Variation between Turnip mosaic virus Isolates in Zhejiang Province,China and Evidence for Recombination

The 3′‐terminal sequences (c. 1700 nt) of the RNA genome of 10 Turnip mosaic virus (TuMV) isolates from different hosts in Zhejiang province, China, were determined. Phylogenetic analysis of the coat protein nucleotide sequences revealed that most TuMV sequences fell into two distinct clusters. The Chinese isolates B1‐B4 (from Brassica spp.) were similar and placed in the largest group (Group 1), while the isolates R1‐R6 (from Raphanus) were usually placed in a distinct but smaller group (Group 2). There were only approximately 90% identical nucleotides between the two groups. However, one isolate (R5) showed evidence of recombination in that the region between nucleotides 430 and 450, from the start of the coat protein gene and its 3′‐terminus, was a Group 1 type.     

Molecular and Biological Analysis of Potato virus M (PVM) Isolates from the Czech Republic

The sequences of the 3′‐terminal region of four Czech Potato virus M isolates VIRUBRA 4/007, VIRUBRA 4/009, VIRUBRA 4/016 and VIRUBRA 4/035 were determined and compared with sequences of PVM isolates available in GenBank. Among the Czech isolates, VIRUBRA 4/007 and 4/016 as well as VIRUBRA 4/016 and 4/035 showed the highest nucleotide identity (93%). Isolates VIRUBRA 4/007, 4/016 and 4/035 were most similar to the PV0273 isolate from Germany and to the wild isolate from Russia. Interestingly, isolate VIRUBRA 4/009 significantly differed from the other three Czech isolates and was the only European isolate that showed the highest nucleotide identity with American isolates. Moreover, the PVM isolates from the Czech Republic and Germany differed in their host range. Phylogenetic analysis based on ORF5 coding for coat protein showed that the Czech isolates could be classified in two of the three groupings of the phylogenetic tree obtained. This is the first report on molecular and biological analysis of the genome sequences of PVM isolates from the Czech Republic.     

Molecular Analysis of ORF6, ORF7 and ORF8 of Beet yellows virus Iranian Isolate

Beet yellows virus (BYV), a member of the Closteroviridae family, is one of the most important sugar beet yellowing viruses. The nine ORFs of BYV genome encode different proteins required for BYV life cycle. We sequenced a part of the genome of BYV Iranian isolate consisting of ORF6, ORF7 and ORF8. The primer pair BYVA/Z was used for amplification of this region in RT‐PCR. The amplicon (1615 bp) was cloned and sequenced. Comparisons showed the amplified segment is corresponding to ORF6, ORF7 and ORF8 of BYV genome encoding coat protein, p20 and p21 proteins, respectively. The ORF7 of BYV Iranian isolate overlaps with ORF6 and ORF8 in four and 26 nucleotides at 5′ and 3′ ends, respectively. The ORF7 of Iranian isolate of BYV was sequenced completely. However, approximately 24 nt. from the beginning of ORF6 and 23 nt. from end of ORF8, including the stop codon, were not determined. ORF6, ORF7 and ORF8 showed the highest similarity at nucleotide (98.3, 99.4 and 99.2%) and amino acid (97.4, 98.9 and 100%) sequence levels, with BYV Ukrainian isolate. Phylogenetic analysis of the deduced amino acid sequences of ORF6, ORF7 and ORF8 revealed closer relationship of Iranian isolate of BYV with BYV Ukrainian isolate than other BYV isolates available at GenBank.     

Coat Protein Gene of Cymbidium mosaic virus from Vanilla fragrans in Reunion Island

Nucleotide and amino acid sequences of the coat protein (CP) of 12 isolates of Cymbidium mosaic virus from Vanilla fragrans in Reunion Island (CyMV‐R) were compared with each other and with those of previously described Asian strains. Alignment revealed that CyMV‐R isolates were highly homologous, suggesting that one strain is prevalent in Reunion. This strain also showed high homology with the Korean CyMV‐K2 and Singapore CyMV‐S2 strains, but nucleotide additions resulted in the carboxy‐terminal ends of the CP sequences differing from those of the Korean CyMV‐K1 and Singapore CyMV‐K1 strains.     

