Genomic and eco-epidemiological investigations in Uruguay reveal local Chikungunya virus transmission dynamics during its expansion across the Americas in 2023.

Uruguay experienced its first Chikungunya virus outbreak in 2023, resulting in a significant burden to its healthcare system. We conducted analysis based on real-time genomic surveillance (30 novel whole genomes) to offer timely insights into recent local transmission dynamics and eco-epidemiological factors behind its emergence and spread in the country.

Genomics-based timely detection of Dengue Virus type I genotypes I and V in Uruguay.

We report the first whole-genome sequences of Dengue Virus type I genotypes I and V from Uruguay, including the first cases ever reported in the country. Through timely genomic analysis, identification of these genotypes was possible, aiding in timely public health responses and intervention strategies to mitigate the impact of dengue outbreaks.

Genomic and eco-epidemiological investigations in Uruguay reveal local Chikungunya virus transmission dynamics during its expansion across the Americas in 2023.

Uruguay experienced its first Chikungunya virus outbreak in 2023, resulting in a significant burden to its healthcare system. We conducted analysis based on real-time genomic surveillance (30 novel whole genomes) to offer timely insights into recent local transmission dynamics and eco-epidemiological factors behind its emergence and spread in the country.

Emergence and spreading of the largest SARS-CoV-2 deletion in the Delta AY.20 lineage from Uruguay.

The genetic variability of SARS-CoV-2 (genus Betacoronavirus, family Coronaviridae) has been scrutinized since its first detection in December 2019. Although the role of structural variants, particularly deletions, in virus evolution is little explored, these genome changes are extremely frequent. They are associated with relevant processes, including immune escape and attenuation. Deletions commonly occur in accessory ORFs and might even lead to the complete loss of one or more ORFs. This scenario poses an interesting question about the origin and spreading of extreme structural rearrangements that persist without compromising virus viability. Here, we analyze the genome of SARS-CoV-2 in late 2021 in Uruguay and identify a Delta lineage (AY.20) that experienced a large deletion (872 nucleotides according to the reference Wuhan strain) that removes the 7a, 7b, and 8 ORFs. Deleted viruses coexist with wild-type (without deletion) AY.20 and AY.43 strains. The Uruguayan deletion is like those identified in Delta strains from Poland and Japan but occurs in a different Delta clade. Besides providing proof of the circulation of this large deletion in America, we infer that the 872-deletion arises by the consecutive occurrence of a 6-nucleotide deletion, characteristic of delta strains, and an 866-nucleotide deletion that arose independently in the AY.20 Uruguayan lineage. The largest deletion occurs adjacent to transcription regulatory sequences needed to synthesize the nested set of subgenomic mRNAs that serve as templates for transcription. Our findings support the role of transcription sequences as a hotspot for copy-choice recombination and highlight the remarkable dynamic of SARS-CoV-2 genomes.

Consecutive deletions in a unique Uruguayan SARS-CoV-2 lineage evidence the genetic variability potential of accessory genes.

Deletions frequently occur in the six accessory genes of SARS-CoV-2, but most genomes with deletions are sporadic and have limited spreading capability. Here, we analyze deletions in the ORF7a of the N.7 lineage, a unique Uruguayan clade from the Brazilian B.1.1.33 lineage. Thirteen samples collected during the early SARS-CoV-2 wave in Uruguay had deletions in the ORF7a. Complete genomes were obtained by Illumina next-generation sequencing, and deletions were confirmed by Sanger sequencing and capillary electrophoresis. The N.7 lineage includes several individuals with a 12-nucleotide deletion that removes four amino acids of the ORF7a. Notably, four individuals underwent an additional 68-nucleotide novel deletion that locates 44 nucleotides downstream in the terminal region of the same ORF7a. The simultaneous occurrence of the 12 and 68-nucleotide deletions fuses the ORF7a and ORF7b, two contiguous accessory genes that encode transmembrane proteins with immune-modulation activity. The fused ORF retains the signal peptide and the complete Ig-like fold of the 7a protein and the transmembrane domain of the 7b protein, suggesting that the fused protein plays similar functions to original proteins in a single format. Our findings evidence the remarkable dynamics of SARS-CoV-2 and the possibility that single and consecutive deletions occur in accessory genes and promote changes in the genomic organization that help the virus explore genetic variations and select for new, higher fit changes.

