PMC:7033720 / 13140-16434 JSONTXT

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    LitCovid-PubTator

    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. Table 2. Minor nucleotide variant identified from WHU01 and WHU02 genomes. Strain Region Variant Start Poisiton End Position Length Change Coverage Polymorphism Type VariantFrequency (%) P-value WHU01 1a T 221 221 1 C → T 27 SNP (transition) 14.80 6.70E-07 WHU01 1a A 1103 1103 1 T → A 119 SNP (transversion) 5.00 5.40E-14 WHU01 1a A 1820 1820 1 G → A 97 SNP (transition) 11.30 2.00E-27 WHU01 1a G 3916 3916 1 A → G 113 SNP (transition) 5.30 3.90E-14 WHU01 1a TT 3919 3920 2 AA → TT 110 Substitution 5.50 1.30E-13 WHU01 1a T 3923 3923 1 C → T 108 SNP (transition) 5.60 3.00E-14 WHU01 1a T 5701 5701 1 C → T 247 SNP (transition) 5.30 5.70E-29 WHU01 1a G 8892 8892 1 A → G 69 SNP (transition) 5.80 5.40E-10 WHU01 1a A 8895 8895 1 T → A 65 SNP (transversion) 6.20 4.20E-10 WHU01 1a G 8975 8975 1 A → G 59 SNP (transition) 5.10 6.50E-08 WHU01 1a C 9114 9114 1 T → C 43 SNP (transition) 7.00 7.70E-07 WHU01 1a   11,081 11,081 1 (T)8 → (T)7 78 Deletion (tandem repeat) 12.80 1.20E-20 WHU01 1a C 13,074 13,074 1 T → C 110 SNP (transition) 5.50 3.30E-14 WHU01 1a TT 13,282 13,283 2 AA → TT 78 → 79 Substitution 5.10 9.40E-10 WHU01 1b A 15,079 15,079 1 C → A 57 SNP (transversion) 8.80 1.30E-13 WHU01 1b T 18,252 18,252 1 A → T 192 SNP (transversion) 6.30 5.50E-23 WHU01 1b T 19,163 19,163 1 C → → T 89 SNP (transition) 19.10 1.90E-47 WHU01 1b A 20,234 20,234 1 C → A 67 SNP (transversion) 6.00 1.20E-09 WHU01 S A 22,315 22,315 1 G → A 182 SNP (transition) 6.60 4.70E-28 WHU01 S A 22,447 22,447 1 C → A 54 SNP (transversion) 5.60 2.00E-07 WHU01 S C 24,322 24,322 1 A → C 325 SNP (transversion) 38.50 0 WHU01 Other ORF A 26,313 26,313 1 G → A 29 SNP (transition) 10.30 1.50E-08 WHU02 1a T 1100 1100 1 C → T 390 SNP (transition) 6.70 1.50E-56 WHU02 1a A 1103 1103 1 T → A 391 SNP (transversion) 5.90 3.10E-51 WHU02 1a A 1820 1820 1 G → A 382 SNP (transition) 5.20 1.00E-41 WHU02 1a C 6823 6822 0 +C 129 Insertion 5.40 2.50E-16 WHU02 1a A 10,778 10,778 1 T → A 323 SNP (transversion) 5.30 2.40E-32 WHU02 1a T 11,366 11,366 1 A → T 250 SNP (transversion) 6.00 4.40E-31 WHU02 1a T 11,562 11,562 1 C → T 397 SNP (transition) 13.60 1.30E-138 WHU02 1b T 13,692 13,692 1 A → T 356 SNP (transversion) 7.00 1.60E-57 WHU02 1b C 14,306 14,306 1 T → C 279 SNP (transition) 7.90 9.20E-50 WHU02 1b A 14,315 14,315 1 G → A 244 SNP (transition) 10.70 6.90E-57 WHU02 Other ORF A 26,504 26,504 1 G → A 63 SNP (transition) 6.30 1.50E-10

