Level Of Nucleotide Sequence Identity Research Articles

Molecular Epidemiology of Klebsiella pneumoniae from Clinical Bovine Mastitis in Northern Area of China, 2018–2019

Klebsiella pneumoniae ( K. pneumonia , KpI) is a predominate inducement of bovine mastitis, which is associated with high mortality and milk yield reduction. However, data is lacking on the molecular characteristics of bovine K. pneumoniae , limiting the risk assessment of its transmission through the food chain. Herein, we investigated the prevalence of K. pneumoniae in 6301 clinical mastitis (CM) milk samples from dairy cattle in northern area of China. In total, 183 K. pneumoniae isolates were recovered, with detection rates of 3.0% and 2.8% in 2018 and 2019, respectively. Like human clinical K. pneumoniae , all CM K. pneumoniae isolates belonged to one of three phylogroups: KpI ( n = 143), Klebsiella. quasipneumoniae subsp. similipneumoniae (KpII-B) ( n = 37), and Klebsiella variicola (KpIII) ( n = 3). We detected the extended-spectrum β-lactamase-encoding genes bla SHV-2a , bla CTX-M-14 , and bla CTX-M-15 , as well as clpC , lpfA , lacI , lacZ , lacY , and the fecABDEIR operon in the KpI isolates, which may contribute to their pathogenicity and host adaptability in cows. The high prevalence of KpI in dairy farms may be problematic, as it showed relatively higher rates of antibiotic resistance and virulence gene carriage than the KpII-B and KpIII isolates. Furthermore, we observed distinct differences in population structure between CM- and human infection-associated KpI isolates, with the genes associated with invasive infection in humans rarely being observed in bovine isolates, indicating that few CM-associated K. pneumoniae isolates pose a threat to human health. Nevertheless, bovine KpII-B isolates shared a high level of nucleotide sequence identity with isolates from human infections and frequently carried the nitrogen-fixation gene nif , suggesting an association between KpII-B isolates from cattle and humans, and plant-derived bacteria.

Genetic characterization and phylogenetic analysis of porcine deltacoronavirus (PDCoV) in Shandong Province, China

Porcine deltacoronavirus (PDCoV) is the etiological agent of acute diarrhoea and vomiting in pigs, threatening the swine industry worldwide. Although several PDCoV studies have been conducted in China, more sequence information is needed to understand the molecular characterization of PDCoV. In this study, the partial ORF1a, spike protein (S) and nucleocapsid protein (N) were sequenced from Shandong Province between 2017 and 2018. The sequencing results for the S protein from 10 PDCoV strains showed 96.7 %–99.7 % nucleotide sequence identity with the China lineage strains, while sharing a lower level of nucleotide sequence identity, ranging from 95.7 to 96.8%, with the Vietnam/Laos/Thailand lineage strains. N protein sequencing analysis showed that these strains showed nucleotide homologies of 97.3%–99.3% with the reference strains. Phylogenetic analyses based on S protein sequences showed that these PDCoV strains were classified into the China lineage. The discontinuous 2 + 3 aa deletions at 400–401 and 758–760 were found in the Nsp2 and Nsp3 coding region in five strains, respectively, with similar deletions having been identified in Vietnam, Thailand, and Laos. Three novel patterns of deletion were observed for the first time in the Nsp2 and Nsp3 regions. Importantly, those findings suggest that PDCoV may have undergone a high degree of variation since PDCoV was first detected in China.