Genome Sequences of SARS-CoV-2 P.1 (Variant of Concern) and P.2 (Variant of Interest) Identified in Uruguay.

Two severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants associated with increased transmission and immune evasion, P.1 and P.2, emerged in Brazil and spread throughout South America. Here, we report genomes corresponding to these variants that were recently detected in Uruguay. These P.1 and P.2 genomes share all substitutions that are characteristic of these variants.

Multiple gene genealogies reveal important relationships between species of Phaeophleospora infecting Eucalyptus leaves.

The majority of Eucalyptus species are native to Australia, but worldwide there are over 3 million ha of exotic plantations, especially in the tropics and subtropics. Of the numerous known leaf diseases, three species of Phaeophleospora can cause severe defoliation of young Eucalyptus; Phaeophleospora destructans, Phaeophleospora eucalypti and Phaeophleospora epicoccoides. Phaeophleospora destructans has a major impact on seedling survival in Asia and has not, as yet, been found in Australia where it is considered a serious threat to the biosecurity of native eucalypts. It can be difficult to distinguish Phaeophleospora species based on symptoms and micromorphology and an unequivocal diagnostic tool for quarantine purposes would be useful. In this study, a multiple gene genealogy of these Phaeophleospora species and designed specific primers has been constructed to detect their presence from leaf samples. The phylogenetic position of these Phaeophleospora species within Mycosphaerella was established. They are closely related to each other and to other important Eucalyptus pathogens, Mycosphaerella nubilosa, Mycosphaerella cryptica and Colletogloeopsis zuluensis. The specific primers developed can now be used for diagnostic and screening purposes within Australia.

Multi-gene phylogenies and phenotypic characters distinguish two species within the Colletogloeopsis zuluensis complex associated with Eucalyptus stem cankers.

Colletogloeopsis zuluensis, previously known as Coniothyrium zuluense, causes a serious stem canker disease on Eucalyptus spp. grown as non-natives in many tropical and sub-tropical countries. This stem canker disease was first reported from South Africa and it has subsequently been found on various species and hybrids of Eucalyptus in other African countries as well as in countries of South America and South-East Asia. In previous studies, phylogenetic analyses based on DNA sequence data of the ITS region suggested that all material of C. zuluensis was monophyletic. However, the occurrence of the fungus in a greater number of countries, and analyses of DNA sequences with additional isolates has challenged the notion that a single species is involved with Coniothyrium canker. The aim of this study was to consider the phylogenetic relationships amongst C. zuluensis isolates from all available locations and to support these analyses with phenotypic and morphological comparisons. Individual and combined phylogenies were constructed using DNA sequences from the ITS region, exons 3 through 6 of the beta-tubulin gene, the intron of the translation elongation factor 1-alpha gene, and a partial sequence of the mitochondrial ATPase 6 gene. Both phylogenetic data and morphological characteristics showed clearly that isolates of C. zuluensis represent at least two taxa. One of these is C. zuluensis as it was originally described from South Africa, and we provide an epitype for it. The second species occurs in Argentina and Uruguay, and is newly described as C. gauchensis. Both fungi are serious pathogens resulting in identical symptoms. Recognising them as different species has important quarantine consequences.

First record of Colletogloeopsis zuluense comb. nov., causing a stem canker of Eucalyptus in China.

Coniothyrium zuluense causes a serious canker disease of Eucalyptus in various parts of the world. Very little is known regarding the taxonomy of this asexual fungus, which was provided with a name based solely on morphological characteristics. In this study we consider the phylogenetic position of C. zuluense using DNA-based techniques. Distance analysis using 18S and ITS regions revealed extensive sequence divergence relative to the type species of Coniothyrium, C. palmarum and species of Paraconiothyrium. Coniothyrium zuluense was shown to be an anamorph species of Mycosphaerella, a genus that includes a wide range of Eucalyptus leaf and stem pathogens. Within Mycosphaerella it clustered with taxa having pigmented, verruculose, aseptate conidia that proliferate percurrently and sympodially from pigmented conidiogenous cells arranged in conidiomata that vary from being pycnidial to acervular. The genus Colletogloeopsis is emended to include species with pycnidial conidiomata, and the new combination Colletogloeopsis zuluense is proposed. This is also the first report of the pathogen from China where it is associated with stem cankers on Eucalyptus urophylla.