A mixture of begomoviruses in leaf curl-affected tobacco in Karnataka, South India

Tobacco leaf curl is widespread in several states in India including Andhra Pradesh, Gujarat, Karnataka, Bihar and West Bengal. Tobacco leaf curl virus (TbLCV) isolates collected from five different parts of India induced four distinct symptom phenotypes (group I, II, III & IV) on tobacco cultivars Samsun and Anand 119 (Valand & Muniyappa, 1992). PCR was performed on DNA extracted from group I and IV leaf curl‐affected tobacco from Karnataka, India using degenerate begomovirus‐specific primers. Subsequent cloning and sequencing of PCR products revealed preliminary evidence for the presence of at least three begomoviruses in the affected material following alignment of a 333 bp region of the coat protein gene (CP). The complete CP and common region (CR) of two putative begomoviruses, Tobacco leaf curl virus‐Karnataka1 (TbLCV‐Kar1) and Tobacco leaf curl virus‐Karnataka2 (TbLCV‐Kar2), were sequenced using PCR clones obtained with designed sequence‐specific primers. Phylogenetic analysis of the CP and CR of TbLCV‐Kar1 and TbLCV‐Kar2 placed them in the Asian Old World begomovirus cluster. The two viruses differed from each other significantly in both the CP gene and the CR (< 90% nucleotide sequence identity). This difference, in conjunction with distinct iterative sequences strongly suggests that these begomoviruses are distinct from one another. Group I and IV tobacco were also found to harbour a possible third begomovirus following the 333 bp CP alignment. Comparison of TbLCV‐Kar1 and TbLCV‐Kar2 with other geminiviruses, showed that both sequences shared high nucleotide sequence identity (> 90%) with other begomoviruses in either the CP or CR, thereby suggesting these viruses to be possible strains of other reported begomoviruses. Combined comparison of the CP and CR sequences however, suggests that the two viruses are not strains of other reported begomoviruses, but may be distinct begomoviruses that could have arisen through recombination events during mixed infections. Phylogenetic comparison demonstrated no significant homology between the Indian tobacco begomoviruses and a tobacco‐infecting begomovirus from Zimbabwe, again showing that as with other geminiviruses, there is a geographic basis for phylogenetic relationships rather than an affiliation with tobacco as a host.     

水稻条纹病毒中国分离物和日本分离物RNA2节段序列比较

测定了来源于我国水稻条纹叶枯病常年流行区的云南楚雄(CX)及病害暴发区的江苏洪泽(HZ)的水稻条纹病毒(RSV)2个分离物RNA2全长序列,其长度分别为3506bp和3514 bp.与已报道的日本T和O分离物RNA2序列进行比较的结果表明,这4个分离物可分为两组,其中,HZ、T和O分离物为一组,组内分离物之间,RNA2的毒义链(vRNA2)及RNA2的毒义互补链(vcRNA2)上的ORF的核苷酸一致性分别为97.2%～98.0%和96.8%～97.1%,5′端和3′端非编码区的序列则完全一致.但HZ分离物与T分离物的亲缘关系更为密切,其基因间隔区(IR)与T和O分离物的等长.另一组为我国CX分离物,组与组之间,vRNA2及vcRNA2上的ORF的核苷酸一致性分别为95.0%～95.7%和93.9%～94.4%.CX分离物的IR与HZ分离物相比缺失了一段8 nt的片段.5′端非编码区的序列完全一致,但3′末端非编码区有一个碱基的差异.这些结果表明,RSV在自然界的分子变异与其地理分布具有密切的关系.此外,非编码区序列的高度保守性暗示着它们在病毒基因转录和复制的调控方面具有重要的功能.本文还讨论了RSV的分子流行病学.     

Analysis of Coat Protein of Peanut stunt virus Subgroup II Isolates from Alfalfa Fields in West Iran

Alfalfa fields in three western provinces of Iran were surveyed for Peanut stunt virus (PSV) during 2011 and 2012. Forty‐seven of 115 samples tested (41%) were infected with PSV. Phylogenetic analysis using coat protein (CP) gene sequences showed that the Iranian isolates belong to the subgroup II of PSV. Pairwise identity analysis revealed four groups representing four phylogenetic subgroups. PSV strains in subgroups III and IV are closely related to each other, as supported by the lowest nucleotide diversity, high pairwise nucleotide identity and high haplotype diversity as evidence of a recent population expansion after a genetic bottleneck. Using the maximum likelihood method, amino acid 86S in the CP gene of the Iranian PSV isolates was found to be under positive selection, although the likelihood ratio test statistics is not significant. This is the first report of the occurrence and phylogenetic relationships of Iranian PSV isolates in west Iran.     

