Phylogenetic Analysis of MERSCoV in Human and Camels in Iraq

Abstract

The present study was conducted to evaluate the genetic relationship among Middle East respiratory syndrome coronavirus (MERSCoV) of human and camels origin at the period from October 2015 to February 2016.One hundred samples were collected from camel and 100 from human. Nighty four from nasal swabs and six from oropharyngeal swabs Camel samples secerned by immunochromatographic assay (ICA) for detection of viral antigen. The total percentage of ICA positivity was 28%. Human and camel samples subjected to Revers transcription real time- PCR and carried out by RNA extraction by using specific primers and Taq- Man-Probe for detection of nucleocapsid gene 113 bp. The total positive result in camels were 15% ,there was no significant difference between sex and type of samples, in relation to the age group the results showed that age group more than ten years of camel was the heights percent. With significant difference at P<0.05. According to the months of the year October recorded the highest infection rate with significant difference at p<0.05. the result of RT-qPCR according to the regions of study showed that Al-shinafyah in western borders of Iraq-Saudi was the highest infection rate 35% .On the other hand ,100 human 81 nasal swabs and 19 bronchial lavage samples were collected from pilgrims and non-pilgrims. The total positive result was 5%. The pilgrims recorded the highest infection rate. The results of conventional PCR by using specific primers for detection of Nucleocapsid gene (217 bp) of MERSCoV. The results were confirmative. Three human and 11 camel positive samples were used in further sequencing and phylogenetic analysis by extraction and purification of the PCR products. Our clones sequence submitted in GenBank-NCBI for accession number.
The phylogenetic tree construction and analysis results showed that most of Iraqi variants of camel and human were located in clade-B in which Saudi Arabia strains were clustered. One of our clones (MERS-Iq.2Huh) of accession number KX150500.1 was located in clade-A in the same branch of Jordanian strain while bat corona virus, SARS corona and neoromica corona virus was out group clustered in separated branch.