landrace sweetpotato varieties and one introduced cultivar (NIS 91 from the International Potato Centre, Peru) were sampled from six regions of Tanzania. DNA was extracted (2) and amplified by PCR using primers (MastvKF: 5'-GACAGACCCCTAGGGTGA-3'; MastvsR 5'-ACTGCATATAGTACATGCCACA-3') designed in this study to amplify partial, putative movement and coat protein gene sequences of Sweetpotato symptomless virus 1 (SPSMV-1) (GenBank Accession No. FJ560945) (2). Products of the expected size were detected in seven samples (varieties Ex-London, Ex-Lyawaya, Gairo, Hombolo, Kagole white, Mbeya, and Shangazi) representing four regions surveyed (Dodoma, Mbeya, Morogoro, and Kagera). PCR products from five samples were sequenced (396 nt; GenBank Accession Nos. HQ316938 to HQ316942) and found to be identical to each other and the isolate described originally in Peru (2). Amplification with primers (BadnaBKF: 5'-CAAATTAGGAGGCAGATAAATG-3'; BadnaBsR: 5'-GGTCTTCTTATGTTCCACCTT-3') designed in this study according to the sequence of Sweetpotato virus B (SPBV-B) (GenBank Accession No.FJ560944) resulted in products of the expected size in three samples (varieties Ex-Lyawaya, Gairo, and Hombolo collected in Mbeya, Morogoro, and Dodoma, respectively) that were positive also for SPSMV-1. Sequences of the products (787 nt; HQ316935 to HQ316937) were nearly identical (99.4%). They were 96.8 to 96.9% similar to a region (nts 830-1616) of Sweetpotato virus A (SPBV-A; FJ560943) (2), whereas they were only 83.2 to 83.6 % similar to the corresponding region (1,486 to 2,272 nt) of SPBV-B (FJ560944) (2). No virus was detected in cv. NIS 91. All plants sampled exhibited mild mottling or mosaic symptoms, but a contribution to the symptoms by other untested viruses cannot be excluded because few of the large number of sweetpotato viruses have been studied in Africa (4). To our knowledge, this is the first report of SPSMV-1 and SPBV-A outside South America and in sweetpotatoes grown in the field. The results show that the two viruses are distributed widely in local sweetpotato varieties in Tanzania, which suggests that they may be found in other sweetpotato-growing areas where they have not been studied. While the yield losses caused by SPSMV-1 and SPBV-A remains to be studied, the data from this study are of practical importance in terms of regional and international exchange of sweetpotato germplasm. References: (1) V. Aritua et al. Plant Pathol. 56:324, 2007. (2) J. F. Kreuze et al. Virology 388:1, 2009. (3) T. Paprotka et al. Virus Res. 149:224, 2010. (4) F. Tairo et al. Mol. Plant Pathol. 6:199, 2005.

Evolution of cassava brown streak disease-associated viruses

Cassava brown streak disease (CBSD) has occurred in the Indian Ocean coastal lowlands and some areas of Malawi in East Africa for decades, and makes the storage roots of cassava unsuitable for consumption. CBSD is associated with Cassava brown streak virus (CBSV) and the recently described Ugandan cassava brown streak virus (UCBSV) [picorna-like (+)ssRNA viruses; genus Ipomovirus; family Potyviridae]. This study reports the first comprehensive analysis on how evolution is shaping the populations of CBSV and UCBSV. The complete genomes of CBSV and UCBSV (four and eight isolates, respectively) were 69.0-70.3 and 73.6-74.4% identical at the nucleotide and polyprotein amino acid sequence levels, respectively. They contained predictable sites of homologous recombination, mostly in the 3'-proximal part (NIb-HAM1h-CP-3'-UTR) of the genome, but no evidence of recombination between the two viruses was found. The CP-encoding sequences of 22 and 45 isolates of CBSV and UCBSV analysed, respectively, were mainly under purifying selection; however, several sites in the central part of CBSV CP were subjected to positive selection. HAM1h (putative nucleoside triphosphate pyrophosphatase) was the least similar protein between CBSV and UCBSV (aa identity approx. 55%). Both termini of HAM1h contained sites under positive selection in UCBSV. The data imply an on-going but somewhat different evolution of CBSV and UCBSV, which is congruent with the recent widespread outbreak of UCBSV in cassava crops in the highland areas (>1000 m above sea level) of East Africa where CBSD has not caused significant problems in the past.

Genetically distinct strains of Cassava brown streak virus in the Lake Victoria basin and the Indian Ocean coastal area of East Africa

Six isolates of Cassava brown streak virus (CBSV, genus Ipomovirus; Potyviridae) from the Lake Victoria basin in Uganda and Tanzania were characterized. Virus particles were 650 nm long. The complete coat protein (CP)-encoding sequences (1,101 nucleotides, nt) were 90.7-99.5 and 93.7-99.5% identical at the nt and amino acid (aa) levels, respectively. The 3' untranslated region was 225, 226 or 227 nt long. These eight isolates were only 75.8-77.5% (nt) and 87.0-89.9% (aa) identical when compared to the partial CP sequences (714 nt) of six CBSV isolates characterized previously from the costal lowlands of Tanzania and Mozambique. Hence, two genetically different and geographically separated populations of CSBV exist in East Africa.

Some molecular characteristics of three viruses from SPVD-affected sweet potato plants in Egypt

Sweet potato feathery mottle virus (SPFMV, genus Potyvirus, family Potyviridae), Sweet potato chlorotic stunt virus (SPCSV, genus Crinivirus, family Closteroviridae) and sweet potato virus G (SPVG) were detected in naturally infected sweet potato plants grown in the Delta region in Egypt. Before this study, SPVG was reported only from China. Two isolates of SPFMV and one isolate of SPVG were characterized for the 3'-proximal genomic sequences. Phylogenetic analyses indicated that the SPFMV isolates belong to the "russet crack" strain group (RC). Serological tests using monoclonal antibodies, and phylogenetic analysis of a partial sequence of the Hsp70 gene, indicated that the Egyptian SPCSV belongs to the so-called non-East African strain group of SPCSV.

Coat protein sequence analysis reveals occurrence of new strains of Sweet potato feathery mottle virus in Uganda and Tanzania

The 3'-proximal part (1.8 kb) of the Sweet potato feathery mottle virus (SPFMV) genome was studied in four SPFMV isolates collected from farmers' fields in western Uganda (SPFMV-Bny), eastern Uganda (SPFMV-Sor) and Bagamoyo district, Tanzania (SPFMV-TZ1 and SPFMV-TZ2). Unlike the other three SPFMV isolates, SPFMV-Sor was not detected with the polyclonal antisera to SPFMV. It showed moderately high coat protein (CP) nucleotide (93.3-96.7%) and amino acid (93.6-96.8%) sequence identity to the isolates of the SPFMV strain group C. In contrast, identities (78.1-80.1%, and 79.9-83.1%) to isolates of the SPFMV strain groups O, RC, and the East African (EA) strain group were low. Similar to some isolates (SPFMV-CH2 and SPFMV-6) of strain group C, but different from other SPFMV isolates, SPFMV-Sor contained a deletion of 6 nucleotides in the CP-encoding region (CP amino acid positions 62-63). Phylogenetic analysis of the CP sequences indicated that SPFMV-Sor belongs to the SPFMV strain group C that has not been reported from Africa. Sequence data were obtained for the first time from Tanzanian SPFMV isolates in this study, and phylogenetic analysis indicated that they belong to the strain group EA, which is unique to East Africa.