Journal: bioRxiv

Article Title: Severity of SARS-CoV-2 infection as a function of the interferon landscape across the respiratory tract of COVID-19 patients

doi: 10.1101/2021.03.30.437173

Figure Lengend Snippet: ( A-C ) Age distribution ( A ), number ( B ) and percentage ( C ) of females and males in cohorts of patients (Swab −, Swab + and BALF) analyzed in . ( D-K ) Percentage of patients that express (Expressed, black bars) or not (Undetected, red bars) IFNL1 ( D ), IFNL2,3 ( E ), IFNL4 ( F ), IFNB1 ( G ), IFNA2 ( H ), IFNA4 ( I ), IL1B ( J ), and IL6 ( K ) in SARS-CoV-2 + swabs (Swab +) and in the BALF from SARS-CoV-2 + patients (BALF). Statistics: ( A ) One-way ANOVA test with Turkey’s post-hoc test: ns, not significant ( P >0.05); * P <0.05, ** P <0.01, *** P <0.001, and **** P <0.0001. ( D-K ) Fisher’s exact test; ns, not significant ( P >0.05); * P <0.05, ** P <0.01, *** P <0.001, and **** P <0.0001.

Article Snippet: IFNL1 ( Hs01050642_gH) , IFNL2,3 ( Hs04193047_gH) , IFNL4 (Hs04400217_g1), IFNB1 (Hs01077958_s1), IFNA2 (Hs00265051_s1) , IFNA4 (Hs01681284_sH) , IL1B (Hs01555410_m1) and IL6 (Hs00174131_m1) expression was assessed with respect to the housekeeping gene GAPDH (Hs99999905_m1).

Techniques:

Journal: bioRxiv

Article Title: Severity of SARS-CoV-2 infection as a function of the interferon landscape across the respiratory tract of COVID-19 patients

doi: 10.1101/2021.03.30.437173

Figure Lengend Snippet: ( A-H ) IFNL1 ( A ), IFNL2,3 ( B ), IFNL4 ( C ), IFNB1 ( D ), IFNA2 ( E ), IFNA4 ( F ), IL1B ( G ), and IL6 ( H ) mRNA expression was evaluated in nasopharyngeal swabs from SARS-CoV-2-negative (Swab −) and -positive (Swab +) subjects and in the BALF from SARS-CoV-2-positive patients (BALF). Expression is plotted as log2 ( gene / GAPDH mRNA + 0.5 x gene-specific minimum). Each dot represents a patient. Median with range is depicted. Statistics: ( A-H ) Kruskal-Wallis test with Dunn’s post-hoc test: ns, not significant ( P >0.05); * P <0.05, ** P <0.01, *** P <0.001, and **** P <0.0001.

Article Snippet: IFNL1 ( Hs01050642_gH) , IFNL2,3 ( Hs04193047_gH) , IFNL4 (Hs04400217_g1), IFNB1 (Hs01077958_s1), IFNA2 (Hs00265051_s1) , IFNA4 (Hs01681284_sH) , IL1B (Hs01555410_m1) and IL6 (Hs00174131_m1) expression was assessed with respect to the housekeeping gene GAPDH (Hs99999905_m1).

Techniques: Expressing

Journal: bioRxiv

Article Title: Severity of SARS-CoV-2 infection as a function of the interferon landscape across the respiratory tract of COVID-19 patients