Natural Infection by Tospoviruses of Cucurbitaceous and Fabaceous Vegetable Crops in India

Natural infection of tospoviruses on three cucurbitaceous (Cucumis sativus, cucumber; Luffa acutangula, ridge gourd; Citrullus lanatus, watermelon) and three fabaceous (Vigna unguiculata, cowpea; Phaseolus vulgaris, French bean; Dolichos lablab, sem) vegetable crops in India was identified on the basis of nucleocapsid protein (NP) gene characteristics. The complete NP gene of the cowpea isolate from Kerala and the sem isolate from Tamil Nadu was 831 nucleotides long, encoding a protein of 276 amino acids. For other Tospovirus isolates from cucumber, French bean, ridge gourd and watermelon, the partial NP gene (291 nt) was sequenced. Comparative NP gene sequence analyses revealed that fabaceous isolates shared maximum identity both at the nucleotide (92–97%) and amino acid (93–97%) levels with the corresponding region of Groundnut bud necrosis virus (GBNV), whereas cucurbitaceous isolates shared maximum identity both at nucleotide (93–99%) and amino acid (95–98%) levels with the corresponding region of Watermelon bud necrosis virus (WBNV), results suggesting that the Tospovirus isolates infecting fabaceous hosts should be regarded as strain of GBNV, whereas those infecting cucurbitaceous hosts as a strain of WBNV. Nucleocapsid protein gene was conserved both in GBNV and WBNV isolates originating from different hosts and locations.     

Detection and molecular characterisation of Potato virus S of weed reservoirs in Iran

Potato virus S causes destructive disease on the plants. In this research, 44 weed samples symptomless were collected during 2015 from Fars, Razavi Khorasan and Kerman provinces of Iran. The coat protein (CP) and 11 K genes from eight PVS isolates were amplified, cloned and sequenced. PVS was detected in eight weed samples including: one sample of Solanum nigrum, two samples of Chenopodium botrytis, three samples of Chenopodium album and two samples of Amaranthus hybridus. Phylogenetic analysis showed that seven Iranian isolates fell into group I, II near to European isolates and one Iranian isolate formed a separate group. Comparison of coat protein and 11 k nucleotide indicated that all Iranian isolates belonged to Ordinary strain and there were 79–100% identity among the eight Iranian isolates and the world isolates of PVS. The highest identity was between Iranian and Ukraine isolates. Recombination analysis identified four recombinant isolates among eight new Iranian isolates.     

Begomoviruses Associated with Yellow Leaf Curl Disease of Tomato in Iran*

The occurrence of Tomato yellow leaf curl virus (TYLCV; genus Begomovirus, family Geminiviridae) in the major tomato‐growing areas of Iran was determined using TAS‐ELISA and PCR. The nucleotide sequences of the coat protein (CP) gene and intergenic region (IR) of eight Iranian isolates were determined. CP nucleotide identities among the Iranian isolates were 96–98%, and showed 94–96% identity with TYLCV‐IR [IR:Ira:98] and TYLCV‐IL [IL:Reo:86]. However, they showed low identity (68–69%) with ToLCIRV‐[IR:Ira]. Sequence analyses of IR indicated that seven Iranian isolates had sequence identity of 93–100% with each other, and 76% identity with the Jiroft isolate; identities of 75–79% with TYLCV‐IR[IR:Ira:98] were observed in every case, and 59–62% identity with ToLCIRV‐[IR:Ira]. The IR nucleotide sequences of Iranian isolates showed 92–93% identity with TYLCV‐IL[IL:Reo:86], except the Jiroft isolate (75%). The CP and IR sequence analyses suggested that eight Iranian TYLCV isolates probably differ from ToLCIRV‐[IR:Ira]. Based on IR sequence comparisons and phylogenetic analyses, the Iranian isolates were divided into two groups. The first major group (A), consists of seven virus isolates, was most closely related to TYLCV‐IL[IL:Reo:86], and relatively divergent from TYLCV‐IR [IR:Ira:98] and ToLCIRV‐[IR:Ira]. However, the Jiroft isolate from group B did not show high similarity with TYLCV‐IR[IR:Ira:98], ToLCIRV‐[IR:Ira], and TYLCV‐IL[IL:Reo:86], suggesting that the isolate may be a divergent variant. The differences are in a range that suggests different strains or species from TYLCV‐IR[IR:Ira:98] and ToLCIRV‐[IR:Ira] are probably associated with tomato yellow leaf curl disease in Iran.     

