Genotyping of Corona virus infections in Baghdad city

Abstract

Background: The discovery of genotypes linked to geographic and temporal infectious clusters suggests that genotyping analysis can be used to track and monitor the transmission of corona virus. Objective: To explore the clinical value of causative agent for corona virus infection (CoVI) by using different genes (SARS-HCoV2 ORF1ab JINZA1 and JINZA2 gene and HCoV NL63, HCoV OC43 and HCoV 229E in the diagnosis of causative agent for corona virus disease and severity of infection to know speed transmission this pandemic and control of disease. Patients and methods: Different types from human samples included nasal swabs, throat swabs and blood samples(plasma) from patients with CoVI and pneumonia. To diagnosis SARS-HCoV2 ORF1ab JINZA1 and JINZA2 gene, and HCoV NL63 gene, HCoV OC43 gene and HCoV 229E gene. The positive ratio of SARS-HCoV2 ORF1ab gene in the diagnosis of COVID-19 pneumonia confirmed by conventional PCR then gene sequencing by sanger method by using PCR product were sent for Sanger sequencing using ABI3730XL, automated DNA sequences, by Macrogen Corporation Korea. The results were received by email then analyzed using geneious software. Results: Assay for CoV the results shown P = 0.001 Highly sign. (P<0.01) within NL63 gene from nasal and throat swab positive n = 2 (10.53%) while negative n =17 (89.47 %) and P = 0.00 Highly sign. (P<0.01) within CT for NL63 gene positive n = 2 (4 %) while negative n = 48 (96 %). In addition to CoV result by PCR were P = 0.033 Sign. (P<0.05), positive n =17 (34%) and negative n =33 (66 %) from total n =50, and P = 0.019 Sign. (P<0.05) within SARSHCOV2 ORF1ab gene from nasal swab by PCR positive n =4(21.05%), negative n =15(78.95%) from total n =19 and P = 0.648 Non sign. (P>0.05) 229E gene from nasal and throat swab positive n =11(57.9%), negative n =8 (42.1%) from total n=19 (100%). While undetectable from OC43HCOV gene by real time PCR and by conventional PCR that indicated all results were negative for blood samples and from nasal and throat swab: Conclusion: Genotyping very important to know type of gene caused corona virus infection by using PCR real time PCR and conventional PCR indicated the study on the present other types of corona virus were HCOV 229E and NL63 HCOV and PCR product confirmed by Sanger sequencing using ABI3730XL, automated DNA sequences, the results concluded discovery two new isolates called SARSHCOV2ORF1ab JINZA1 gene and SARSHCOV2ORF1ab JINZA2 gene in Baghdad/Iraq patients and submitted in National Center for Biotechnology Information. SARSHCOV2ORF1ab JINZA1 OK486620 gene and JINZA2 OK586822 gene. The names of both genes according to name of PhD student Jnan Jafar Baksh, Supervisal Prof. Dr. Nazar Shiyaa Mohammed and Assist prof. Dr. Ahmed Saadi Hassan. BLAST results indicated because transmission by travel between Iraq and USA. Both of two patient’s loss of their life due to severity of infection for JINZA1 and JINZA2 and were critical class for this pandemic.Recommendation: 1) Chosen specific primers for specific gene to avoid coinfection with other viruses and using confirmed tests include real time PCR or conventional PCR and gene sequencing for genotyping for corona virus to know speed viral transmission and control of disease: 2) Nasal swab and throat swab for detection from corona virus mostly greatest than blood samples because viral load higher and development molecular techniques and instruments for detection from virus when very low viral load.