Sequences of S-surface of Human COVID-19

Aims: Diagnosing the Coronavirus and viruses that share infection for different age groups through real time PCR, as well as using the Sanger sequencing method to homology sequence identity between local human Coronavirus isolate and NCBI-BLAST submitted Coronavirus isolate. Study Design: Cross section. Place and Duration of Study: From the central health laboratory and quarantine centers, work was carried out in different places for the purpose of diagnosis in Al-Hakim and Al-Sadr Teaching Hospital and the Central Health Center in addition to the private laboratories, between April 2020 and July 2021. Methodology: Diagnosing the virus through qRTPCR, PCR and sanger sequencing. Sample: We included 300 patients (174 men, 128 women; age range 1883years) with from people who were infected for the first time with the Coronavirus and repeated infections with the virus with other viruses that affect the respiratory system. Results: The current study showed that the number of cases of Coronavirus infection (110) case, Influenza virus (90) case, Parainfluenzavirus (65) case, Metapneumovirus (108)case and Rhinovirus (95)case for the period from 4-4-2020 up to 26-26 7-2021 all viruses were diagnosed through qReal time PCR technique by designing primers according to the location NCBI Regarding the sequences test, the results showed the percentage of similarity with the studied strains at a rate ranging between (99.92 78 %). Conclusion: Most of the infections with the Coronavirus are common with respiratory viruses in different proportions, in addition to the fact that the age group (51-61) year is more infected, and (110) case of Influenza shares with the Coronavirus more infection and the results of Sanger sequences between(99.92 78 %). Original Research Article Alameedy; JPRI, 33(60B): 2571-2576, 2021; Article no.JPRI.81813 2572


INTRODUCTION
In December of 2019, a novel strain of coronaviruses, SARS-CoV-2, was revealed prominent to an occurrence of transmittable illness affecting a global pandemic. Coronaviruses were a great family of viruses well-known for contaminate together persons and different organisms. The persons, SARS-CoV-2 coronavirus contagions can source several infections beginning the corporate cold to other acute infections such as (middle east and severe acute respiratory Syndrome) [1].
A healthy cell is infected by the attachment of coronaviruses to a healthy target cell by binding to special receptors located on the membrane of an uninfected cell. The glycoprotein Spike (S) is the single membrane that helps bind to the target cells, which can fuse with the viral cells [2].
Through studies about appearance of new variants of the virus and the presence of the SARS-CoV-2 Spike (S) protein gene that contains one of the main mutations that have an effect on the function of the protein and its ability to infect uninfected cells [3].
In calculation to the variation that causes the mutation in the Spike (S) protein gene, added mutations have currently been discovered. Where all parts of the genome represent the genes that contain mutations, which are important in the preparation of the vaccine as well as the therapeutic research of the virus [4].
By knowing the next generation sequence of the SARS-CoV-2 viral genome, we can identify the variants that occur virus disaster and based on protocol for early ARTIC SARS-CoV-2 sequencing in January 2020 which was approved by several scientific organizations around the world and later published the original protocol in September 2020 which was considered the most common for sequencing SARS-CoV-2 [5].

Quantitve Real Time PCR Technique
This technique was relied on for the diagnosis of viral infection, and an extraction was used from (Canvax Higher Purity™ Viral DNA/RNA

RNA Sequencing Methods
Ten samples were selected out of 110 positive for genetic Sequencing. Conventional PCR products of positive S-Covid-19 and S-SARS-CoV-2. IBS_m_S2 were sent to Macrogen Company in Korea by for performing the RNA sequencing by (AB RNA sequencing system). The RNA sequencing analysis for S-Covid-19 and S-SARS-CoV-2. IBS_mS 2 genotyping. PCR master mix was elaborated by using GoTaq® Green Mater Mix Kit (Promega, LOT. 0000401B40,USA), Iqon PCR Ladder Cat. No.: A610641 (dsDNA ladder with bands from 100 bp to 3.000 bp). All PCR products were electrophoresed on agarose gel with ethidium bromide and visualized under UV light.The multiple alignment analysis was based on Clustal alignment analysis, and NCBI-BLAST for the homology sequence identity.

RESULTS AND DISCUSSION
The current study showed that the number of cases of Coronavirus infection (110) (25)] ,and the number 174 cases of males infected was higher than females 128 cases. Through our study, we noticed a difference in age groups in infection, where the age group (40-50)years was more susceptible to infected. In the study [6]. In 15 countries, we noticed that the age group (+80 )years had the highest infection, while in India the age group (20-29 )years in addition to the recovery rates of males were higher than females in India, and the death rate also varied.
In Iraq, through our study, no age group is excluded, because the collection of samples did not include all governorates of Iraq and all cities. Samples were taken according to the consent of the patient or the patient for the purpose of conducting the study.
Regarding the sequences test, the results showed the percentage of similarity with the studied strains at a rate ranging between ( 99.92 -78 %) as shown in the Table (2), ten samples were selected based on the concentration of the virus cycles, different age groups, gender in addition to the sample source areas at the time of collection.
Sanger sequence analysis of the Coronavirus variants. All 10 samples that amplified with both the S-Covid-19 in 20-11-2020 and S-SARS-CoV-2 IBS_mS 2 primers from 20 -11-2020 up to 10-3-2021. Table 2 appear the six results were the percentage of NCBI-BLAST homology sequence identity between (99.92 -95.32 %), while the S-SARS-CoV-2 IBS_mS from 7-10 samples, the percentage ranged between (89.19 -78 %), and all samples were sent to the NCBI for the purpose of recording it.

CONCLUSION
The number of cases of Coronavirus infection (110) case, Influenza virus (90) case, Parainfluenzavirus (65) case, Metapneumovirus (108)case and Rhinovirus (95)case, and the age group (51-61) year has the highest infection rate, and the incidence of males174 cases is higher than females128 cases.

CONSENT
Samples were taken according to the consent of the patient or the patient for the purpose of conducting the study.

ETHICAL APPROVAL
As per international standard or university standard written ethical approval has been collected and preserved by the author(s).

DISCLAIMER
The products used for this research are commonly and predominantly use products in our area of research and country. There is absolutely no conflict of interest between the authors and producers of the products because we do not intend to use these products as an avenue for any litigation but for the advancement of knowledge. Also, the research was not funded by the producing company rather it was funded by personal efforts of the authors