ABSTRACT
Novel coronavirus (nCoV) namely "SARS-CoV-2" is being found responsible for current PANDEMIC commenced from Wuhan (China) since December 2019 and has been described with epidemiological linkage to China in about 221 countries and territories until now. In this study we have characterized the genetic lineage of SARS-CoV-2 and report the recombination within the genus and subgenus of coronaviruses. Phylogenetic relationship of thirty nine coronaviruses belonging to its four genera and five subgenera was analyzed by using the Neighbor-joining method using MEGA 6.0. Phylogenetic trees of full length genome, various proteins (spike, envelope, membrane and nucleocapsid) nucleotide sequences were constructed separately. Putative recombination was probed via RDP4. Our analysis describes that the "SARS-CoV-2" although shows great similarity to Bat-SARS-CoVs sequences through whole genome (giving sequence similarity 89%), exhibits conflicting grouping with the Bat-SARS-like coronavirus sequences (MG772933 and MG772934). Furthermore, seven recombination events were observed in SARS-CoV-2 (NC_045512) by RDP4. But not a single recombination event fulfills the high level of certainty. Recombination mostly housed in spike protein genes than rest of the genome indicating breakpoint cluster arises beyond the 95% and 99% breakpoint density intervals. Genetic similarity levels observed among "SARS-CoV-2" and Bat-SARS-CoVs advocated that the latter did not exhibit the specific variant that cause outbreak in humans, proposing a suggestion that "SARS-CoV-2" has originated possibly from bats. These genomic features and their probable association with virus characteristics along with virulence in humans require further consideration.
O novo coronavírus (nCoV), nomeadamente "SARS-CoV-2", foi considerado responsável pela pandemia atual iniciada em Wuhan (China) desde dezembro de 2019 e foi descrito com ligação epidemiológica à China em cerca de 221 países e territórios até agora. Neste estudo, caracterizamos a linhagem genética do SARS-CoV-2 e relatamos a recombinação dentro do gênero e subgênero dos coronavírus. A relação filogenética de 39 coronavírus pertencentes a seus quatro gêneros e cinco subgêneros foi analisada usando o método de Neighbour-joining usando MEGA 6.0. Árvores filogenéticas do genoma de comprimento total, várias proteínas (espícula, envelope, membrana e nucleocapsídeo), sequências de nucleotídeos foram construídas separadamente. A recombinação putativa foi testada via RDP4. Nossa análise descreve que o "SARS-CoV-2", embora mostre grande semelhança com as sequências de Bat-SARS-CoVs em todo o genoma (dando semelhança de sequência de 89%), exibe agrupamento conflitante com as sequências de coronavírus do tipo Bat-SARS (MG772933 e MG772934) Além disso, sete eventos de recombinação foram observados em SARS-CoV-2 (NC045512) por RDP4. Mas nem um único evento de recombinação preenche o alto nível de certeza. A recombinação está alojada mais em genes de proteína de pico, principalmente, do que no resto do genoma, indicando que o cluster de ponto de interrupção surge além dos intervalos de densidade de ponto de interrupção de 95% e 99%. Os níveis de similaridade genética observados entre "SARS-CoV-2" e Bat-SARS-CoVs defendem que o último não exibe a variante específica que causa surto em humanos, sugerindo que "SARS-CoV-2" tenha se originado possivelmente de morcegos. Essas características genômicas e sua provável associação com as características do vírus, juntamente com a virulência em humanos, requerem uma consideração mais aprofundada.
Subject(s)
Phylogeny , Severe acute respiratory syndrome-related coronavirus/geneticsABSTRACT
English Lavender (Lavandula angustifolia Mill.) has been considered an alternative crop to tobacco in Hatay Province of Turkey because of its great production potential. As a new, nonnative crop, diseases and pests of lavender are not well known in the region. In summer 2010, root rot symptoms were observed with an average incidence of 45% in a 2-year-old lavender nursery in Hatay. Initial symptoms of chlorosis and wilting were followed by progressive death of the plants starting at the shoot tips. An oomycetous species was isolated consistently from the stems and roots of diseased plants on potato dextrose agar (PDA) amended with several fungicides and antibiotics. The culture of the single-zoospore isolate produced arachnoid growth on PDA. Chlamydospores of the isolate were approximately 35.0 µm in diameter. The isolate produced papillate, caduceus, hyaline sporangia in different shapes ranging from spherical to ellipsoidal. Sporangia with short pedicels (5 µm) were 35.0 to 57.5 × 27.5 to 42.5 µm with a length/width ratio of 1.2 to 1.8. On the basis of symptoms and morphology of the organism, the pathogen was identified as Phytophthora palmivora (E.J. Butler) E.J. Butler (3). Identification of the isolate was also confirmed by comparison of the sequence of the nuclear ribosomal internal transcribed spacer (ITS) region with reference isolates. The ITS region of rDNA was amplified by PCR with primers ITS1/ITS4 and sequenced (GenBank Accession No. JF777117). BLAST analysis of the sequence obtained showed a 99 to 100% homology with P. palmivora. Pathogenicity tests were performed on 12 greenhouse-grown 2-year-old lavender plants in 2-liter pots containing a steamed sand/peat/soil mixture. After rooting, the plants were inoculated by placing mycelial plugs from a 1-week-old culture of the isolate into an incision made at the base of each plant. Control plants were treated with plugs of sterile PDA. Inoculated plants were kept at 27°C for 5 weeks. Similar symptoms developed on the inoculated plants within 4 weeks after inoculation. P. palmivora was consistently reisolated from symptomatic plants. No symptoms developed on control plants. P. palmivora attacks a wide range of crop species including lavenders (1,2,4). To our knowledge, this is the first report of a root rot caused by P. palmivora, a new pathogen of lavender in Turkey. References: (1) S. Davino et al. Plant Dis. 86:561, 2002. (2) D. C. Erwin and O. K. Ribeiro. Phytophthora Diseases Worldwide. The American Phytopathological Society, St Paul, MN, 1996. (3) D. J. Stamps. C.M.I. Descr. Fungi Bact. 831:1, 1985. (4) G. A. Torres et al. Plant Dis. 94:1163, 2010.