Caracterización genotípica de 80 cepas del género Mycobacterium en Uruguay / Genotype characterization of 80 strains of Mycobacterium in Uruguay

Los métodos tradicionales de identificación fenotípica del género Mycobacterium son lentos y poco sensibles, requiriéndose cuatro a seis semanas para lograr un diagnóstico apropiado a partir de un cultivo positivo. Los procedimientos moleculares han permitido acortar este período, obteniéndose resultados entre las 36 a 72 horas. En nuestro país la incidencia de M. tuberculosis es baja y no existen datos acerca de con qué frecuencia los casos diagnosticados como tuberculosis pulmonar son en realidad causados por Mycobacterium no tuberculosis (MNT), normalmente saprofitas. Desde el punto de vista terapéutico, el diagnóstico etiológico a través de la identificación precisa de la especie de Mycobacterium infectante resulta un aporte significativo, dado que el tratamiento y el manejo de sus contactos son diferentes según sea la especie involucrada. Por estas razones se introdujo en nuestro laboratorio el diagnóstico de Mycobacterium a través de su identificación genotípica. Para ello se eligieron dos marcadores moleculares de ADN: la secuencia de inserción IS6110, característica de los genomas del complejo M. tuberculosis, y la secuencia del gen ribosomal 16s (ADNr 16s) para estudiar la identidad específica dentro del género Mycobacterium. Una vez puestas a punto las técnicas moleculares seleccionadas, se procedió al estudio retrospectivo de una colección de 80 aislamientos, identificados como Mycobacterium por métodos fenotípicos. La mayoría de los aislamientos (75/80) resultaron cepas del complejo M. tuberculosis. Los restantes cinco fueron identificados como cepas MNT, tres de ellas causantes de infecciones pulmonares.

Summary Traditional methods to determine phenotype identification for mycobacterium are longer as compared with cellular procedures (4 to 6 weeks and 36 to 72 hours respectively). In Uruguay, the incidence of tuberculosis Mycobacterium is low and data on pulmonary tuberculosis cases but caused by non-tuberculosis Mycobacterium (MNT) -normally saprophytes- is lacking. From a therapeutic point of view, diagnosis based on an accurate identification of Mycobacterium infectant may be significant since treatment and management differ according to the strain found. Two DNA molecular markers were chosen in our laboratory to diagnose Mycobacterium through genotype identification: IS6110 insertion element and ribosomal DNA sequences 16s (DNAr 16s) to determine specific identity within Mycobacterium. Once selected molecular techniques were updated, we undertook a retrospective study of 80 isolates identified as Mycobacterium by phenotype methods. Most of the isolates (75/80) were tuberculosis Mycobacterium strains. The remained five were identified as MNT strains, of which three caused pulmonary infections.

Résumé Les méthodes traditionnelles d'identification phénotypi-que du genre Mycobacterium sont lentes et peu sensibles, quatre à six semaines étant nécessaires pour avoir un diagnostic approprié à partir d'une culture positive. Les procédés moléculaires ont permis de raccourcir cette période: on obtient des résultants au bout de 36-72 heures. Dans notre pays, l'incidence de M. tuberculosis est basse et il n'y a pas de registres pour savoir la fréquence avec laquelle les cas diagnostiqués comme tuberculose pulmonaire sont en réalité causés par Mycobacterium non tuberculose (MNT), normalement saprophytes. Du point de vue thérapeutique, le diagnostic étiolo-gique à travers l'identification précise de l'espèce de mycobacterium infectante est un apport important, étant donné que le traitement varie selon l'espèce en question. Voilà pourquoi on a introduit dans notre laboratoire le diagnostic de Mycobacterium à travers son identification génotypique. Pour ce faire, on a choisi deux marqueurs moléculaires d'ADN: la séquence d'insertion IS6110, caractéristique des génomes du complexe M.tuberculose, et la séquence du gène ribosome 16s (ADN 16s) pour étudier l'identité spécifique dans le genre Mycobacterium. Une fois mises à point les techniques moléculaires sélectionnées, on fait une étude rétrospective d'une collec-tion de 80 isolements, identifiés comme Mycobacterium par des méthodes phénotypiques. La plupart des isolements (75/80) étaient des cèpes du complexe M. tuberculose. Les autres cinq ont été identifiés comme des cèpes MNT, dont trois étant la cause d'infections pulmonaires.