    LitCovid-PD-FMA-UBERON

    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. Table 2. Minor nucleotide variant identified from WHU01 and WHU02 genomes. Strain Region Variant Start Poisiton End Position Length Change Coverage Polymorphism Type VariantFrequency (%) P-value WHU01 1a T 221 221 1 C → T 27 SNP (transition) 14.80 6.70E-07 WHU01 1a A 1103 1103 1 T → A 119 SNP (transversion) 5.00 5.40E-14 WHU01 1a A 1820 1820 1 G → A 97 SNP (transition) 11.30 2.00E-27 WHU01 1a G 3916 3916 1 A → G 113 SNP (transition) 5.30 3.90E-14 WHU01 1a TT 3919 3920 2 AA → TT 110 Substitution 5.50 1.30E-13 WHU01 1a T 3923 3923 1 C → T 108 SNP (transition) 5.60 3.00E-14 WHU01 1a T 5701 5701 1 C → T 247 SNP (transition) 5.30 5.70E-29 WHU01 1a G 8892 8892 1 A → G 69 SNP (transition) 5.80 5.40E-10 WHU01 1a A 8895 8895 1 T → A 65 SNP (transversion) 6.20 4.20E-10 WHU01 1a G 8975 8975 1 A → G 59 SNP (transition) 5.10 6.50E-08 WHU01 1a C 9114 9114 1 T → C 43 SNP (transition) 7.00 7.70E-07 WHU01 1a   11,081 11,081 1 (T)8 → (T)7 78 Deletion (tandem repeat) 12.80 1.20E-20 WHU01 1a C 13,074 13,074 1 T → C 110 SNP (transition) 5.50 3.30E-14 WHU01 1a TT 13,282 13,283 2 AA → TT 78 → 79 Substitution 5.10 9.40E-10 WHU01 1b A 15,079 15,079 1 C → A 57 SNP (transversion) 8.80 1.30E-13 WHU01 1b T 18,252 18,252 1 A → T 192 SNP (transversion) 6.30 5.50E-23 WHU01 1b T 19,163 19,163 1 C → → T 89 SNP (transition) 19.10 1.90E-47 WHU01 1b A 20,234 20,234 1 C → A 67 SNP (transversion) 6.00 1.20E-09 WHU01 S A 22,315 22,315 1 G → A 182 SNP (transition) 6.60 4.70E-28 WHU01 S A 22,447 22,447 1 C → A 54 SNP (transversion) 5.60 2.00E-07 WHU01 S C 24,322 24,322 1 A → C 325 SNP (transversion) 38.50 0 WHU01 Other ORF A 26,313 26,313 1 G → A 29 SNP (transition) 10.30 1.50E-08 WHU02 1a T 1100 1100 1 C → T 390 SNP (transition) 6.70 1.50E-56 WHU02 1a A 1103 1103 1 T → A 391 SNP (transversion) 5.90 3.10E-51 WHU02 1a A 1820 1820 1 G → A 382 SNP (transition) 5.20 1.00E-41 WHU02 1a C 6823 6822 0 +C 129 Insertion 5.40 2.50E-16 WHU02 1a A 10,778 10,778 1 T → A 323 SNP (transversion) 5.30 2.40E-32 WHU02 1a T 11,366 11,366 1 A → T 250 SNP (transversion) 6.00 4.40E-31 WHU02 1a T 11,562 11,562 1 C → T 397 SNP (transition) 13.60 1.30E-138 WHU02 1b T 13,692 13,692 1 A → T 356 SNP (transversion) 7.00 1.60E-57 WHU02 1b C 14,306 14,306 1 T → C 279 SNP (transition) 7.90 9.20E-50 WHU02 1b A 14,315 14,315 1 G → A 244 SNP (transition) 10.70 6.90E-57 WHU02 Other ORF A 26,504 26,504 1 G → A 63 SNP (transition) 6.30 1.50E-10