Diversity and recombination analysis of Cotton leaf curl Multan virus: a highly emerging begomovirus in northern India

BackgroundCotton leaf curl disease (CLCuD), caused by begomoviruses in association with satellite molecules, is a major threat to cotton production causing enormous losses to cotton crop in most of the cotton growing countries including Indian subcontinent. In this study, isolates of begomovirus and satellite molecules associated with CLCuD were collected from North India (Haryana, New Delhi). They were amplified employing rolling circle replication mechanism, cloned, sequenced and, their phylogenetic and recombination analysis was performed.ResultsThe five Cotton leaf curl Multan virus (CLCuMuV) isolates investigated in this study showed monopartite organization of the genome typical of Old World begomoviruses. Nucleotide sequence analyses assigned them as the strains of CLCuMuV and were designated as CLCuMuV-SR13, CLCuMuV-SR14, CLCuMuV-ND14, CLCuMuV-ND15 and CLCuMuV-SR15. The genome of CLCuMuV-SR13 shared a highest level of nucleotide sequence identity (98%) with CLCuMuV (JN678804), CLCuMuV-SR14 and CLCuMuV-SR15 exhibited 96% with CLCuMuV (KM096471), while isolates CLCuMuV-ND15 and CLCuMuV-SR15 revealed 96% sequence identity with CLCuMuV (AY765253). The four betasatellite molecules investigated in this study shared 95–99% nucleotide sequence identity with Cotton leaf curl Multan betasatellite (CLCuMB) from India. The betasatellite molecules were designated as CLCuMB-SR13, CLCuMB-SR14, CLCuMB-ND14 and CLCuMB-ND15. Alphasatellite molecules in this study, designated as GLCuA-SR14, GLCuA-ND14 and GLCuA-SR15, revealed 98% identity with Guar leaf curl alphasatellite (GLCuA) reported from Pakistan.ConclusionThe phylogenetic and recombination studies concluded that the isolates of CLCuMuV genomes undertaken in this study have a potential recombinant origin. Remarkably, significant recombination was detected in almost all the genes with contribution of Cotton leaf curl Kokhran Virus (CLCuKoV) in IR, V1, V2, C1, C4 and C5 regions and of CLCuMuV in C2 region of CLCuMuV-SR14. CLCuKoV also donated in C2, C3 regions of CLCuMuV-ND14; V1, V2, C2 and C3 regions of CLCuMuV-ND15 and C1 of CLCuMuV-SR15. Altogether, these observations signify the uniqueness in Indian CLCuMuV isolates showing contribution of CLCuKoV in all the genes. An interesting observation was frequent identification of GLCuA in CLCuD leaf samples.

A Role for Tetracycline Selection in Recent Evolution of Agriculture-Associated Clostridium difficile PCR Ribotype 078.

The increasing clinical importance of human infections (frequently severe) caused by Clostridium difficile PCR ribotype 078 (RT078) was first reported in 2008. The severity of symptoms (mortality of ≤30%) and the higher proportion of infections among community and younger patients raised concerns. Farm animals, especially pigs, have been identified as RT078 reservoirs. We aimed to understand the recent changes in RT078 epidemiology by investigating a possible role for antimicrobial selection in its recent evolutionary history. Phylogenetic analysis of international RT078 genomes (isolates from 2006 to 2014, n = 400), using time-scaled, recombination-corrected, maximum likelihood phylogenies, revealed several recent clonal expansions. A common ancestor of each expansion had independently acquired a different allele of the tetracycline resistance gene tetM Consequently, an unusually high proportion (76.5%) of RT078 genomes were tetM positive. Multiple additional tetracycline resistance determinants were also identified (including efflux pump tet40), frequently sharing a high level of nucleotide sequence identity (up to 100%) with sequences found in the pig pathogen Streptococcus suis and in other zoonotic pathogens such as Campylobacter jejuni and Campylobacter coli Each RT078 tetM clonal expansion lacked geographic structure, indicating rapid, recent international spread. Resistance determinants for C. difficile infection-triggering antimicrobials, including fluoroquinolones and clindamycin, were comparatively rare in RT078. Tetracyclines are used intensively in agriculture; this selective pressure, plus rapid, international spread via the food chain, may explain the increased RT078 prevalence in humans. Our work indicates that the use of antimicrobials outside the health care environment has selected for resistant organisms, and in the case of RT078, has contributed to the emergence of a human pathogen.IMPORTANCEClostridium difficile PCR ribotype 078 (RT078) has multiple reservoirs; many are agricultural. Since 2005, this genotype has been increasingly associated with human infections in both clinical settings and the community. Investigations of RT078 whole-genome sequences revealed that tetracycline resistance had been acquired on multiple independent occasions. Phylogenetic analysis revealed a rapid, recent increase in numbers of closely related tetracycline-resistant RT078 (clonal expansions), suggesting that tetracycline selection has strongly influenced its recent evolutionary history. We demonstrate recent international spread of emergent, tetracycline-resistant RT078. A similar tetracycline-positive clonal expansion was also identified in unrelated nontoxigenic C. difficile, suggesting that this process may be widespread and may be independent of disease-causing ability. Resistance to typical C. difficile infection-associated antimicrobials (e.g., fluoroquinolones, clindamycin) occurred only sporadically within RT078. Selective pressure from tetracycline appears to be a key factor in the emergence of this human pathogen and the rapid international dissemination that followed, plausibly via the food chain.