Characterization of Viruses Infecting Potato Plants from a Single Location in Shetland,an Isolated Scottish Archipelago

Sequence data were obtained from 29 isolates of Potato virus A (PVA), Potato virus S (PVS), Potato virus V (PVV) and Potato virus X (PVX) infecting nine tubers from Shetland, one of the most remote inhabited islands in the United Kingdom. These isolates were sequenced in the coat protein region, as were 29 Scottish mainland isolates of the same four potato virus species, and these 58 isolates were compared to previously published sequence data. This has allowed the characterization of viruses from a relatively isolated location, where there is little production of ware potatoes and no seed potato production. Phylogenetic homogeneity of the Shetland isolates of PVS and PVV was apparent. PVX was more heterogeneous, and Shetland isolates cluster with the Scottish isolates in a group which includes Asian and European isolates. For PVA, the majority of the Shetland and Scottish mainland isolates formed a predominantly Scottish grouping, with the remaining Shetland and Scottish mainland isolates clustering with a previously characterized Scottish isolate. There were three main groups of PVA, of which the Scottish grouping was the only one which did not have a fully characterized representative. To extend the characterization of PVA, the nucleotide sequence of the full polyprotein region encoding all the gene products of an isolate from Shetland was determined.     

Book Review

To study the variability and to identify the species of Begomovirus associated with yellow mosaic disease of blackgram in Andhra Pradesh, India, infected blackgram samples were collected from six districts belonging to three regions of Andhra Pradesh. The total DNA was isolated by modified CTAB method and amplified with coat protein gene-specific primers (RHA-F and AC abut) resulting in 900?bp gene product. The PCR products were cloned, sequenced and deposited in GenBank. The sequence analysis of six clones showed that the size of amplified CP gene of YMV was 920?bp. Based on nucleotide sequence identity of six isolates representing three regions of Andhra Pradesh, the isolates from Rayalaseema and Telangana region are the same variant of YMV (>99.5% identity) and isolate from coastal Andhra is another variant of YMV (>95.4%) when compared with other region isolates. Comparison of CP gene sequence of YMV-TPT isolate with 27 other isolates in database revealed more than 93.2 and 86.2% identity with MYMIV isolates and less than 80 and 64% identity with MYMY isolates that originate from Indian sub-continent and South-East Asia at nucleotide and amino acid level, respectively. Phylogenetic tree based on CP gene sequences of six isolates with other isolates from GenBank formed unique cluster with MYMIV. Hence the YMV infecting blackgram in Andhra Pradesh is caused by MYMIV rather than MYMY as reported in Tamil Nadu which is adjoining state in southern India.     

Low Genetic Diversity of the Coat Protein Gene among Blueberry Red Ringspot Virus Isolates

Blueberry red ringspot virus (BRRSV) isolates have been investigated for genetic diversity. Nucleotide sequences of the coat protein (CP) gene of 19 isolates from Poland, Czech Republic, Slovenia and the United States were analysed. The nucleotide and amino acid sequence identity were 92–100% and 89–100%, respectively. Estimations of the distribution of synonymous and non‐synonymous changes indicated negative selection within the analysed CP gene and confirmed the genetic stability of the virus. At a capsid protein level, our results revealed BRRSV to be distinct from other, recombination‐prone pararetroviruses.     

Sequence Diversity of the Nucleoprotein Gene of Peanut bud necrosis virus Isolates from South India

Peanut bud necrosis virus (PBNV), genus Tospovirus (family Bunyaviridae), is an important virus infecting peanut and other crops in South India. PBNV isolates naturally infecting groundnut, brinjal, tomato, black gram, field bean, cowpea, cotton, jute, taro and Calotropis plants were collected from different regions of South India and characterized. Infection was confirmed by direct antigen‐coating enzyme‐linked immunosorbent assay (DAC‐ELISA) using PBNV‐specific antiserum. The coat protein gene was further amplified using PBNV coat protein‐specific primers. The amplicon (830 bp) was cloned and sequenced; sequence analysis revealed that the N gene shared 93–100% and 95–100% sequence identity with PBNV at the nucleotide and amino acid levels, respectively.