    LitCovid-PD-CLO

    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. Table 2. Minor nucleotide variant identified from WHU01 and WHU02 genomes. Strain Region Variant Start Poisiton End Position Length Change Coverage Polymorphism Type VariantFrequency (%) P-value WHU01 1a T 221 221 1 C → T 27 SNP (transition) 14.80 6.70E-07 WHU01 1a A 1103 1103 1 T → A 119 SNP (transversion) 5.00 5.40E-14 WHU01 1a A 1820 1820 1 G → A 97 SNP (transition) 11.30 2.00E-27 WHU01 1a G 3916 3916 1 A → G 113 SNP (transition) 5.30 3.90E-14 WHU01 1a TT 3919 3920 2 AA → TT 110 Substitution 5.50 1.30E-13 WHU01 1a T 3923 3923 1 C → T 108 SNP (transition) 5.60 3.00E-14 WHU01 1a T 5701 5701 1 C → T 247 SNP (transition) 5.30 5.70E-29 WHU01 1a G 8892 8892 1 A → G 69 SNP (transition) 5.80 5.40E-10 WHU01 1a A 8895 8895 1 T → A 65 SNP (transversion) 6.20 4.20E-10 WHU01 1a G 8975 8975 1 A → G 59 SNP (transition) 5.10 6.50E-08 WHU01 1a C 9114 9114 1 T → C 43 SNP (transition) 7.00 7.70E-07 WHU01 1a   11,081 11,081 1 (T)8 → (T)7 78 Deletion (tandem repeat) 12.80 1.20E-20 WHU01 1a C 13,074 13,074 1 T → C 110 SNP (transition) 5.50 3.30E-14 WHU01 1a TT 13,282 13,283 2 AA → TT 78 → 79 Substitution 5.10 9.40E-10 WHU01 1b A 15,079 15,079 1 C → A 57 SNP (transversion) 8.80 1.30E-13 WHU01 1b T 18,252 18,252 1 A → T 192 SNP (transversion) 6.30 5.50E-23 WHU01 1b T 19,163 19,163 1 C → → T 89 SNP (transition) 19.10 1.90E-47 WHU01 1b A 20,234 20,234 1 C → A 67 SNP (transversion) 6.00 1.20E-09 WHU01 S A 22,315 22,315 1 G → A 182 SNP (transition) 6.60 4.70E-28 WHU01 S A 22,447 22,447 1 C → A 54 SNP (transversion) 5.60 2.00E-07 WHU01 S C 24,322 24,322 1 A → C 325 SNP (transversion) 38.50 0 WHU01 Other ORF A 26,313 26,313 1 G → A 29 SNP (transition) 10.30 1.50E-08 WHU02 1a T 1100 1100 1 C → T 390 SNP (transition) 6.70 1.50E-56 WHU02 1a A 1103 1103 1 T → A 391 SNP (transversion) 5.90 3.10E-51 WHU02 1a A 1820 1820 1 G → A 382 SNP (transition) 5.20 1.00E-41 WHU02 1a C 6823 6822 0 +C 129 Insertion 5.40 2.50E-16 WHU02 1a A 10,778 10,778 1 T → A 323 SNP (transversion) 5.30 2.40E-32 WHU02 1a T 11,366 11,366 1 A → T 250 SNP (transversion) 6.00 4.40E-31 WHU02 1a T 11,562 11,562 1 C → T 397 SNP (transition) 13.60 1.30E-138 WHU02 1b T 13,692 13,692 1 A → T 356 SNP (transversion) 7.00 1.60E-57 WHU02 1b C 14,306 14,306 1 T → C 279 SNP (transition) 7.90 9.20E-50 WHU02 1b A 14,315 14,315 1 G → A 244 SNP (transition) 10.70 6.90E-57 WHU02 Other ORF A 26,504 26,504 1 G → A 63 SNP (transition) 6.30 1.50E-10