Independent evolution of porcine reproductive and respiratory syndrome virus 2 with genetic heterogeneity in antigenic regions of structural proteins in Korea.

Porcine reproductive and respiratory syndrome virus (PRRSV) is an economically important pathogen that affects the global swine industry. The continuous evolution of this virus has made control and prevention difficult, which emphasizes the importance of monitoring currently circulating PRRSV strains. In this study, we investigated the genetic characteristics of whole structural genes of 35 PRRSV-2 isolates that circulated between 2012 and 2017 in Korea. Genetic and phylogenetic analysis demonstrated that a recently identified PRRSV-2 shared a relatively low level of nucleotide sequence identity that ranged from 86.2% to 92.8%; however, they were clustered into four distinct Korean field clades, except KU-N1702, in ORF2-7-based phylogeny. KU-N1702 was closely related to the NADC30-like strains that were identified in the USA and China. Amino acid sequence analysis showed that the GP5 neutralizing epitope was conserved among the KU viruses. In contrast, the viruses had genetic mutations in key residues for viral neutralization within GP5 and M. For minor structural proteins, neutralizing epitopes, aa 41-55 of GP2, 61-75 of GP3, and 51-65 of GP4, were variable among the KU viruses. Bioinformatics demonstrated diversifying evolution within the GP2 and GP4 neutralizing epitopes and the emergence of a novel glycosylation site within the GP3and GP4 neutralizing epitopes. Taken together, these data provide evidence that Korean PRRSV-2 evolved independently in Korea, with genetic heterogeneity in antigenic regions of structural proteins.

Molecular characterization of a distinct monopartite begomovirus associated with betasatellites and alphasatellites infecting Pisum sativum in Nepal.

Pea (Pisum sativum) plants exhibiting leaf distortion, yellowing, stunted growth and reduction in leaf size from Rampur, Nepal were shown to be infected by a begomovirus in association with betasatellites and alphasatellites. The begomovirus associated with the disease showed only low levels of nucleotide sequence identity (<91%) to previously characterized begomoviruses. This finding indicates that the pea samples were infected with an as yet undescribed begomovirus for which the name Pea leaf distortion virus (PLDV) is proposed. Two species of betasatellite were identified in association with PLDV. One group of sequences had high (>78%) nucleotide sequence identity to isolates of Ludwigia leaf distortion betasatellite (LuLDB), and the second group had less than 78% to all other betasatellite sequences. This showed PLDV to be associated with either LuLDB or a previously undescribed betasatellite for which the name Pea leaf distortion betasatellite is proposed. Two types of alphasatellites were identified in the PLDV-infected pea plants. The first type showed high levels of sequence identity to Ageratum yellow vein alphasatellite, and the second type showed high levels of identity to isolates of Sida yellow vein China alphasatellite. These are the first begomovirus, betasatellites and alphasatellites isolated from pea.

