Genomic perspectives of SARS CoV-2 in liver disease patients with its clinical correlation: A single centre retrospective study (preprint)

Background: Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2), is a causative agent of current global pandemic of Coronavirus disease-19 (COVID-19). Due to propagated outbreak and global vaccination drive an immense immunological selection pressure has been exerted on SARS CoV-2 leading to evolution of new variants. This study was performed to compare the mutational and clinical profile of liver disease patients infected with different variants of SARS CoV-2. Methodology: This was a single-centre, retrospective, cohort study in which clinicogenomic analysis of liver disease (LD) patients infected with SARS CoV-2 was performed. Complete demographic and clinical details were retrieved from Hospital Information System (HIS). QC-threshold passed FASTA files containing sequences from COVID-19 patients (n=174) were compared with a reference genome of SARS-CoV-2 isolate named Wuhan-Hu-1 (NCBI Reference Sequence: NC_045512.2) for mutational analysis. Results: Out of 232 finally analysed patients 137 (59.1%) were LD-CoV (+) and 95 (40.9%) were LD-CoV(-). LD patients with comorbidities were affected more with COVID-19 (p=0.002). On comparing the outcome in the terms of mortality, LD-CoV (+) had 2.29 times (OR 2.29, CI 95%, 1.25-4.29) higher of odds of succumbing to COVID-19 (p=0.006). Multivariate regression analysis revealed, abdominal distention (p=0.05), severe COVID-19 pneumonia (p=0.046) and the change in serum bilirubin levels (p=0.005) as well as Alkaline phosphatase (ALP) levels (p=0.003) to have an association with adverse outcome in LD patients with COVID-19. In Delta (22%) and Omicron (48%) groups, Spike gene harboured maximum mutations. On comparing the mutations between LD-CoV(+/D) and LD-CoV(+/O) a total of nine genes had more mutations in LD-CoV(+/O) whereas three genes had more mutations in LD-CoV(+/D). Conclusion: We concluded that LD patients are more susceptible to COVID-19 as compared to a healthy adult with associated adverse clinical outcomes in terms of mortality and morbidity. Therefore this special group should be given priority while devising and introducing new vaccination and vaccination policies. The infection with different variants did not result in different outcome in our group of patients. Keywords: COVID-19, SARS CoV-2, Delta, Omicron, Liver disease

Elevated Plasma Levels of ICAM1 Predict Mortality in COVID-19 and Sepsis Patients with Liver Cirrhosis (preprint)