    LitCovid-PD-CHEBI

    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. Table 2. Minor nucleotide variant identified from WHU01 and WHU02 genomes. Strain Region Variant Start Poisiton End Position Length Change Coverage Polymorphism Type VariantFrequency (%) P-value WHU01 1a T 221 221 1 C → T 27 SNP (transition) 14.80 6.70E-07 WHU01 1a A 1103 1103 1 T → A 119 SNP (transversion) 5.00 5.40E-14 WHU01 1a A 1820 1820 1 G → A 97 SNP (transition) 11.30 2.00E-27 WHU01 1a G 3916 3916 1 A → G 113 SNP (transition) 5.30 3.90E-14 WHU01 1a TT 3919 3920 2 AA → TT 110 Substitution 5.50 1.30E-13 WHU01 1a T 3923 3923 1 C → T 108 SNP (transition) 5.60 3.00E-14 WHU01 1a T 5701 5701 1 C → T 247 SNP (transition) 5.30 5.70E-29 WHU01 1a G 8892 8892 1 A → G 69 SNP (transition) 5.80 5.40E-10 WHU01 1a A 8895 8895 1 T → A 65 SNP (transversion) 6.20 4.20E-10 WHU01 1a G 8975 8975 1 A → G 59 SNP (transition) 5.10 6.50E-08 WHU01 1a C 9114 9114 1 T → C 43 SNP (transition) 7.00 7.70E-07 WHU01 1a   11,081 11,081 1 (T)8 → (T)7 78 Deletion (tandem repeat) 12.80 1.20E-20 WHU01 1a C 13,074 13,074 1 T → C 110 SNP (transition) 5.50 3.30E-14 WHU01 1a TT 13,282 13,283 2 AA → TT 78 → 79 Substitution 5.10 9.40E-10 WHU01 1b A 15,079 15,079 1 C → A 57 SNP (transversion) 8.80 1.30E-13 WHU01 1b T 18,252 18,252 1 A → T 192 SNP (transversion) 6.30 5.50E-23 WHU01 1b T 19,163 19,163 1 C → → T 89 SNP (transition) 19.10 1.90E-47 WHU01 1b A 20,234 20,234 1 C → A 67 SNP (transversion) 6.00 1.20E-09 WHU01 S A 22,315 22,315 1 G → A 182 SNP (transition) 6.60 4.70E-28 WHU01 S A 22,447 22,447 1 C → A 54 SNP (transversion) 5.60 2.00E-07 WHU01 S C 24,322 24,322 1 A → C 325 SNP (transversion) 38.50 0 WHU01 Other ORF A 26,313 26,313 1 G → A 29 SNP (transition) 10.30 1.50E-08 WHU02 1a T 1100 1100 1 C → T 390 SNP (transition) 6.70 1.50E-56 WHU02 1a A 1103 1103 1 T → A 391 SNP (transversion) 5.90 3.10E-51 WHU02 1a A 1820 1820 1 G → A 382 SNP (transition) 5.20 1.00E-41 WHU02 1a C 6823 6822 0 +C 129 Insertion 5.40 2.50E-16 WHU02 1a A 10,778 10,778 1 T → A 323 SNP (transversion) 5.30 2.40E-32 WHU02 1a T 11,366 11,366 1 A → T 250 SNP (transversion) 6.00 4.40E-31 WHU02 1a T 11,562 11,562 1 C → T 397 SNP (transition) 13.60 1.30E-138 WHU02 1b T 13,692 13,692 1 A → T 356 SNP (transversion) 7.00 1.60E-57 WHU02 1b C 14,306 14,306 1 T → C 279 SNP (transition) 7.90 9.20E-50 WHU02 1b A 14,315 14,315 1 G → A 244 SNP (transition) 10.70 6.90E-57 WHU02 Other ORF A 26,504 26,504 1 G → A 63 SNP (transition) 6.30 1.50E-10