Complete Genome Sequence of a Novel Wild tomato mosaic virus Isolate Infecting Nicotiana tabacum in China

Virus particles of approximately 740–760 nm in length and 13 nm in diameter were observed from a diseased Nicotiana tabacum (tobacco) plant in Sichuan Province, China. The complete genomic sequence of the virus isolate XC1 was determined to contain 9659 nucleotides without 3′ terminal poly(A) tail. XC1 has a genome typical of members of the genus Potyvirus, encoding a large polyprotein of 3075 amino acids. Putative proteolytic cleavage sites and a number of well characterized functional motifs were identified by sequence comparisons with those of known potyviruses. Sequence comparison revealed that XC1 shared the highest level of nucleotide sequence identity (76.5%) with Wild tomato mosaic virus (WTMV). Phylogenetic analysis showed that XC1 was closely related to the WTMV Guangdong isolate with an identity of 94.3% between CP gene sequence of the two viruses. We thus named XC1 WTMV-XC-1 as a novel isolate of WTMV. The full sequence of WTMV-XC-1 may serve as a basis for future investigations on the gene diversity of WTMV.

First report of a begomovirus associated with betasatellites infecting spinach (Spinacia oleracea) in India

Spinach (Spinacia oleracea) leaves with vein yellowing and reduced leaf size were observed in Rasidpura, Rajasthan Province, India. The complete DNA-A and betasatellite sequences of the virus isolated from infected spinach leaves were determined and comprised 2,753 and 1,367 nucleotides, respectively. The sequence had the highest level of nucleotide sequence identity (88 %) with an isolate of Papaya leaf curl virus and likely represents a new species, for which we propose the name Spinach yellow vein Sikar virus. This is the first report of a Begomovirus associated with satellite molecules infecting the host S. oleracea in India.

Molecular identification and biological characterisation of a begomovirus associated with okra enation leaf curl disease in India

An unusual symptom was noted in okra originating from Haryana state (India) consisting of leaf curl associated with enations. These were distinct from the leaf curl and/or vein yellowing symptoms usually shown by okra. PCR-mediated amplification was used to show the presence of a begomovirus and the complete genome sequences were determined for seven isolates. The sequences showed high levels of nucleotide sequence identity (91.9–99.1 %). In comparison to begomovirus sequences available in the databases the okra sequences showed the highest levels of nucleotide sequence identity (84.5 to 87.1 %) with Mesta yellow vein mosaic virus (MeYVV) and thus were classified as belonging to a novel begomovirus species, tentatively named Okra enation leaf curl virus. In common with the majority of begomoviruses, Okra enation leaf curl virus (OELCuV) was shown to have a recombinant origin. Analysis of the transmission characteristics of a wild-type virus isolate by Bemisia tabaci showed the minimum acquisition access period to be 1 h and the minimum inoculation access period to be 30 min, with female insects transmitting with a greater efficiency than male insects. Under controlled conditions the host range of the virus was shown to be very narrow, limited to two species in the family Malvaceae, okra (Abelmoschus esculentus) and hollyhock (Althaea rosea), and seven in the family Solanaceae.

Multiple NUCLEAR FACTOR Y transcription factors respond to abiotic stress in Brassica napus L.

