Evolutionary analysis of LMP-1 genetic diversity in EBV-associated nasopharyngeal carcinoma: Bioinformatic insights into oncogenic potential.

EBV latent membrane protein 1 (LMP-1) is an important oncogene involved in the induction and maintenance of EBV infection and the activation of several cell survival and proliferative pathways. The genetic diversity of LMP-1 has an important role in immunogenicity and tumorigenicity allowing escape from host cell immunity and more metastatic potential of LMP-1 variants. This study explored the evolutionary of LMP-1 in EBV-infected patients at an advanced stage of nasopharyngeal carcinoma (NPC). Detection of genetic variability in LMP-1 genes was carried out using Sanger sequencing. Bioinformatic analysis was conducted for translation and nucleotide alignment. Phylogenetic analysis was used to construct a Bayesian tree for a deeper understanding of the genetic relationships, evolutionary connections, and variations between sequences. Genetic characterization of LMP-1 in NPC patients revealed the detection of polymorphism in LMP-1 Sequences. Motifs were identified within three critical LMP-1 domains, such as PQQAT within CTAR1 and YYD within CTAR2. The presence of the JACK3 region at specific sites within CTAR3, as well as repeat regions at positions (122-132) and (133-143) within CTAR3, was also annotated. Additionally, several mutations were detected including 30 and 69 bp deletions, 33 bp repeats, and 15 bp insertion. Although LMP-1 strains appear to be genetically diverse, they are closely related to 3 reference strains: prototype B95.8, Med- 30 bp deletion, and Med + 30 bp deletion. In our study, one of the strains harboring the 30 bp deletion had both bone and bone marrow metastasis which could be attributed to the fact that LMP-1 is involved in tumor metastasis, evasion and migration of NPC cells. This study provided valuable insights into genetic variability in LMP-1 sequences of EBV in NPC patients. Further functional studies would provide a more comprehensive understanding of the molecular characteristics, epidemiology, and clinical implications of LMP-1 polymorphisms in EBV-related malignancies.

Chromosome-Scale Assembly of the Complete Genome Sequence of Leishmania (Mundinia) procaviensis Isolate 253, Strain LV425.

Leishmania (Mundinia) procaviensis is a parasitic kinetoplastid that was first isolated from a rock hyrax in Namibia in 1975. We present the complete genome sequence of Leishmania (Mundinia) procaviensis isolate 253, strain LV425, sequenced using combined short- and long-read technologies. This genome will contribute to our understanding of hyraxes as a Leishmania reservoir.

The emergence of an imported variant of dengue virus serotype 2 in the Jazan region, southwestern Saudi Arabia.

BACKGROUND: Dengue virus (DENV) infection is a global economic and public health concern, particularly in tropical and subtropical countries where it is endemic. Saudi Arabia has seen an increase in DENV infections, especially in the western and southwestern regions. This study aims to investigate the genetic variants of DENV-2 that were circulating during a serious outbreak in Jazan region in 2019. METHODS: A total of 482 serum samples collected during 2019 from Jazan region were tested with reverse transcription-polymerase chain reaction (RT-PCR) to detect and classify DENV; positive samples underwent sequencing and bioinformatics analyses. RESULTS: Out of 294 positive samples, type-specific RT-PCR identified 58.8% as DENV-2 but could not identify 41.2%. Based on sequencing and bioinformatics analyses, the samples tested PCR positive in the first round but PCR negative in the second round were found to be imported genetic variant of DENV-2. The identified DENV-2 imported variant showed similarities to DENV-2 sequences reported in Malaysia, Singapore, Korea and China. The results revealed the imported genetic variant of DENV-2 was circulating in Jazan region that was highly prevalent and it was likely a major factor in this outbreak. CONCLUSIONS: The emergence of imported DENV variants is a serious challenge for the dengue fever surveillance and control programmes in endemic areas. Therefore, further investigations and continuous surveillance of existing and new viral strains in the region are warranted.

Molecular Characterization of Leishmania Species among Patients with Cutaneous Leishmaniasis in Asir Province, Saudi Arabia.

