[PMC free article] [PubMed] [Google Scholar] 53. cell epitopes that are highly conserved in: (= 9)= 11)= 11); Group 2 with mild symptoms (i.e., Inpatient only, = 32); Group 3 with moderate symptoms (i.e., ICU admission, = 11) and Group 4 with severe symptoms (i.e., ICU admission +/? Intubation or death, = Tos-PEG3-NH-Boc 9). As expected, compared to the asymptomatic group, all of the 3 symptomatic groups (i.e., mild, moderate and severe) had higher percentages of comorbidities, including diabetes (22% to 64%), hypertension (64% to 78%), cardiovascular disease (11% to 18%) and obesity (9% to 50%) (Table 1). The final Group 5 was comprised of unexposed healthy individuals (controls), with no history of COVID-19 or contact with COVID-19 patients (= 10) collected prior to 2019. All subjects were enrolled at the University of California Irvine under Institutional Review Board-approved protocols (IRB # 2020C5779). A written informed consent was received from all participants prior to inclusion in this study. Sequence comparison among SARS-CoV-2 and previous Coronavirus strains: We retrieved 81,963 human SARS-CoV-2 genome sequences from GISAID database representing countries from North America, South America, Central America, Europe, Asia, Oceania, and Africa (Fig. 1). Furthermore, the full-length sequences of SARS-CoV strains (SARS-CoV-2-Wuhan-Hu-1 (“type”:”entrez-nucleotide”,”attrs”:”text”:”MN908947.3″,”term_id”:”1798172431″,”term_text”:”MN908947.3″MN908947.3), SARS-CoV-Urbani (“type”:”entrez-nucleotide”,”attrs”:”text”:”AY278741.1″,”term_id”:”30027617″,”term_text”:”AY278741.1″AY278741.1), HKU1-Genotype B (“type”:”entrez-nucleotide”,”attrs”:”text”:”AY884001″,”term_id”:”85372431″,”term_text”:”AY884001″AY884001), CoV-OC43 (“type”:”entrez-nucleotide”,”attrs”:”text”:”KF923903″,”term_id”:”701216735″,”term_text”:”KF923903″KF923903), CoV-NL63 (“type”:”entrez-nucleotide”,”attrs”:”text”:”NC_005831″,”term_id”:”49169782″,”term_text”:”NC_005831″NC_005831), CoV-229E (“type”:”entrez-nucleotide”,”attrs”:”text”:”KY983587″,”term_id”:”1198382572″,”term_text”:”KY983587″KY983587)) and MERS (“type”:”entrez-nucleotide”,”attrs”:”text”:”NC_019843″,”term_id”:”667489388″,”term_text”:”NC_019843″NC_019843)) found in the human host were obtained from the NCBI GenBank. SARS-CoV-2 genome sequences from bat (RATG13 (“type”:”entrez-nucleotide”,”attrs”:”text”:”MN996532.2″,”term_id”:”1916859392″,”term_text”:”MN996532.2″MN996532.2), ZXC21 (“type”:”entrez-nucleotide”,”attrs”:”text”:”MG772934.1″,”term_id”:”1369125429″,”term_text”:”MG772934.1″MG772934.1), YN01 (EPI_ISL_412976), YN02(EPI_ISL_412977)), and pangolin (GX-P2V (“type”:”entrez-nucleotide”,”attrs”:”text”:”MT072864.1″,”term_id”:”1824829169″,”term_text”:”MT072864.1″MT072864.1), GX-P5E (“type”:”entrez-nucleotide”,”attrs”:”text”:”MT040336.1″,”term_id”:”1808708909″,”term_text”:”MT040336.1″MT040336.1), GX-P5L (“type”:”entrez-nucleotide”,”attrs”:”text”:”MT040335.1″,”term_id”:”1808708899″,”term_text”:”MT040335.1″MT040335.1), GX-P1E (“type”:”entrez-nucleotide”,”attrs”:”text”:”MT040334.1″,”term_id”:”1808708889″,”term_text”:”MT040334.1″MT040334.1), GX-P4L (“type”:”entrez-nucleotide”,”attrs”:”text”:”MT040333.1″,”term_id”:”1808708879″,”term_text”:”MT040333.1″MT040333.1), GX-P3B (“type”:”entrez-nucleotide”,”attrs”:”text”:”MT072865.1″,”term_id”:”1824829254″,”term_text”:”MT072865.1″MT072865.1), MP789 (“type”:”entrez-nucleotide”,”attrs”:”text”:”MT121216.1″,”term_id”:”1817977257″,”term_text”:”MT121216.1″MT121216.1), Guangdong-P2S (EPI_ISL_410544)) were obtained from NCBI (www.ncbi.nlm.nih.gov/nuccore) and GSAID (www.gisaid.org). More so, the SARS-CoV strains from bat (WIV16 (“type”:”entrez-nucleotide”,”attrs”:”text”:”KT444582.1″,”term_id”:”940378824″,”term_text”:”KT444582.1″KT444582.1), WIV1 (“type”:”entrez-nucleotide”,”attrs”:”text”:”KF367457.1″,”term_id”:”556015142″,”term_text”:”KF367457.1″KF367457.1), YNLF_31C (“type”:”entrez-nucleotide”,”attrs”:”text”:”KP886808.1″,”term_id”:”916354744″,”term_text”:”KP886808.1″KP886808.1), Rs672 (“type”:”entrez-nucleotide”,”attrs”:”text”:”FJ588686.1″,”term_id”:”255733149″,”term_text”:”FJ588686.1″FJ588686.1), recombinant strain (“type”:”entrez-nucleotide”,”attrs”:”text”:”FJ211859.1″,”term_id”:”213990612″,”term_text”:”FJ211859.1″FJ211859.1), camel (“type”:”entrez-nucleotide”,”attrs”:”text”:”KT368891.1″,”term_id”:”922058628″,”term_text”:”KT368891.1″KT368891.1, “type”:”entrez-nucleotide”,”attrs”:”text”:”MN514967.1″,”term_id”:”1755169566″,”term_text”:”MN514967.1″MN514967.1, “type”:”entrez-nucleotide”,”attrs”:”text”:”KF917527.1″,”term_id”:”570348501″,”term_text”:”KF917527.1″KF917527.1, “type”:”entrez-nucleotide”,”attrs”:”text”:”NC_028752.1″,”term_id”:”971483139″,”term_text”:”NC_028752.1″NC_028752.1), and civet (Civet007, A022, B039)) were also retrieved from the NCBI GenBank. The sequences were aligned using ClustalW algorithm in MEGA X. Open in a separate window Figure 1. Evolutionary comparison of genome sequences among beta-Coronavirus strains isolated from humans and animals:(A) Phylogenetic analysis performed between SARS-CoV-2 strains (obtained from humans (and camels ((“type”:”entrez-nucleotide”,”attrs”:”text”:”KT368891.1″,”term_id”:”922058628″,”term_text”:”KT368891.1″KT368891.1, “type”:”entrez-nucleotide”,”attrs”:”text”:”MN514967.1″,”term_id”:”1755169566″,”term_text”:”MN514967.1″MN514967.1, “type”:”entrez-nucleotide”,”attrs”:”text”:”KF917527.1″,”term_id”:”570348501″,”term_text”:”KF917527.1″KF917527.1, “type”:”entrez-nucleotide”,”attrs”:”text”:”NC_028752.1″,”term_id”:”971483139″,”term_text”:”NC_028752.1″NC_028752.1), and civet (Civet007, A022, B039)). The human SARS-CoV-2 genome sequences are represented from six continents. (B) Phylogenetic analysis performed among SARS-CoV-2 strains from human and Tos-PEG3-NH-Boc other species with previous strains of SARS/MERS-CoV showed minimum genetic distance between the TIMP1 first SARS-CoV-2 isolate Wuhan-Hu-1 reported from the Wuhan Seafood market with bat strains hCoV-19-bat-Yunnan-RmYN02, bat-CoV-19-ZXC21, and hCoV-19-bat-Yunnan-RaTG13. This makes the bat strains nearest precursor to the human-SARS-CoV-2 strain. (C) Genetic distances based on Maximum Composite Likelihood model among the human, bat, pangolin, civet cat and camel genome sequences. Results indicate least genetic distance among SARS-CoV-2 isolate Wuhan-Hu-1 and bat strains bat-CoV-19-ZXC21 (0.1), hCoV-19-bat-Yunnan-RaTG13 (0.1), and hCoV-19-bat-Yunnan-RmYN02 (0.2). (D) Evolutionary analysis performed among the human-SARS-CoV-2 genome sequences reported from six continents and SARS-CoV-2 genome sequences obtained from bats (= 1574), Asia (= 7533), North America (= 19659), South America (= 1303), Europe (= 48752), Tos-PEG3-NH-Boc and Oceania region (= 3142) as on August 18, 2020. (F) Complete genome tree derived from 81,963 outbreak SARS-CoV-2 genome sequences submitted from Asian, African, North American, South American, European, and Oceanian regions. Sequence Tos-PEG3-NH-Boc conservation analysis of SARS-CoV-2: The SARS-CoV-2-Wuhan-Hu-1 (“type”:”entrez-nucleotide”,”attrs”:”text”:”MN908947.3″,”term_id”:”1798172431″,”term_text”:”MN908947.3″MN908947.3) protein sequence was Tos-PEG3-NH-Boc compared with SARS-CoV and MERS-CoV specific protein sequences obtained from human, bat, pangolin, civet and camel. The Sequence Variation Analysis was performed on the consensus aligned protein sequences from each virus strain. This Sequence Homology Analysis identified consensus protein sequences from the SARS-CoV and MERS-CoV and predicted the Epitope Sequence Analysis. SARS-CoV-2 CD8 and CD4 T Cell Epitope Prediction: Epitope prediction was carried out using the twelve proteins predicted for the reference SARS-CoV-2 isolate, Wuhan-Hu-1. The corresponding SARS-CoV-2 protein accession identification numbers.