Members of the plant NUCLEAR FACTOR Y (NF-Y) family are composed of the NF-YA, NF-YB, and NF-YC subunits. In Brassica napus (canola), each of these subunits forms a multimember subfamily. Plant NF-Ys were reported to be involved in several abiotic stresses. In this study, we demonstrated that multiple members of thirty three BnNF-Ys responded rapidly to salinity, drought, or ABA treatments. Transcripts of five BnNF-YAs, seven BnNF-YBs, and two BnNF-YCs were up-regulated by salinity stress, whereas the expression of thirteen BnNF-YAs, ten BnNF-YBs, and four BnNF-YCs were induced by drought stress. Under NaCl treatments, the expression of one BnNF-YA10 and four NF-YBs (BnNF-YB3, BnNF-YB7, BnNF-YB10, and BnNF-YB14) were greatly increased. Under PEG treatments, the expression levels of four NF-YAs (BnNF-YA9, BnNF-YA10, BnNF-YA11, and BnNF-YA12) and five NF-YBs (BnNF-YB1, BnNF-YB8, BnNF-YB10, BnNF-YB13, and BnNF-YB14) were greatly induced. The expression profiles of 20 of the 27 salinity- or drought-induced BnNF-Ys were also affected by ABA treatment. The expression levels of six NF-YAs (BnNF-YA1, BnNF-YA7, BnNF-YA8, BnNF-YA9, BnNF-YA10, and BnNF-YA12) and seven BnNF-YB members (BnNF-YB2, BnNF-YB3, BnNF-YB7, BnNF-YB10, BnNF-YB11, BnNF-YB13, and BnNF-YB14) and two NF-YC members (BnNF-YC2 and BnNF-YC3) were greatly up-regulated by ABA treatments. Only a few BnNF-Ys were inhibited by the above three treatments. Several NF-Y subfamily members exhibited collinear expression patterns. The promoters of all stress-responsive BnNF-Ys harbored at least two types of stress-related cis-elements, such as ABRE, DRE, MYB, or MYC. The cis-element organization of BnNF-Ys was similar to that of Arabidopsis thaliana, and the promoter regions exhibited higher levels of nucleotide sequence identity with Brassica rapa than with Brassica oleracea. This work represents an entry point for investigating the roles of canola NF-Y proteins during abiotic stress responses and provides insight into the genetic evolution of Brassica NF-Ys.

Genetic and antigenic characterization of a newly emerging porcine circovirus type 2b mutant first isolated in cases of vaccine failure in Korea.

This study describes the genetic and antigenic characterization of a newly emerging porcine circovirus type 2b (PCV2b) mutant first isolated in cases of vaccine failure in Korea. The full genome of the PCV2b isolates (SNUVR130689 and SNUVR140004) is 1,767 base pairs (bp) in length. The size of ORF1 is 945 bp, encoding a protein of 314 amino acids (aa), and the size of ORF2 is 705 bp, encoding a protein of 234 aa, which is 1 aa longer than that of the common PCV2 (233 aa). Korean PCV2b mutant strains had higher levels of nucleotide sequence identity to other PCV2b mutant strains (99.7-99.8 %) than to reference PCV2a (94.5-95.0 %) and PCV2b (95.5-96.1 %) strains. There was no difference in antigenic reactivity among PCV2a, PCV2b and PCV2b mutant strains to the polyclonal and monoclonal PCV2a antibodies. PCV2b mutant strains have distinct genetic characteristics but similar antigenic reactivity when compared to common PCV2a and 2b strains.

Recurrent horizontal transfers of Chapaev transposons in diverse invertebrate and vertebrate animals.

Horizontal transfer (HT) of a transposable element (TE) into a new genome is regarded as an important force to drive genome variation and biological innovation. In addition, HT also plays an important role in the persistence of TEs in eukaryotic genomes. Here, we provide the first documented example for the repeated HT of three families of Chapaev transposons in a wide range of animal species, including mammals, reptiles, jawed fishes, lampreys, insects, and in an insect bracovirus. Multiple alignments of the Chapaev transposons identified in these species revealed extremely high levels of nucleotide sequence identity (79–99%), which are inconsistent with vertical evolution given the deep divergence time separating these host species. Rather, the discontinuous distribution amongst species and lack of purifying selection acting on these transposons strongly suggest that they were independently and horizontally transferred into these species lineages. The detection of Chapaev transposons in an insect bracovirus indicated that these viruses might act as a possible vector for the horizontal spread of Chapaev transposons. One of the Chapaev families was also shared by lampreys and some of their common hosts (such as sturgeon and paddlefish), which suggested that parasite–host interaction might facilitate HTs.