Anthroponotic cutaneous leishmaniais (ACL) and zoonotic cutaneous leishmaniasis (ZCL) caused by Leishmania tropica and Leishmania major, respectively, are endemic vector-borne diseases in southern Saudi Arabia. In 2021, an outbreak of cutaneous leishmaniasis occurred in the province of Asir. The main objective of our investigation was to analyze the epidemiological features of CL in southern Saudi Arabia. The ministry of health recorded 194 CL patients between January and December 2021 from the Asir province. Our findings showed that the majority of CL patients (87.1%) originated from the governorates of Khamis-Mushait and Abha. Most of the patients were males (62.3%). While CL affected all age groups, those under 13 years old were the most affected (38.1%). For both genders, CL patients were mostly Saudi citizens (90.7%) compared to non-Saudi expatriates. The majority of CL patients (75.2%) suffered from a single lesion, and the majority of lesions (61.3%) were located on the face. The seasonal prevalence of CL showed two peaks, a small one in July-August and a larger one in March. Of a total of 194 Giemsa slides samples, 188 showed positive amplification of Leishmania ITS1 gene. Based on PCR-RFLP and PCR-HMR, 183 patients showed positive amplification of L. tropica and five patients showed positive amplification of L. major. Phylogenetic analysis revealed a clear distinct separation between L. major and L. tropica sequences. Our results provided strong evidence of the pre-domination of L. tropica, the main etiological agent of ACL in Asir province. We reported for the first time the presence of L. major, an etiological agent of ZCL in the study areas. The co-circulation of ACL and ZCL highlighted the complexity of the epidemiology of CL in southern Saudi Arabia, and subsequently, further studies to identify competent vectors and reservoir hosts for the establishment of control strategies are needed.

DNA Barcoding of Potential Mosquito Disease Vectors (Diptera, Culicidae) in Jazan Region, Saudi Arabia.

The conventional morphological characterization of mosquito species remains heavily used for species identification in Jazan, Saudi Arabia. It requires substantial expertise and time, as well as having difficulty in confirming identity of morphologically similar species. Therefore, to establish a reliable and accurate identification system that can be applied to understanding spatial distribution of local mosquito species from the Jazan region, DNA barcoding was explored as an integrated tool for mosquito species identification. In this study, 44 adult mosquito specimens were analyzed, which contain 16 species belong to three genera of potential mosquito disease vectors (Aedes, Anopheles, and Culex). The specimens were collected from the Jazan region located in southwest Saudi Arabia. These included old and preserved mosquito voucher specimens. In addition, we assessed the genetic distance based on the generated mitochondrial partial COI DNA barcodes to detect cryptic diversity across these taxa. Nine mosquito species belonging to three genera were successfully barcoded and submitted to GenBank, namely: Aedes aegypti, Aedes caspius, Aedes vexans, Aedes vittatus, Anopheles arabiensis, Culex pipiens, Culex quinquefasciatus, Culex sitiens, and Culex tritaeniorhynchus. Of these nine species, Aedes vexans, Aedes vittatus, Culex sitiens, and Culex tritaeniorhynchus were registered in GenBank for the first time from Saudi Arabia. The DNA barcodes generated a 100% match to known barcodes of these mosquito species, that also matched with the morphological identification. Ae. vexans was found to be either a case of cryptic species (subspecies) or a new species from the region. However, more research has to be conducted to prove the latter. This study directly contributes to the development of a molecular reference library of mosquito species from the Jazan region and Saudi Arabia. The library is essential for confirmation of species in support of existing mosquito surveillance and control programmes.

Chromosome-Scale Assembly of the Complete Genome Sequence of Porcisia hertigi, Isolate C119, Strain LV43.

Porcisia hertigi is a parasitic kinetoplastid first isolated from porcupines (Coendou rothschildi) in central Panama in 1965. We present the complete genome sequence of P. hertigi, isolate C119, strain LV43, sequenced using combined short- and long-read technologies. This complete genome sequence will contribute to our knowledge of the parasitic genus Porcisia.

Chromosome-scale genome sequencing, assembly and annotation of six genomes from subfamily Leishmaniinae.

We provide the raw and processed data produced during the genome sequencing of isolates from six species of parasites from the sub-family Leishmaniinae: Leishmania martiniquensis (Thailand), Leishmania orientalis (Thailand), Leishmania enriettii (Brazil), Leishmania sp. Ghana, Leishmania sp. Namibia and Porcisia hertigi (Panama). De novo assembly was performed using Nanopore long reads to construct chromosome backbone scaffolds. We then corrected erroneous base calling by mapping short Illumina paired-end reads onto the initial assembly. Data has been deposited at NCBI as follows: raw sequencing output in the Sequence Read Archive, finished genomes in GenBank, and ancillary data in BioSample and BioProject. Derived data such as quality scoring, SAM files, genome annotations and repeat sequence lists have been deposited in Lancaster University's electronic data archive with DOIs provided for each item. Our coding workflow has been deposited in GitHub and Zenodo repositories. This data constitutes a resource for the comparative genomics of parasites and for further applications in general and clinical parasitology.