doi: 10.1101/2021.03.30.437173

Figure Lengend Snippet: ( A-H ) IFNL1 (A ), IFNL2,3 (B ), IFNL4 ( C ), IFNB1 ( D ), IFNA2 ( E ), IFNA4 ( F ), IL1B ( G ), and IL6 ( H ) mRNA expression is plotted against mean viral RNA CT in SARS-CoV-2 + swabs. ( A-H ) Expression is plotted as log2 ( gene / GAPDH mRNA + 0.5 x gene-specific minimum). Each dot represents a patient. Linear regression lines (continuous line) and 95% confidence interval (dashed line and shaded area) are depicted in red. Spearman correlation coefficients (r) and p-value (p) are indicated. ( I-P ) IFNL1 (I ), IFNL2,3 (J ), IFNL4 ( K ), IFNB1 ( L ), IFNA2 ( M ), IFNA4 ( N ), IL1B ( O ), and IL6 ( P ) mRNA expression is plotted against mean viral RNA CT in swabs from SARS-CoV-2 + patients over 70-year-old (≥ 70, blue dots and lines) and below 70-year-old (< 70, orange dots and lines). ( I-P ) Expression is plotted as log2 ( gene / GAPDH mRNA + 0.5 x gene-specific minimum). Each dot represents a patient. Linear regression (continuous lines) and 95% confidence interval (dashed line and shaded area) are depicted. Spearman correlation coefficients (r) and p-value (p) are indicated in blue and in orange for ≥70 and <70 year-old patients respectively.

Article Snippet: IFNL1 ( Hs01050642_gH) , IFNL2,3 ( Hs04193047_gH) , IFNL4 (Hs04400217_g1), IFNB1 (Hs01077958_s1), IFNA2 (Hs00265051_s1) , IFNA4 (Hs01681284_sH) , IL1B (Hs01555410_m1) and IL6 (Hs00174131_m1) expression was assessed with respect to the housekeeping gene GAPDH (Hs99999905_m1).

Techniques: Expressing

Journal: bioRxiv

Article Title: Severity of SARS-CoV-2 infection as a function of the interferon landscape across the respiratory tract of COVID-19 patients

doi: 10.1101/2021.03.30.437173

Figure Lengend Snippet: ( A-H ) IFNL1 ( A ), IFNL2,3 ( B ), IFNL4 ( C ), IFNB1 ( D ), IFNA2 ( E ), IFNA4 ( F ), IL1B ( G ), and IL6 ( H ) mRNA expression in SARS-CoV-2 + swabs divided in viral load terciles (“+++”, “++”, “+”) defined by mean viral RNA CT (<20, >20 and <30, > 30) in patients over 70 years old (≥70, blue dots and lines) and below 70 years old (< 70, orange dots and lines). Expression is plotted as log2 ( gene / GAPDH mRNA + 0.5 x gene-specific minimum). Each dot represents a patient. Median with range is depicted. ( I-O ) Odds ratio of expressing IFNL2,3 ( I ), IFNL4 ( J ), IFNB1 ( K ), IFNA2 ( L ), IFNA4 ( M ), IL1B ( N ), and IL6 ( O ) mRNA in “+++” and “++” with respect to “+” SARS-CoV-2 + swabs in ≥70 (blue dots and lines) and < 70 (orange dots and lines) patients. Symbols represent the odds ratio. Error bars represent the 95% confidence interval associated to the odds ratio. NE: not estimable, J) no patient in group expresses IFNL4 , N) all patients in group express IL1B . Statistics: ( A-H ) Multiple Mann-Whitney tests with Holm-Šídák method: ns, not significant ( P >0.05); * P <0.05, ** P <0.01, *** P <0.001, and **** P <0.0001. ( I-O ) Odds ratio: ns, not significant ( P >0.05); # P <0.05, ## P <0.01, ### P <0.001. Interaction analysis: ns, not significant ( P >0.05); * P <0.05, ** P <0.01, *** P <0.001.

Article Snippet: IFNL1 ( Hs01050642_gH) , IFNL2,3 ( Hs04193047_gH) , IFNL4 (Hs04400217_g1), IFNB1 (Hs01077958_s1), IFNA2 (Hs00265051_s1) , IFNA4 (Hs01681284_sH) , IL1B (Hs01555410_m1) and IL6 (Hs00174131_m1) expression was assessed with respect to the housekeeping gene GAPDH (Hs99999905_m1).