A distinct strain of chickpea chlorotic dwarf virus (genus Mastrevirus, family Geminiviridae) identified in cotton plants affected by leaf curl disease

As part of a study to determine the diversity of whitefly-transmitted viruses (genus Begomovirus, family Geminiviridae) associated with cotton leaf curl disease in Pakistan, leaf samples from cotton plants showing typical leaf curl disease symptoms were collected in various locations of Punjab province. Sequence analysis of full-length virus clones (~2.7 kb) showed plants to be infected with the begomovirus cotton leaf curl Burewala virus, the only virus identified in cotton in the Punjab since 2001. Surprisingly, a second virus, the leafhopper-transmitted chickpea chlorotic dwarf virus (CpCDV) of the genus Mastrevirus (family Geminiviridae), was identified in a small number of plants. The sequences of four CpCDV isolates from cotton originating from geographically distinct areas in Punjab were obtained. Analysis of the sequences showed them to represent a distinct, newly identified strain of CpCDV with the highest levels of nucleotide sequence identity to isolates of CpCDV strains C and D that have been identified previously in Pakistan. CpCDV has not been identified previously in cotton. The significance of this finding is discussed.

Association of Tomato leaf curl Joydebpur virus and a betasatellite with leaf curl disease of eggplant

Leaf samples (five) from brinjal/eggplant fields showing upward leaf curling symptoms were collected from Varanasi, Uttar Pradesh state, India. The full length genome of begomovirus and associated betasatellite were amplified by PCR, cloned and sequenced. Sequences of homologous DNA-A and its betasatellite in all samples were the same. The samples failed to amplify DNA-B, suggesting that the begomovirus associated with leaf curl disease of eggplant was monopartite. The complete genome (homologous of DNA-A) consists of 2758 nts, whereas the betasatellite has 1352 nts and the genome organization is typical of Old World begomoviruses. The sequence analysis showed high levels of nucleotide sequence identity (79.8–91.7%) of virus with Tomato leaf curl Joydebpur virus (ToLCJoV) infecting chilli in India, suggesting it as a strain of ToLCJoV based on the current ICTV taxonomic criteria for begomovirus strain demarcation. However, the betasatellite associated was identified as a variant of Tomato leaf curl Bangladesh betasatellite (ToLCBDB), with which it shared highest sequence identity of 84.7–94.8%. Phylogenetic analyses of the genome further supported the above results. The recombination analyses of both genome and betasatellite showed that a major part of genome sequences are derived from begomoviruses (ToLCJoV, ChiLCuV, AEV) infecting chilli, tomato, ageratum and betasatellite from PaLCuB as the foremost parents in evolution, suggesting this as a new recombinant virus strain. This is the first report of a monopartite begomovirus and a betasatellite molecule associated with the leaf curl disease of eggplant.

A divergent insect-specific flavivirus that causes overt cytopathic effect in a mosquito cell-line

