Ahmed Alqaffas

Human Cytomegalovirus (HCMV) is a member of the betaherpesvirinae subfamily of the
Herpesvirus family. HCMV infection is common among adults worldwide, with an estimated
seroprevalence of 66 to 95%, depending on the geographic region (Zuhair et al., 2019). Although
most of the virus genomic content has been studied extensively, the terminal repeating region
sequences remain understudied. Two main challenges hindered the study of the region: a)
limitations of sequencing… Show more

Human Cytomegalovirus (HCMV) is a member of the betaherpesvirinae subfamily of the
Herpesvirus family. HCMV infection is common among adults worldwide, with an estimated
seroprevalence of 66 to 95%, depending on the geographic region (Zuhair et al., 2019). Although
most of the virus genomic content has been studied extensively, the terminal repeating region
sequences remain understudied. Two main challenges hindered the study of the region: a)
limitations of sequencing technologies; and b) misassembly of the repeats due to its complex
4
nature. Here I show a novel bioinformatics pipeline that takes advantage of PacBio's long reads
to resolve the challenges mentioned earlier. Implementation of the pipeline yielded results that
supported previous assumptions of the terminal region, showed evidence of new findings, and
provided in-depth analysis of the terminal repeat known as the a sequence. Show less

Long-read, single-molecule DNA sequencing technologies have triggered a revolution in genomics by enabling the determination of large, reference-quality genomes in ways that overcome some of the limitations of short-read sequencing. However, the greater length and higher error rate of the reads generated on long-read platforms make the tools used for assembling short reads unsuitable for use in data assembly and motivate the development of new approaches. We present LoReTTA (Long Read… Show more

Long-read, single-molecule DNA sequencing technologies have triggered a revolution in genomics by enabling the determination of large, reference-quality genomes in ways that overcome some of the limitations of short-read sequencing. However, the greater length and higher error rate of the reads generated on long-read platforms make the tools used for assembling short reads unsuitable for use in data assembly and motivate the development of new approaches. We present LoReTTA (Long Read Template-Targeted Assembler), a tool designed for performing de novo assembly of long reads generated from viral genomes on the PacBio platform. LoReTTA exploits a reference genome to guide the assembly process, an approach that has been successful with short reads. The tool was designed to deal with reads originating from viral genomes, which feature high genetic variability, possible multiple isoforms, and the dominant presence of additional organisms in clinical or environmental samples. LoReTTA was tested on a range of simulated and experimental datasets and outperformed established long-read assemblers in terms of assembly contiguity and accuracy. The software runs under the Linux operating system, is designed for easy adaptation to alternative systems, and features an automatic installation pipeline that takes care of the required dependencies. A command-line version and a user-friendly graphical interface version are available under a GPLv3 license at https://bioinformatics.cvr.ac.uk/software/ with the manual and a test dataset. Show less

Human cytomegalovirus shed in infant urine was isolated and serially passaged in fibroblasts in the presence or absence of neutralizing antibodies. Comparison of the genome sequences of representative viruses Ig-KG-H2 (passed with antibody) and ϕ-KG-B5 (passed without antibody) revealed the presence of several mutations in each virus.

Analyzed viral genomic variants between multiple strains propagating in different media.
The bioinformatics analysis is done by generating a new pipeline to deal with common sequencing issues and viral genome-specific issues.

The goal of this shared group project is to fully annotate de novo phage sequences and submit a whole genome annotated sequence to ASM.