[ES] En este trabajo, se detectó por primera vez el virus de la clorosis amarilla de las cucurbitáceas (CCYV, cucurbit chlorotic yellows virus) infectando pepino y calabacín en Argelia. El CCYV (género Crinivirus, familia Closteroviridae) forma parte de un complejo de virus transmitidos por la mosca blanca Bemisia tabaci, que causan enfermedades de amarillamiento en las cucurbitáceas. Se obtuvo la secuencia completa del gen que codifica la proteína de la cápside (CP) y secuencias parciales de los genes RdRp y Hsp70 de un aislado argelino de CCYV y se compararon con las secuencias presentes en las bases de datos. ToLCNDV (género Begomovirus, familia Geminiviridae) también se detectó por primera vez infectando plantas de cucurbitáceas en Argelia. ToLCNDV es un begomovirus bipartito que causa importantes epidemias en cultivos económicamente valiosos de las familias Solanaceae y Cucurbitaceae. Se obtuvo la secuencia genómica completa de un aislado de ToLCNDV de pepino de Argelia (ToLCNDV-Biskra). La alineación de las secuencias de nucleótidos de los segmentos de ADN-A y ADN-B reveló identidades del 98,7% y 97,6%, respectivamente, con los segmentos de los aislados de la cuenca del Mediterráneo, mientras que la identidad con los aislados de Asia fue de aproximadamente del 90% y 81%. Los aislados presentes en la cuenca mediterránea son monofiléticos y forman un único grupo, mientras que los aislados de la cepa asiática presentan una mayor variabilidad genética y forman varios grupos. Todos los aislados de Argelia mostraron una variación de nucleótidos muy baja. Solo se observó una duplicación de 17 nucleótidos en el ADNB de algunos aislados que daría lugar a una proteína de movimiento 53 aminoácidos más larga, aunque la funcionalidad de esta supuesta proteína es desconocida. A pesar de esa duplicación, no se detectaron eventos de recombinación entre los aislados secuenciados. La baja variación genética podría dificultar la detección de recombinantes. / [CA] En aquest treball, es va detectar per primera vegada el virus de la clorosi groga de les cucurbitàcies (CCYV, cucurbit chlorotic yellows virus) infectant cogombres i carabassetes a Algèria. El CCYV (gènere Crinivirus, família Closteroviridae) forma part d'un complex de virus transmesos per mosca blanca que causen malalties d'esgrogueïment en les cucurbitàcies. Es va realitzar la determinació de la seqüència completa de la proteïna de la càpsida (CP) i seqüències parcials dels gens RdRp i Hsp70 d'un aïllat algerià de CCYV i es van comparar amb les seqüències publicades en les bases de dades. ToLCNDV (gènere Begomovirus, família Geminiviridae) també va ser detectat per primera vegada infectant plantes de cucurbitàcies a Algèria. ToLCNDV és un begomovirus bipartit que causa importants epidèmies en cultius econòmicament valuosos de les famílies Solanaceae i Cucurbitaceae. Es va obtindre la seqüència genòmica completa d'un aïllat de ToLCNDV de cogombre d'Algèria (ToLCNDV-Biskra). La alineació de les seqüències de nucleòtids del segments d'ADN-A i ADN-B van mostrar identitats del 98.7% i 97.6%, respectivament, amb els segments corresponents dels aïllats de la conca del Mediterrani, mentre que la identitat amb els aïllats d'Àsia va ser d'aproximadament el 90% i 81%. Els aïllats presents a la conca del Mediterrani són monofilètics i formen un únic grup, mentre que els aïllats de la soca asiàtica presenten una major variabilitat genètica i s'agrupen en diversos grups. Tots els aïllats algerians van mostrar una variació de nucleòtids molt baixa. Només es va observar una duplicació de 17 nucleòtids en d'ADNB d'alguns aïllats que lonaria lloc a una proteïna de moviment 53 aminoàcids més llarga, encara que la funcionalitat d¿aquesta suposada proteïnaés desconeguda. A més, malgrat la duplicació, no es van detectar esdeveniments de recombinació entre els aïllats seqüenciats. La baixa variació genètica podria dificultar la detecció de recombinants. / [EN] In this work, cucurbit chlorotic yellows virus (CCYV) was first detected infecting cucumber and zucchini in Algeria. CCYV (genus Crinivirus, family Closteroviridae) is part of a complex of whitefly-transmitted viruses that cause yellowing disease in cucurbits. Determination of the complete CP, and partial RdRp and Hsp70 sequences of an Algerian CCYV isolate was conducted to unveil the evolutionary relationships with the published isolates in databases. The phylogenetic analysis showed that the Algerian isolate clustered into group I together with the majority of the reported CCYV isolates. ToLCNDV (genus Begomovirus, family Geminiviridae) was also detected for the first time infecting cucurbit plants in Algeria. ToLCNDV is a bipartite begomovirus that causes major epidemics in economically valuable crops. epidemics in economically valuable crops of the Solanaceae and Cucurbitaceae families. Cucurbitaceae. The complete genome sequence of a ToLCNDV isolate from Algerian cucumber (ToLCNDV from Algeria (ToLCNDV-Biskra) was obtained. Alignment of the nucleotide sequences of the A-DNA and B-DNA segments revealed the identity of the DNA-A and DNA-B segments revealed identities of 98.7% and 97.6%, respectively, with