The genus Flavivirus (Flaviviridae) includes over seven dozen known enveloped viruses with ssRNA genomes, the evolution, geographic dispersion and epidemiology of which seems to have been shaped both by environmental constraints (involving ecological factors and human activities), and by their replication in vertebrate and invertebrate hosts. Most bona-fide flaviviruses have been classified as mosquito or tick-borne viruses, although for some no known invertebrate vector has yet been found. Over time, a divergent cluster including viral agents that seem to be specific of insect (Insect-Specific Flaviviruses-ISF) has been associated with the genus. The classification of ISF as flaviviruses is supported by their genomic organization, protein hydropathy plots, conserved polyprotein cleavage sites and enzyme domains, which are similar to those of classical flaviviruses. However, they are antigenically distinct, and share approximately the same level of nucleotide sequence identity with other members of the genus, as when compared to the members of the two other genera in the Flaviviridae family.This work reports the initial characterization, including near full-length sequence analysis, of an ISF which seems to form a divergent lineage within the ISF radiation (Figure 1), as indicated by phylogenetic analysis based on ac multiple sequence alignment of the NS5 flavivirus coding sequence. This virus, tentatively designated OCFV (Ochlerotatus caspius flavivirus) was isolated from clarified macerates of a pool of Aedes (Ochlerotatus) caspius (Pallas, 1771) adult mosquitoes (lab code number 174) using the Ae. albopictus-derived C6/36 cell line. The mosquitoes from which OCFV was isolated were collected using CDC-traps baited with CO2, and are amongst those found in high densities in the coastal, and estuarine, districts of Setúbal and Faro. Detection of viral genomes by RT-PCR using RNA directly extracted from supernatants of C6/36 infected cultures, collected 24h post-infection, indicated that the virus replicates rapidly in these cells. Nevertheless, but as expected for an ISF, it does not replicate in Vero cells. Unexpectedly, unlike most ISF OCFV seems to cause overt cytopathic effect in C6/36 cells, which rapidly detach from a solid support and round-up soon (24-48h) after infection. Electron-microscope analysis of thin-sections of C6/36 cells at 48h post-infection with OCFV revealed nuclear hyperplasy, and an evident enlargement of the intracisternal space of the nuclear envelope, which is filled by multiple sized vesicles. In some cells, a complex network of apparent membrane trabeculae was also clearly evident (Figure 2A). Viral particles seem to assemble at the endoplasmatic reticulum, from which viruses reach the cell surface by vesicular transport (Figure 2B). Unexpectedly for a flavivirus, but as previously observed, viral particles also seem to gemulate directly from the cytoplasmic membrane (Figure 2C).

Genetic diversity and distribution of a distinct strain of Chili leaf curl virus and associated betasatellite infecting tomato and pepper in Oman

Tomato and pepper are widely grown in Oman for local consumption. A countrywide survey was conducted during 2010–2011 to collect samples and assess the diversity of begomoviruses associated with leaf curl disease of tomato and pepper. A virus previously only identified on the Indian subcontinent, chili leaf curl virus (ChLCV), was found associated with tomato and pepper diseases in all vegetable grown areas of Oman. Some of the infected plant samples were also found to contain a betasatellite. A total of 19 potentially full-length begomovirus and eight betasatellite clones were sequenced. The begomovirus clones showed >96% nucleotide sequence identity, showing them to represent a single species. Comparisons to sequences available in the databases showed the highest levels of nucleotide sequence identity (88.0–91.1%) to isolates of the “Pakistan” strain of ChLCV (ChLCV-PK), indicating the virus from Oman to be a distinct strain, for which the name Oman strain (ChLCV-OM) is proposed. An analysis for recombination showed ChLCV-OM likely to have originated by recombination between ChLCV-PK (the major parent), pepper leaf curl Lahore virus and a third strain of ChLCV. The betasatellite sequences obtained were shown to have high levels of identity to isolates of tomato leaf curl betasatellite (ToLCB) previous shown to be present in Oman. For the disease in tomato Koch's postulates were satisfied by Agrobacterium-mediated inoculation of virus and betasatellites clones. This showed the symptoms induced by the virus in the presence of the betasatellite to be enhanced, although viral DNA levels were not affected. ChLCV-OM is the fourth begomovirus identified in tomato in Oman and the first in Capsicum. The significance of these findings is discussed.

A new, previously undescribed monopartite begomovirus infecting Premna serratifolia in Vietnam

The complete genome sequence of a monopartite begomovirus isolate infecting Creek Premna (Premna serratifolia L.) plants that exhibited leaf curl, vein swelling, and enation symptoms in Nha Trang, Vietnam, was cloned and sequenced. It comprises 2,753 nucleotides (JQ793786) and has a typical organization of begomoviruses DNA-A with AV1 and AV2 open reading frames (ORFs) in the viral-sense strand and AC1, AC2, AC3, AC4 and AC5 ORFs in the complementary-sense strand. The full-length genome sequence of the isolate (clone VN7) shared the highest level of nucleotide sequence identity (83 %) with the isolate IN:Pusa:Tb:10 of tobacco leaf curl Pusa virus (HQ180391). The phylogenetic relationship of VN7 to other begomoviruses was also investigated. VN7 grouped most closely with a clade containing begomoviruses from China, India and Japan. According to the current taxonomic criteria for the genus Begomovirus, family Geminiviridae, the isolate VN7 represents a new species, herein named "Premna leaf curl virus" (PrLCV).