    LitCovid-sentences

    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. Table 2. Minor nucleotide variant identified from WHU01 and WHU02 genomes. Strain Region Variant Start Poisiton End Position Length Change Coverage Polymorphism Type VariantFrequency (%) P-value WHU01 1a T 221 221 1 C → T 27 SNP (transition) 14.80 6.70E-07 WHU01 1a A 1103 1103 1 T → A 119 SNP (transversion) 5.00 5.40E-14 WHU01 1a A 1820 1820 1 G → A 97 SNP (transition) 11.30 2.00E-27 WHU01 1a G 3916 3916 1 A → G 113 SNP (transition) 5.30 3.90E-14 WHU01 1a TT 3919 3920 2 AA → TT 110 Substitution 5.50 1.30E-13 WHU01 1a T 3923 3923 1 C → T 108 SNP (transition) 5.60 3.00E-14 WHU01 1a T 5701 5701 1 C → T 247 SNP (transition) 5.30 5.70E-29 WHU01 1a G 8892 8892 1 A → G 69 SNP (transition) 5.80 5.40E-10 WHU01 1a A 8895 8895 1 T → A 65 SNP (transversion) 6.20 4.20E-10 WHU01 1a G 8975 8975 1 A → G 59 SNP (transition) 5.10 6.50E-08 WHU01 1a C 9114 9114 1 T → C 43 SNP (transition) 7.00 7.70E-07 WHU01 1a   11,081 11,081 1 (T)8 → (T)7 78 Deletion (tandem repeat) 12.80 1.20E-20 WHU01 1a C 13,074 13,074 1 T → C 110 SNP (transition) 5.50 3.30E-14 WHU01 1a TT 13,282 13,283 2 AA → TT 78 → 79 Substitution 5.10 9.40E-10 WHU01 1b A 15,079 15,079 1 C → A 57 SNP (transversion) 8.80 1.30E-13 WHU01 1b T 18,252 18,252 1 A → T 192 SNP (transversion) 6.30 5.50E-23 WHU01 1b T 19,163 19,163 1 C → → T 89 SNP (transition) 19.10 1.90E-47 WHU01 1b A 20,234 20,234 1 C → A 67 SNP (transversion) 6.00 1.20E-09 WHU01 S A 22,315 22,315 1 G → A 182 SNP (transition) 6.60 4.70E-28 WHU01 S A 22,447 22,447 1 C → A 54 SNP (transversion) 5.60 2.00E-07 WHU01 S C 24,322 24,322 1 A → C 325 SNP (transversion) 38.50 0 WHU01 Other ORF A 26,313 26,313 1 G → A 29 SNP (transition) 10.30 1.50E-08 WHU02 1a T 1100 1100 1 C → T 390 SNP (transition) 6.70 1.50E-56 WHU02 1a A 1103 1103 1 T → A 391 SNP (transversion) 5.90 3.10E-51 WHU02 1a A 1820 1820 1 G → A 382 SNP (transition) 5.20 1.00E-41 WHU02 1a C 6823 6822 0 +C 129 Insertion 5.40 2.50E-16 WHU02 1a A 10,778 10,778 1 T → A 323 SNP (transversion) 5.30 2.40E-32 WHU02 1a T 11,366 11,366 1 A → T 250 SNP (transversion) 6.00 4.40E-31 WHU02 1a T 11,562 11,562 1 C → T 397 SNP (transition) 13.60 1.30E-138 WHU02 1b T 13,692 13,692 1 A → T 356 SNP (transversion) 7.00 1.60E-57 WHU02 1b C 14,306 14,306 1 T → C 279 SNP (transition) 7.90 9.20E-50 WHU02 1b A 14,315 14,315 1 G → A 244 SNP (transition) 10.70 6.90E-57 WHU02 Other ORF A 26,504 26,504 1 G → A 63 SNP (transition) 6.30 1.50E-10