Techniques: Expressing, MANN-WHITNEY

Journal: bioRxiv

Article Title: Severity of SARS-CoV-2 infection as a function of the interferon landscape across the respiratory tract of COVID-19 patients

doi: 10.1101/2021.03.30.437173

Figure Lengend Snippet: ( A-L ) Swabs from a cohort of SARS-CoV-2 + patients with known disease severity including ICU inpatients and hospitalized patients (HOSP, black dots and lines) and home-isolated patients (HI, red dots and lines) were analyzed. ( A-H ) IFNL1 ( A ), IFNL2,3 ( B ), IFNL4 ( C ), IFNB1 ( D ), IFNA2 ( E ), IFNA4 ( F ), IL1B ( G ), and IL6 ( H ) mRNA expression is plotted against mean viral RNA CT. Expression is plotted as log2 ( gene / GAPDH mRNA + 0.5 x gene-specific minimum). Each dot represents a patient. Linear regression lines (continuous line) and 95% confidence interval (dashed line and shaded area) are depicted. Spearman correlation coefficients (r) and p-value (p) are indicated in black and in red for HOSP and HI patients respectively. ( I ) K-means clustering based on the expression of IFNA2, IFNB1 IFNL1, IFNL2,3 , IL1B was used to determine clusters 1-3 (Cluster 1 n=15, Cluster 2 n=8, Cluster 3 n=6). The color indicates the relative gene expression. Viral load tercile, age group and severity are annotated. Viral load terciles (“+++”, “++”, “+”) are defined by mean viral RNA CT (<20, >20 and <30, > 30). Age groups are defined as <70 or ≥70-year old patients. Severity groups are defined as follows: HI=home isolated, HOSP (non ICU)=Hospitalized patients that did not require ICU admission, HOSP (ICU)=Hospitalized patients admitted to the ICU. ( J ) IFNL1, IFNL2,3 , IFNA2, IFNB1, IL1B mRNA expression within clusters identified in . Expression is plotted as log2 ( gene / GAPDH mRNA + 0.5 x gene-specific minimum). Each dot represents a patient. Violin plots are depicted. ( K ) Percentage of patients with the indicated disease severity within clusters identified in . ( L ) Odds ratio of patients in Cluster 2 and Cluster 1 being hospitalized relative to patients in Cluster 3 (Clusters identified in ). Symbols represent the odds ratio. Error bars represent the 95% confidence interval associated to the odds ratio. Statistics: ( L ) Odds ratio: ns, not significant ( P >0.05); * P <0.05, ** P <0.01, *** P <0.001.

Article Snippet: IFNL1 ( Hs01050642_gH) , IFNL2,3 ( Hs04193047_gH) , IFNL4 (Hs04400217_g1), IFNB1 (Hs01077958_s1), IFNA2 (Hs00265051_s1) , IFNA4 (Hs01681284_sH) , IL1B (Hs01555410_m1) and IL6 (Hs00174131_m1) expression was assessed with respect to the housekeeping gene GAPDH (Hs99999905_m1).

Techniques: Isolation, Expressing, Gene Expression

Journal: Liver International

Article Title: PDCD1 and IFNL4 genetic variants and risk of developing hepatitis C virus‐related diseases

doi: 10.1111/liv.14667

Figure Lengend Snippet: Frequencies of PD‐1 and IFNL4 genotypes in patients with HCV‐related diseases and in blood donors

Article Snippet: Genotyping of IFNL4 rs12979860 and rs117648444 (C>T, P70S) was performed using custom TaqMan SNP genotyping assays (Applied Biosystems) on a 7900HT Fast Real‐Time PCR system (Applied Biosystems).

Techniques:

Journal: Liver International

Article Title: PDCD1 and IFNL4 genetic variants and risk of developing hepatitis C virus‐related diseases

doi: 10.1111/liv.14667

Figure Lengend Snippet: Genomic positions of IFNL4 genetic variants in samples homozygous at rs12979860. In addition to rs12979860, eight different SNPs were identified in 24 of 36 samples. Three SNPs (including one in exon 3) have not previously been reported. The table below the gene diagram indicates the genotype at each polymorphism for all 36 samples

Article Snippet: Genotyping of IFNL4 rs12979860 and rs117648444 (C>T, P70S) was performed using custom TaqMan SNP genotyping assays (Applied Biosystems) on a 7900HT Fast Real‐Time PCR system (Applied Biosystems).

