The revolutionary breakthrough in molecular diagnostics have greatly affected the health care industry, in terms of specificity and sensitivity in diagnosing and monitoring infectious diseases by DNA sequencing and amplification methods. DNA sequencing methods are gravely helpful in detecting mutations (genetic shifts and drifts) of viruses, because they change their genetic code so easily causing problems in their diagnosis. Thankfully, these techniques made life so much easier, commercially available and cheap kits provide us with an accurate diagnosis in the shortest time possible, which influences the heath care of patients in providing early treatment options (Cobo, 2012).
‘ Dengue Virus in Saudi Arabia
One of the medically important viruses in Saudi Arabia’s western province is the dengue virus (DEV-1), transmitted by mosquitos and the causative agent of dengue fever. Since 1994, multiple outbreaks have been reported of positive cases of dengue fever especially in Hajj and Omrah season because of the heavy crowds. Research has been conducted regarding DENV-1 in Saudi Arabia, but none sequenced the whole genome of the virus until recently. In the beginning of this year 2015, a group of Saudi scientist for the first time published an article coding the whole genome of the common DENV-1 in SA. Which is very helpful in diagnosis, as well as to be used as a reference genome to be compared with if any novel serotypes were to be developed in the future (Esam I Azhar1, 2015).
DENV genome sequencing
First, the viral RNA was extracted by cellular culture method; then the RNA fragments were amplified using RT-PCR (reverse transcriptase PCR) with the help of an ABI Veriti thermal cycler. Unnecessary sequences were removed from agarose gel by using QIAquick Gel Extraction Kit. Finally, an ABI 3500 Automatic Sequencer was used and sequencing was completed. “The complete viral sequence was assembled and deposited in the GenBank with the following accession number (GenBank: KJ649286; DENV-1-Jeddah-1-2011)” (Esam I Azhar1, 2015).
‘ Epstein-Barr virus
EBV is the causative agent of many lymphatic malignancies, nasopharyngeal carcinoma, gastric carcinoma and infectious mononucleosis. Genotyping of EBV strains is very important in classifying diseases and predicting response to therapy (Gulley, 2001).
EBV genome sequencing
In 2013, a group of Chinese scientist were interested in sequencing the genome of a specific EBV from cell line C666-1; that causes a distinct type of head and neck cancer (NPC). They performed a100-bases pair-end massive parallel sequencing along with PCR amplification, and successfully sequenced the whole genome of EBV (C666-1). “(GenBank accession number: KC617875), finally, concluded that C666-1 contains a representative NPC-associated EBV genome and might serve as an important model
for studying the roles or function of viral proteins in NPC tumorigenesis (Tso1, 2013).
‘ Human Papilloma Virus (HPV)
HPV is the causative agent of cervical cancer and genital warts, the third widely spread cancer in women and most prevalent in America; associated with high mortality rate. Deadly consequences arise from late diagnosis of cervical cancer, which could have been prevented if an efficient diagnostic tool was sensitive enough to detect the presence of HPV (Meiring, 2012).
HPV Genome sequencing
For some reason many of the HIV+ve women in Africa for example, are missed for having specific strains of HPV. A Cohort study was established to unravel the reason behind this. The result were as follows “Illumina sequencing identified a total of 16 HPV genotypes in the selected specimen, with four genotypes (HPV-30, 74, 86 and 90) not included in the commercial kit. The prevalence’s of HPV-30, 74, 86 and 90 in 109 HIV positive South African women were found to be 14.6%, 12.8%, 4.6% and 8.3% respectively” (Meiring, 2012).