Biology subjects

Lott, M.

Publications and source records attributed to Lott, M..

3 recordsLinked to original sources

bioRxiv2022

Genomic Surveillance of SARS CoV2 in COVID-19 vaccinated healthcare workers in Lebanon.

The emergence of SARS-CoV-2 variants including the Delta and Omicron along with waning of vaccine-induced immunity over time contributed to increased rates of breakthrough infection specifically among healthcare workers (HCWs). SARS-CoV-2 genomic surveillance is an important tool for timely detection and characterization of circulating variants as well as monitoring the emergence of new strains. Our study is the first national SARS-CoV-2 genomic surveillance among HCWs in Lebanon. We collected 250 samples from five hospitals across Lebanon between December 2021 and January 2022. We extracted viral RNA and performed whole genome sequencing using the Illumina NextSeq 500 platform. A total of 133 (57.1%) samples belonging to the Omicron (BA.1.1) sub-lineage were identified, as well as 44 (18.9%) samples belonging to the BA.1 sub-lineage, 28 (12%) belonging to the BA.2 sub-lineage, and only 15 (6.6%) samples belonging to the Delta variant sub-lineage B.1.617.2. These results show that Lebanon followed the global trend in terms of circulating SARS-CoV-2 variants with Delta rapidly replaced by the Omicron variant. This study underscores the importance of continuous genomic surveillance programs in Lebanon for the timely detection and characterization of circulating variants. The latter is critical to guide public health policy making and to timely implement public health interventions.

genomics↗

bioRxiv2022

LoRTIS Software Suite: Transposon mutant analysis using long-read sequencing

To date transposon insertion sequencing (TIS) methodologies have used short-read nucleotide sequencing technology. However, short-read sequences are unlikely to be matched correctly within repeated genomic regions which are longer than the sequence read. This drawback may be overcome using long-read sequencing technology. We have developed a suite of new analysis tools, the "LoRTIS software suite" (LoRTIS-SS), that produce transposon insertion site mapping data for a reference genome using long-read nucleotide sequence data. Long-read nucleotide sequence data can be applied to TIS, this enables the unique mapping of transposon insertion sites within long genomic repeated sequences. Here we present long-read TIS analysis software, LoRTIS-SS, which uses the Snakemake framework to manage the workflow. A docker image is provided, complete with dependencies and ten scripts are included for experiment specific data processing before or after use of the main workflow. The workflow uses long-read nucleotide sequence data such as those generated by the MinION sequencer (Oxford Nanopore Technologies). The unique mapping properties of long-read sequence data were exemplified by reference to the ribosomal RNA genes of Escherichia coli strain BW25113, of which there are 7 copies of [~]4.9 kbases in length that are at least 99% similar. Of reads that matched within rRNA genes, approximately half matched uniquely. The software workflow outputs data compatible with the established Bio-TraDIS analysis toolkit allowing for existing workflows to be easily upgraded to support long-read sequencing.

bioinformatics↗

bioRxiv2022

Novel mtDNA Imparts the Connective Tissue Disorder of a Tourette Pedigree

Mitochondrial dysfunction is associated with a range of clinical manifestations including neuropsychiatric and metabolic disorder. Here, we reanalyzed a family with an L-Histidine Decarboxylase (HDC) variant previously linked to Tourette syndrome but with associated connective tissue and metabolic features of unknown etiology. We identified a mitochondrial haplogroup J-defining mutation on the haplogroup H background that functionally interacts with the L-Histidine Decarboxylase variant via calcium homeostasis. Our findings establish how a common mtDNA variant on a different mtDNA background can result in mitochondrial dysfunction, demonstrate a role for histaminergic signaling in modifying mitochondrial phenotypes, and link mitochondria dysfunction to connective tissue phenotypes.

genetics↗