Chromosome-Scale Assembly of the Complete Genome Sequence of Leishmania (Mundinia) sp. Ghana, Isolate GH5, Strain LV757.

Leishmania (Mundinia) sp. Ghana is a kinetoplastid parasite isolated in 2015 in Ghana. We report the complete genome sequence of L. (M.) sp. Ghana, sequenced using combined short-read and long-read technologies. This will facilitate greater understanding of this novel pathogen and its relationships within the subgenus Mundinia.

Chromosome-Scale Assembly of the Complete Genome Sequence of Leishmania (Mundinia) enriettii, Isolate CUR178, Strain LV763.

Leishmania (Mundinia) enriettii is a parasitic kinetoplastid first isolated from a guinea pig in Brazil in 1946. We present the complete genome sequence of L. (M.) enriettii, isolate CUR178, strain LV763, sequenced using combined short-read and long-read technologies. This will facilitate a greater understanding of the genome diversity within L. (M.) enriettii.

Chromosome-Scale Assembly of the Complete Genome Sequence of Leishmania (Mundinia) orientalis, Isolate LSCM4, Strain LV768.

Leishmania (Mundinia) orientalis is a kinetoplastid parasite first isolated in 2014 in Thailand. We report the complete genome sequence of L. (M.) orientalis, sequenced using combined short-read and long-read technologies. This will facilitate greater understanding of this novel pathogen and its relationship to other members of the subgenus Mundinia.

LGAAP: Leishmaniinae Genome Assembly and Annotation Pipeline.

We present the LGAAP computational pipeline, which was successfully used to assemble six genomes of the parasite subfamily Leishmaniinae to chromosome-scale completeness from a combination of long- and short-read sequencing data. LGAAP is open source, and we suggest that it may easily be ported for assembly of any genome of comparable size (∼35 Mb).

Chromosome-Scale Assembly of the Complete Genome Sequence of Leishmania (Mundinia) martiniquensis, Isolate LSCM1, Strain LV760.

Leishmania (Mundinia) martiniquensis is a kinetoplastid parasite that was first isolated in 1995 on Martinique. We report the first complete genome for Leishmania martiniquensis from Asia, isolate LSCM1, strain LV760, which was sequenced using combined short-read and long-read technologies. This will facilitate greater understanding of the evolution of the geographically dispersed subgenus Mundinia.

Echocardiographic and Clinical Correlates of Ejection Fraction Among 2000 Patients with Heart Failure in Western Saudi Arabia.

INTRODUCTION: Heart failure (HF) affects about 320,000 Saudi individuals and is associated with a considerable negative impact on the patients' quality of life. In literature, there is a lack of data about the echocardiographic abnormalities of HF patients in Saudi Arabia. AIM OF WORK: To describe the echocardiographic findings of HF patients in Western Saudi Arabia. METHODOLOGY: This was a retrospective record review study conducted on 2000 patients with chronic HF in Saudi Arabia. Demographic, clinical and echocardiographic data were collected and compared among patients with HF with reduced ejection fraction (HFrEF), ie, EF≤40%; HF with mid-range EF (HFmrEF), ie, EF=41-49%; and HF with preserved EF (HFpEF), ie, EF≥50%. RESULTS: Among the 2000 patients studied, females constituted 46.3% of the sample. About 52% of females had HFpEF, whilst 70% of males had HFrEF (p<0.0001). Diastolic dysfunction occurred in 98% of HFpEF versus 78% of HFrEF (p<0.0001). Patients with HFrEF had higher left-ventricular diastolic (LVd) volume (1536 versus 826), higher left-ventricular systolic (LVs) volume (1660 vs 772), higher left atrial volume (1344 vs 875), higher aortic root dimension (1144 vs 929) and lower fractional shortening (FS) (267 vs 1213) than patients with HFpEF (p<0.0001). CONCLUSION: HFpEF was more common among females and was associated with higher rates of diastolic dysfunction and higher FS. HFrEF was prevalent among males and associated with higher LVd, LVs, left atrium volume and aortic root dimensions.