Genome Sequences of COVID-19 from Jordanian Patients in Comparison with the Global Pandemic Strains and the Transmission Route

In this research study, we reported a pioneer investigation on the phylogenetic profile of genomic sequences and the prevalence of COVID-19 strains in Jordan; in comparison with global strains, as part of concerted global efforts in combating the COVID-19 pandemic. A total of 28 genome sequences of the hCoV-19/Jordan strain were employed in this study. The phylogenetic analysis of the genome sequences of hCoV-19/Jordan strain, which was conducted on the databases of NCBI and GASAID revealed that the hCoV-19/ Jordan strain belongs to the G, V, and S clades with distribution coverage rates of 89%, 7% and 4%, respectively. Comparison of the hCoV-19/Jordan clades with global clades distribution profile showed evidently and conclusively, a unique pandemic profile of multiple geographical sources of COVID-19, imported into Jordan primarily through cryptic means from European countries (UK, Belgium, Sweden, Russia) and Morocco, which are entry points into Jordan. This is due to the reciprocal heavy air traffic route between Jordan and the capitals of these European countries, with Morocco being the primary entry point into Jordan. The results of this study represent a marked addition to investigations on the prevalence rate of the hCovid-19/Jordan strain in comparison to the global strains sequences, and provides a better understanding on comparative diagnosis technique for COVID-19 worldwide. Phylogenetic analysis of the top 100 and top 10 taxonomic trees revealed almost identical homology (99.98% 100%) between hCoV-19/Jordan strain and the strains that broke out in Wuhan, the MT642226.1. Furthermore, it can be inferred that there was no marked change in the virus mutation that occurred during the period of this study taking into cognizance the fact that there was identical homology (99.98% 100%) among the 28 sequences of hCoV-19/Jordan strains. Similarly, all sequences of the Jordanian strains of hCoV-19/Jordan How to cite this paper: Mahasneh, I., Ennaji, M. and Abumsimir, B. (2021) Genome Sequences of COVID-19 from Jordanian Patients in Comparison with the Global Pandemic Strains and the Transmission Route. Journal of Biosciences and Medicines, 9, 77-93. https://doi.org/10.4236/jbm.2021.93009 Received: February 12, 2021 Accepted: March 26, 2021 Published: March 29, 2021 Copyright © 2021 by author(s) and Scientific Research Publishing Inc. This work is licensed under the Creative Commons Attribution International License (CC BY 4.0). http://creativecommons.org/licenses/by/4.0/ Open Access


Introduction
Since the World Health Organization (WHO) officially declared the outbreak of COVID-19 a pandemic on March 11, 2020, there has been a global growing interest in research targeted at combating the virus due to the surge in infection, as well as the prevalence rate. This has made it imperative and expedient for all probable preventative measures to be adopted in combating the global surge in infection pending the discovery of a vaccine for the virus. Currently, there are over 40 million confirmed cases globally as reported by WHO. The COVID-19 strain responsible for the current global pandemic was identified early this year as the β-coronavirus (CoV), which belongs to the Coronaviridae family and it has a single positive-strand RNA genome [1] [2] [3]. This strain-type is among several strains of coronaviruses that are pathogenic to humans; most are associated with mild clinical symptoms, with the exception of the Severe Acute Respiratory Syndrome (SARS) coronavirus (SARS-CoV) and it was reported as a novel β-coronavirus two decades ago [4] [5] [6]. In 2012, the same strain-type was detected in Saudi Arabia, and since then, it has been known as the Middle East Respiratory Syndrome (MERS) coronavirus (MERS-CoV) [7] [8]. It was later imported into South Korea, and caused about 2500 confirmed cases of infections [9] [10]. In late December, 2019, after global detection of the COVID-19 strain in many countries, the WHO has declared it as a pandemic on March 11, 2020.
A phylogenetic tree with the geographical mutation transmission of SARS-CoV-2 has previously been reported to have a genome size of about 30 kilobases, and encodes 10 genes of a single positive-stranded RNA (ribonucleic acid) [1] [2] [11]- [17]. Furthermore, a comprehensive study conducted by the World Health Organization [18] (employing 10,022 SARS-CoV-2 genomes from 68 different countries) showed how the SARS-CoV-2 genome has evolved over the years, spreading to different parts of the world. In total, 65,776 variants and 5775 distinct variants, comprised of the most frequent mutations causing the SARS-CoV-2 pandemic were detected by WHO. Additionally, 2969 missense mutations, 1965 synonymous mutations, and 484 mutations in non-coding regions were also discovered by WHO [1]. It was reported by [12] based on data from the public database of the Global Initiative on Sharing All Influenza Data (GISAID) that three major clades of SARS-CoV-2 exists, and have subsequently

Jordan National SARS-CoV-2 Pandemic Surveillance Committee
After the first confirmed case of SARS-CoV-2 infection in Jordan, a National SARS-CoV-2 Pandemic Surveillance Committee was instituted with the National Order number (17) to oversee the SAR-CoV-2 surveillance and combat program.

