An outbreak of a viral respiratory illness (officially named by the World Health Organization 53 coronavirus disease, COVID-19) started around mid-December 2019, in the city of Wuhan, 54 Hubei province, China. The COVID-19 is an infectious disease of the respiratory tract triggered 55 by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) which in severe cases 56 can lead to acute respiratory distress syndrome and death [1] . The disease has rapidly spread 57 to the entire world [2] . On March 11, 2020, the WHO declared COVID-19 to be pandemic. 58 Now, more than 20,730,456 confirmed cases of COVID-19, including 751,154 deaths have 59 been reported worldwide according to WHO. 60 The SARS-CoV-2 genome size varies from 29.8 to 29.9 kb and the 5′ region represent more 61 than two-thirds of the genome that comprises open reading frame (ORF1ab) encoding ORF1ab 62 polyproteins, while the 3′ one third consists of genes encoding structural proteins including 63 surface (S), envelope (E), membrane (M), and nucleocapsid (N) proteins. The SARS-CoV-2 64 comprises 6 accessory proteins, encoded by ORF3a, ORF6, ORF7a, ORF7b, and ORF8 [3, 4] . 65 To date, by genetic homogeneity the closest virus phylogenetically to SARS-CoV-2 is a 66 coronavirus isolated from the horseshoe bat (Bat CoV RaTG13) with an overall genome 67 sequence identity of 96.2 % , which is higher than that of SARS-CoV (<80 % ) [5, 6] . 68 Next generation sequencing provides high-quality, full-scale genome sequences for viral 69 isolates collected in relatively non-biased ways, irrespective of virulence or other unusual 70 properties. Analyzes of the genome sequences gave insight into the pattern of global 71 distribution, the genetic diversity during epidemics and the dynamics of the development of 72 subtypes. SARS-CoV2 database, such as GISAID (www.gisaid.org), the NCBI SARS-CoV2 73 database (https://www.ncbi.nlm.nih.gov/sars-cov-2), and NGDC Genome Warehouse 74 (https://bigd.big.ac.cn/gwh/), make the genomic information publicly available, together with 75 epidemiological data for the sequenced isolates. 76 The development of a statistical system focused on epidemiological, antigenic and genetic 77 knowledge may provide more insight into the rules regulating the appearance and development 78 of antigenically novel mutations and improve the capacity for prevention and regulation of 79 SARS-CoV2 [7, 8] . Studies strongly support an urgent necessity for additional rapid, wide-80 ranging investigations that incorporate genetic data, epidemiological knowledge and graph 81 details of patients with COVID-19 with clinical characteristics [9, 10] . Therefore, we studied the molecular variation among SARS-CoV-2 genomes isolated and sequenced from COVID-83 19 Egyptian patients. calling of the raw data. Two strategies were utilized for genome assembly and these were 126 executed in two independent tracks: The first is de-novo assembly, where the reads were 127 assembled using the IRMA (v0.9.3) workflow. The second is based on reference-based 128 assembly, where the reads were assembled by mapping (aligning) them to a reference genome.
The tmap program (v.512) was used to align the reads to the reference corona virus genome 130 Wuhan 1 (RefSeq; NC_045512.2). The consensus sequence was then computed from the 131 aligned reads. After finishing the assembly, the de-novo assembly was compared against the 132 reference-based assembly to assure consistency of the results. In fact, for this target amplicon 133 based panel, we see that the reference-based assembly is enough to reconstruct the viral 134 sequence. Samples with less than 99% coverage or with gaps larger than 30 bps were excluded.
The final successful set included 61 complete genome sequences and these were uploaded to 136 NCBI/GISAID repositories (Supplementary File S1).
Preparing world datasets: All the complete SARS-CoV2 genome sequences were first retrieved 138 from the GISAID website on 30 June 2020 and all sequences with long internal gaps or 139 ambiguities (larger than 30bps) were excluded. The final dataset included 46,612 sequences.
On October 2020, we updated this dataset and the number of sequences increased to 89632. On 141 these sequences, the following processing was conducted to create different collections of Egyptian dataset: The variations (mutations) in the Egyptian genomes were examined for 187 quality and depth. A variation is filtered out if its depth is less than 50 reads. It is also filtered 188 out if its depth is less than 100, appears only once in our dataset, and did not appear in world Table 5, shows the  contingency table for the variations in Table 3 and the sub-populations listed above. For 207 comparing the distribution of variations in the set of virus genes (Table 2) , we also used Chi 208 square test. The P-value threshold 0.05 is used to confirm or reject differences between the 209 variables in the test. Specifically, P-value > 0.05 means that there is no difference between the 210 two sub-populations (two groups) with respect to the variations (categories) at hand. In this study, three frameshift mutations were detected, one of which was detected in ORF1ab, (Table 1) . that most of the variegations (148 ones) are in the ORF part due to its size (Figure 1 b) . We 266 compared this pattern of distribution in Egyptian world datasets. Chi square).
The table also shows the ratio between the synonymous and non-synonymous mutations in Table 3 lists these variations and their frequencies in world and regional 290 datasets. It is interesting to note that these variations are also abundant in the world and regional sub-sampled from the Nextstrain (Figure 2 ). The tree shows that most of the Egyptian cohorts of 313 samples can be assigned clades G/GR/GH/O (as per GISAID system). in to see the sequence information https://github.com/mabouelhoda/nCovEgypt.
In detail, the phylogenetic study of the full sequences ( Figure 3) of the S1 domain [24, 25] . This mutation with residual glycine 614 (G614) was previously detected 409 to increase at an alarming rate and were observed at low frequency in March (26%), but increased 
The replicase enzyme is shown as two polyproteins (ORF1a and ORF1ab) [27, 28] States of America. One sample was identical to the one from Sweden, England and Israel. One 482 sample was identical to that from the United States of America, Saudi Arabia, India and Colombia.
One sample was the same as that collected from Saudi Arabia.
In conclusion, we detect 204 unique sequence variations in genomes isolated from Egyptian 