PMC:7033720 / 13140-16434 JSONTXT

{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/7033720","sourcedb":"PMC","sourceid":"7033720","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7033720","text":"On 8th January 2020, the genome comparisons and evolutionary analyses were performed. Although some single nucleotide polymorphism (SNP) profiles were identified in the mNGS data (Table 2), the consensus genome sequences obtained from the patient 1 and 2 were identical (GenBank MN988668 and MN988669, respectively). These results indicated that these two individual patients were infected by the same CoV at separate times. We named the two clinical isolates as 2019-nCoV strain WHU01 and WHU02, respectively, according to WHO announcement. Based on the results of genome mapping, our data revealed extremely high viral abundance within the samples: the average genome coverage was 523.6X and 133.7X and the estimated abundance level were 1.5% and 0.62% of total reads sequenced for patient 1 and 2, respectively, suggesting active coronaviral replication in the lungs of both patients.\nTable 2. Minor nucleotide variant identified from WHU01 and WHU02 genomes.\nStrain Region Variant Start Poisiton End Position Length Change Coverage Polymorphism Type VariantFrequency (%) P-value\nWHU01 1a T 221 221 1 C → T 27 SNP (transition) 14.80 6.70E-07\nWHU01 1a A 1103 1103 1 T → A 119 SNP (transversion) 5.00 5.40E-14\nWHU01 1a A 1820 1820 1 G → A 97 SNP (transition) 11.30 2.00E-27\nWHU01 1a G 3916 3916 1 A → G 113 SNP (transition) 5.30 3.90E-14\nWHU01 1a TT 3919 3920 2 AA → TT 110 Substitution 5.50 1.30E-13\nWHU01 1a T 3923 3923 1 C → T 108 SNP (transition) 5.60 3.00E-14\nWHU01 1a T 5701 5701 1 C → T 247 SNP (transition) 5.30 5.70E-29\nWHU01 1a G 8892 8892 1 A → G 69 SNP (transition) 5.80 5.40E-10\nWHU01 1a A 8895 8895 1 T → A 65 SNP (transversion) 6.20 4.20E-10\nWHU01 1a G 8975 8975 1 A → G 59 SNP (transition) 5.10 6.50E-08\nWHU01 1a C 9114 9114 1 T → C 43 SNP (transition) 7.00 7.70E-07\nWHU01 1a   11,081 11,081 1 (T)8 → (T)7 78 Deletion (tandem repeat) 12.80 1.20E-20\nWHU01 1a C 13,074 13,074 1 T → C 110 SNP (transition) 5.50 3.30E-14\nWHU01 1a TT 13,282 13,283 2 AA → TT 78 → 79 Substitution 5.10 9.40E-10\nWHU01 1b A 15,079 15,079 1 C → A 57 SNP (transversion) 8.80 1.30E-13\nWHU01 1b T 18,252 18,252 1 A → T 192 SNP (transversion) 6.30 5.50E-23\nWHU01 1b T 19,163 19,163 1 C → → T 89 SNP (transition) 19.10 1.90E-47\nWHU01 1b A 20,234 20,234 1 C → A 67 SNP (transversion) 6.00 1.20E-09\nWHU01 S A 22,315 22,315 1 G → A 182 SNP (transition) 6.60 4.70E-28\nWHU01 S A 22,447 22,447 1 C → A 54 SNP (transversion) 5.60 2.00E-07\nWHU01 S C 24,322 24,322 1 A → C 325 SNP (transversion) 38.50 0\nWHU01 Other ORF A 26,313 26,313 1 G → A 29 SNP (transition) 10.30 1.50E-08\nWHU02 1a T 1100 1100 1 C → T 390 SNP (transition) 6.70 1.50E-56\nWHU02 1a A 1103 1103 1 T → A 391 SNP (transversion) 5.90 3.10E-51\nWHU02 1a A 1820 1820 1 G → A 382 SNP (transition) 5.20 1.00E-41\nWHU02 1a C 6823 6822 0 +C 129 Insertion 5.40 2.50E-16\nWHU02 1a A 10,778 10,778 1 T → A 323 SNP (transversion) 5.30 2.40E-32\nWHU02 1a T 11,366 11,366 1 A → T 250 SNP (transversion) 6.00 4.40E-31\nWHU02 1a T 11,562 11,562 1 C → T 397 SNP (transition) 13.60 1.30E-138\nWHU02 1b T 13,692 13,692 1 A → T 356 SNP (transversion) 7.00 1.60E-57\nWHU02 1b C 14,306 14,306 1 T → C 279 SNP (transition) 7.90 9.20E-50\nWHU02 1b A 14,315 14,315 1 G → A 244 SNP (transition) 10.70 6.90E-57\nWHU02 Other ORF A 26,504 26,504 1 G → A 63 SNP (transition) 6.30 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