Sequencing of the Full Length Genome of Jordanian SAR-CoV-2 Strains
The (28) genome samples from Jordan (26 from Amman and 2 from Irbid) were subjected to complete genome sequencing in the Scripps Research Institute (TSRI), La Jolla, California, USA as previously described [11]. The resultant se-Journal of Biosciences and Medicines quences were later deposited by the Scripps Research Institute (TSRI) into the databases of the NCBI GenBank (http://www.ncbi.nlm.nih.gov/) and Global Initiative on Sharing All Influenza Data (GISAID) (http://www.gisaid.org/) employing the tag hCoV-19/Jordan vis-à-vis each respective accession number (see Table 1 for details of the accession numbers and other descriptions).

Results
The phylogenetic tree of the hCoV-19/Jordan sequences in comparison with selected global sequences is presented in Figure 1 Table 1. All sequences of the hCoV-19/Jordan strain were complete, exceeding (29,400 bp), and example of the complete sequence of the hCoV-19/Jordan is given in Figure 3, which were therefore compared with similar complete global sequences. The clades and sub-clades descriptions of the genealogical lineage of the hCoV-19/Jordan strain are presented in Table 2; which shows that the hCoV-19/Jordan strain belongs to the G, V, and S clades with spreading frequencies of 89%, 7% and 4%, respectively. Journal of Biosciences and Medicines

Discussion
The phylogenetic analysis of the hCoV-19/Jordan strain constructed from selected global genomes deposited into GISAID for comparison purposes revealed that the 28 genome sequences from Jordan employed in this study were compatible with the evolutionary tree of SARS-CoV-2, and had a complete genome length of 29,400 bp and homology of (99.98% -100%) (Figure 1). This provides a conclusive evidence that the hCoV-19/Jordan is part of the global pandemic strains of SARS-CoV-2. The results of our study showed that the genome length and homology of the hCoV-19/Jordan strain are in consonance with those reported for the SARS-CoV-2 strains globally [1] [3] [11]. The neighbor joining phylogenetic analysis of the top 100 ( Figure 2) and top 10 taxonomic trees ( Figure 3) showed conclusively that the hCoV-19/Jordan strain had almost identical homology (99.98% -100%) with the strains that broke out in Wuhan, the MT642226.1. This suggests that it is the most recent strain, and has a common ancestry with the strains transmitted and detected in Jordan. Similarly, all sequences of the Jordanian strains of hCoV-19/Jordan were compared to the England and American strains and showed identical homology of (99.98% -   (Figure 2 and Figure 3) and as it can be seen from the example of the complete sequence of the hCoV-19/Jordan strain as given in Figure 4.
Comparison of the clades of hCoV-19/Jordan with that of SARS-CoV-2 showed that the most plausible transmission routes are European countries (UK, Belgium, Sweden, Russia) and Morocco, which are entry points into Jordan. This can be attributed to the fact that both the G and V clades reported in this study for hCoV-19/Jordan strain are similar to those reported earlier in these European countries [12] [19]. This further suggests that the strain was transmitted through the heavy air traffic transmission rout between EU countries-Morocco-Jordan) after the strains were transmitted from China to EU countries. This is Journal of Biosciences and Medicines in consonance with previous reports that stated that clade G apparently originated from Shanghai before it was imported into European countries [17] [20] [21].

Conclusion
The results of this study show conclusively a unique pandemic profile of multiple geographical sources of COVID-19 importation into Jordan primarily through UK, Belgium, Sweden, Russia and Morocco, which are entry points into Jordan. This is also due to the reciprocal heavy air traffic route between Jordan and European capitals. It can be inferred based on the identical homology (99.98% -100%) of the 28 sequences of hCoV-19/Jordan strain that there was no marked change in the virus mutation that occurred during the period of this study.