Molecular identification of Ageratum enation virus (AEV) associated with leaf curl disease of tomato(Solanum lycopersicum) in India

Leaf samples of tomato plants showing severe leaf curl symptoms were collected from Pantnagar, Uttarakhand state of India. Full-length clones of a monopartite begomovirus were isolated and complete genome sequence was determined. Genome organization of this virus was found to be similar to those of other old world begomoviruses. Neither alphasatellite nor DNA B component was detected. The DNA-A molecule (2753 nt) sequences showed the highest levels of nucleotide sequence identity of 92.9 to 98.7 % with the DNA-A of Ageratum enation virus (AEV) isolates and less identity of 77.1 to 86.3 % with known tomato-infecting begomoviruses from India. The incidence of AEV in protected cultivation was upto 68.5 % noticed.

First report of Cotton leaf curl Burewala virus infecting Ricinus communis.

Castor bean (Ricinus communis; family Euphorbiaceae) is cul- tivated for the production of oil and as an ornamental plant throughout tropical regions. Leaf samples from castor bean plants with leaf curl and vein thickening were collected from ar- eas around Okara (Pakistan) in 2011. PCR amplification using di- agnostic primers showed the presence of a begomovirus and sub- sequently the specific primer pair (BurNF 5’-CCATGGTTGTG- GCAGTTGATTGACAGATAC-3’; BurNR 5’-CCATGGATT CACGCACAGGGGAACCC-3’) was used to amplify and clone the whole genome of the virus. The complete nucleotide se- quence was determined to be 2,759 nt (accession No. HE985227). Alignments showed the highest levels of nucleotide sequence identity (98.8%) with Cotton leaf curl Burewala virus (CLCuBuV; accession No. JF416947). The virus in castor beans lacks on intact C2 gene, as is typical of CLCuBuV in cotton (Am- rao et al., 2010). An amplification product of ca. 1.4 kb was ob- tained in PCR with primers for betasatellites (Briddon et al., 2002) and the complete nucleotide sequence of a clone was deter- mined to be 1373 nt (HE985228). The sequence showed 96.3% nucleotide sequence identity to the recombinant Cotton leaf curl Multan betasatellite (CLCuMB; JF502389). This is the first re- port of CLCuBuV and its betasatellite infecting castor bean, showing this plant species as an alternate host of the virus.

Complete nucleotide sequences of two begomoviruses infecting Madagascar periwinkle (Catharanthus roseus) from Pakistan

Though Catharanthus roseus (Madagascar periwinkle) is an ornamental plant, it is famous for its medicinal value. Its alkaloids are known for anti-cancerous properties, and this plant is studied mainly for its alkaloids. Here, this plant has been studied for its viral diseases. Complete DNA sequences of two begomoviruses infecting C. roseus originating from Pakistan were determined. The sequence of one begomovirus (clone KN4) shows the highest level of nucleotide sequence identity (86.5%) to an unpublished virus, chili leaf curl India virus (ChiLCIV), and then (84.4% identity) to papaya leaf curl virus (PaLCV), and thus represents a new species, for which the name "Catharanthus yellow mosaic virus" (CYMV) is proposed. The sequence of another begomovirus (clone KN6) shows the highest level of sequence identity (95.9% to 99%) to a newly reported virus from India, papaya leaf crumple virus (PaLCrV). Sequence analysis shows that KN4 and KN6 are recombinants of Pedilanthus leaf curl virus (PedLCV) and croton yellow vein mosaic virus (CrYVMV).