the segments of the isolates from the Algerian segments of the Mediterranean basin isolates, while the identity with the Asian isolates was approximately 90% and 81%, respectively. was approximately 90% and 81%. The isolates present in the Mediterranean Basin are monophyletic and form a single monophyletic and form a single cluster, whereas isolates from the Asian strain have a higher genetic variability and form several clusters. genetic variability and form several clusters. All isolates from Algeria showed very low nucleotide variation. very low nucleotide variation. Only a duplication of 17 nucleotides was observed in the B-DNA of some isolates which would result in a longer 53 amino acid movement protein, although the functionality of this putative protein is unknown. Despite this duplication, no recombination events recombination events were detected among the sequenced isolates. The low genetic variation could hinder the detection of recombinants. / This work was supported by the following grants: Programa de Ayudas de Investigación y Desarrollo (PAID-11-21) of the Universitat Politècnica de València; PID2021-125787OR-C33 funded by MCIN/AEI/10.13039/501100011033 and by “ERDF A way of making Europe”; and PROMETEO project for excellence groups 2021/072 Conselleria de Innovación, Universidades, Ciencia y Sociedad Digital (Generalitat Valenciana). / Kheireddine, A. (2023). First report of Cucurbit Chlorotic Yellows Virus (CCYV) and Tomato Leaf Curl New Delhi Virus (ToLCNDV) in Algeria and Lack of Evidence for Seed Transmission of ToLCNDV in Melon and Pumpkin [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/196840

The cacao swollen shoot disease of Theobroma cacao L. (cacao) is caused by Cacao swollen shoot virus (CSSV; genus, Badnavirus, family, Caulimoviridae). The virus is endemic to West Africa, where it poses a serious threat to cocoa production. Despite efforts to control CSSV spread by replacement of infected trees with tolerant cultivars and mealybug vector management, the disease is widespread in West Africa. In Trinidad, leaf mosaic and vein-banding symptoms have been observed in cacao plants in the field since the 1940s, and recently at the International Cocoa Genebank (ICGT), a custodian of cacao germplasm resources. The strains A and B of the suspect Cacao Trinidad virus (CTV) caused the symptoms, and were thought to be related to CSSV, however, viral causality was not demonstrated, until now. To develop molecular detection methods for CSSV in infected plants, polymerase chain reaction (PCR) amplification of eight regions of the CSSV genome was implemented. The PCR results showed variable amplification frequencies of 19 - 42% at each region, for 124 isolates collected in Cote d'Ivoire and Ghana. Pairwise nucleotide (nt) analyses of the eight regions showed 66-99% shared identities, indicating that CSSV isolates exhibit extensive variability with respect to primer design. The results provided preliminary evidence for the existence of a CSSV complex consisting of four divergent species. The full length genome of 14 CSSV isolates from cacao determined using the Illumina HiSeq platform showed 70-99% shared nt identities. The pairwise nt identities placed CSSV sequences into a group of four distinct species, one of which represented a previously undescribed species. Moreover, the full-length genomes grouped phylogenetically with other badnaviruses and revealed two CSSV subclades with three types of genome arrangements; four, five or six open reading frames (ORFs). Predicted functional protein domains were conserved on each ORF. Two distinct, full-length genome sequences were determined using the Illumina HiSeq platform, from DNA isolated from cacao leaves exhibiting distinct symptoms in Trinidad. The sequences were validated by PCR-amplification and sequencing of overlapping viral genome fragments. Pairwise nt analysis indicated that each genome shared 52-62% nt identities with CSSV and other badnaviruses, suggesting that the two are distinct species. Phylogenetic analysis indicated that the two sequences are not strains of the same virus, as supposed, but they represent two previously undescribed species in the genus, Badnavirus, and they have been named Cacao mild mosaic virus (CaMMV) and Cacao yellow-vein-banding virus (CYVBV). Despite sharing the same host and causing similar symptoms in cacao, CSSV, CaMMV, and CYVBV are phylogenetically-distinct species. The discovery of a CSSV species complex and the identification of three new cacao-infecting badnavirus species will support the development of molecular detection tools using the partial and complete genome sequences determined in this study. The ability to develop validated molecular tools for the detection of CSSV and related viruses, CaMMV and CYVBV, in cacao will aid quarantine efforts and safe movement of germplasm from the ICGT in Trinidad to cacao-growing countries, worldwide. Also, molecular diagnostics tools are expected to be useful in efforts underway to develop CSSV-resistant planting material for countries in West Africa, which are currently experiencing continued or new disease outbreaks.