Techniques:

Journal: Liver International

Article Title: PDCD1 and IFNL4 genetic variants and risk of developing hepatitis C virus‐related diseases

doi: 10.1111/liv.14667

Figure Lengend Snippet: Frequency of IFNL4 genetic variants associated with IFNλ4 in patients and blood donors

Article Snippet: Genotyping of IFNL4 rs12979860 and rs117648444 (C>T, P70S) was performed using custom TaqMan SNP genotyping assays (Applied Biosystems) on a 7900HT Fast Real‐Time PCR system (Applied Biosystems).

Techniques: Expressing, Mutagenesis

Journal: Liver International

Article Title: PDCD1 and IFNL4 genetic variants and risk of developing hepatitis C virus‐related diseases

doi: 10.1111/liv.14667

Figure Lengend Snippet: Boxplot describing the relationship of IFNL4 genotype related to a fully active IFNL4 secretion with a younger median age of HCC patients. HCC patients carrying a fully active (rs12979860‐T/T combined without P70S mutation, rs117648444 C/C) were diagnosed with tumour at younger age compared to those with a reduced expression (rs12979860‐T/T combined with P70S mutation, rs117648444 C/T or T/T), median age 61y and 72y, respectively, P = .02 ANOVA test. Boxes range from the 25th to the 75th percentile with a horizontal black line at the median and vertical lines extending to the 10th and 90th percentiles. These data suggest that IFNL4 levels may represent a risk factor for HCC development

Article Snippet: Genotyping of IFNL4 rs12979860 and rs117648444 (C>T, P70S) was performed using custom TaqMan SNP genotyping assays (Applied Biosystems) on a 7900HT Fast Real‐Time PCR system (Applied Biosystems).

Techniques: Mutagenesis, Expressing

Journal: Liver International

Article Title: PDCD1 and IFNL4 genetic variants and risk of developing hepatitis C virus‐related diseases

doi: 10.1111/liv.14667

Figure Lengend Snippet: Pairwise linkage disequilibrium (LD) relationships between the PD‐1.3, PD‐1.5, PD‐1.7 and IFNL4 rs12979860 polymorphism. A–F, Results from linkage analysis conducted for the polymorphism of blood donors (A), CHC (B), cirrhosis (C), HCC (D), MC (E) and NHL (F) respectively

Article Snippet: Genotyping of IFNL4 rs12979860 and rs117648444 (C>T, P70S) was performed using custom TaqMan SNP genotyping assays (Applied Biosystems) on a 7900HT Fast Real‐Time PCR system (Applied Biosystems).

Techniques:

Journal: Liver International

Article Title: PDCD1 and IFNL4 genetic variants and risk of developing hepatitis C virus‐related diseases

doi: 10.1111/liv.14667

Figure Lengend Snippet: Epistatic interaction defined by PD‐1 and IFNL4 polymorphisms and their associations with HCV‐related diseases compared to patients with a chronic HCV infection

Article Snippet: Genotyping of IFNL4 rs12979860 and rs117648444 (C>T, P70S) was performed using custom TaqMan SNP genotyping assays (Applied Biosystems) on a 7900HT Fast Real‐Time PCR system (Applied Biosystems).

Techniques:

Journal: PLOS ONE

Article Title: Utility of a buccal swab point-of-care test for the IFNL4 genotype in the era of direct acting antivirals for hepatitis C virus

doi: 10.1371/journal.pone.0280551

Figure Lengend Snippet: Comparisons between Genedrive buccal swab and whole blood genotyping: CC, CT, and TT.

Article Snippet: The Genedrive® (previously Epistem) IFNL4 genotyping platform is a small, handheld ‘Point of Care’ (PoC) molecular diagnostic device developed by Genedrive PLC UK.

Techniques:

Journal: PLOS ONE

Article Title: Utility of a buccal swab point-of-care test for the IFNL4 genotype in the era of direct acting antivirals for hepatitis C virus

doi: 10.1371/journal.pone.0280551

Figure Lengend Snippet: Comparisons between Genedrive buccal swab and genome-wide genotyping: CC vs. non-CC.

Article Snippet: The Genedrive® (previously Epistem) IFNL4 genotyping platform is a small, handheld ‘Point of Care’ (PoC) molecular diagnostic device developed by Genedrive PLC UK.

Techniques: Genome Wide, Sequencing