Background: An increased covid-19 mortality has been reported in patients with liver cirrhosis. Given a significant association of endothelial damage with both liver disease and covid-19 severity, we investigated key endothelial injury markers in covid-19 patients with and without cirrhosis. Methods: A cross-sectional study with PCR-confirmed moderate/severe covid-19 hospitalized patients with and without cirrhosis was performed. Cirrhosis patients with bacterial sepsis were also recruited. Soluble plasma bio-markers of endothelial cell injury, including intercellular adhesion molecule 1 (ICAM1), von Willebrand Factor (vWF) antigen, vascular endothelial growth factor receptor 1 (vegfr1), angiopoietin 1 and 2 (Ang1, 2) were measured. Findings: A total of 56 hospitalized patients were included belonging to patients in moderate covid-19 category [covid-19 with liver cirrhosis (n=6); covid-19 without liver cirrhosis (n=8)] and severe covid-19 category [covid-19 with liver cirrhosis (n=10); severe covid-19 without liver cirrhosis (n=15)]. 17 patients were with liver cirrhosis plus bacterial sepsis. ICAM1 levels were increased (p=0.04) while vegfr1 (p<0.0001) and Ang1 (p<0.0001) were reduced in covid-19 patients with cirrhosis, as compared to that in covid-19 patients alone. On univariate logistic regression, ICAM1 (OR=9.81, 95%CI 11.69-155.9, p=0.03) and Ang2 levels (OR=3.72, 95%CI 1.29-21.92, p=0.04) predicted mortality in covid-19 patients with cirrhosis. Among severe covid-19, patients with covid-19 alone had a 28-day mortality of 76.7%, covid-19 plus cirrhosis had 48% while patients with cirrhosis had 23.8%. Endothelial injury biomarkers between cirrhosis patients with sepsis and those with covid-19 did not differ significantly. In cirrhosis patients with severe covid-19 and sepsis analysed together, elevated ICAM1 levels (OR=15, 95% CI 0.2-1380, P<0.05) and MELD score (OR=1.11, 95%CI=1.0-1.26, P<0.03) appeared to be significantly associated with mortality. For these patients, the area under the curve for ICAM1 was 0.721, while that of the MELD score was 0.621. An ICAM1 value higher than 182,150 pg/ml and MELD more than 31.5 was associated with higher mortality in liver cirrhosis patients with covid-19 and sepsis (ICAM1: HR: 5.65, 95% CI 2.16-14.83, p<0.01; MELD:HR: 1.09, 95% CI 1.02-1.16, p< 0.05). Interpretation: The study indicates that in patients with liver cirrhosis, altered levels of endothelial injury markers may be associated with a higher covid-19 and sepsis associated in-hospital mortality. Both elevated ICAM1 and MELD would serve as valuable predictors of covid-19 and sepsis associated mortality in cirrhosis patients. Funding: The study was funded by research funds from the Institute of liver and biliary Sciences (ILBS).Declaration of Interests: All authors declare no competing interestsEthics Approval Statement: The institutional review board approved this study (Ethics protocol no IEC/2020/82/NA01).

Efficacy of Convalescent Plasma Therapy compared to Fresh Frozen Plasma in Severely ill COVID-19 Patients: A Pilot Randomized Controlled Trial (preprint)

Background: The role of convalescent plasma (COPLA) for the treatment of severely ill Corona Virus Disease-2019 is under investigation. We compared the efficacy and safety of convalescent plasma with fresh frozen plasma (FFP) in severe COVID-19 patients. Methods and findings: This was an open-label, single-centre phase II RCT on 29 patients with severe COVID-19 from India. One group received COPLA with standard medical care (SMC) (n=14), and another group received FFP with SMC (n=15). A total of 29 patients were randomized in the two treatment groups. Eleven out of 14 (78.5%) patients remained free of ventilation at day seven in the intervention arm while the proportion was 14 out of 15 (93.3 %) in the control arm (p= 0.258). The median reductions in RR per min at 48-hours in COPLA-group and FFP group were -6.5 and -3 respectively [p=0.004] and at day seven were -14.5 and -10 respectively (p=0.008). The median improvements in percentage O2 saturation at 48-hours were 6.5 and 2 respectively [p=0.001] and at day seven were 10 and 7.5 respectively (p=0.026). In the COPLA-group, the median improvement in PaO2/FiO2 was significantly superior to FFP at 48-hours [41.94 and 231.15, p=0.009], and also at day-7 [5.55 and 77.01 p<0.001]. We did not find significant differences in hospitalization duration between the groups (0.08). Conclusion: COPLA therapy resulted in rapid improvement in respiratory parameters and shortened time to clinical recovery, although no significant reduction in mortality was observed in this pilot trial. We need larger trials to draw conclusive evidence on the use of Convalescent plasma in COVID-19.

Pooled RNA sample reverse transcriptase real time PCR assay for SARS CoV-2 infection: a reliable, faster and economical method. (preprint)

Background: Corona virus disease 2019 (COVID-19) which initially started as a cluster of pneumonia cases in the Wuhan city of China has now become a full blown pandemic. Timely diagnosis of COVID-19 is the key in containing the pandemic and breaking the chain of In low and middle income countries availability of testing kits has become the major bottle neck in testing. Novel methods like pooling of samples are the need of the hour. Method: Extracted RNA samples were randomly placed in pools of 8 on a 96 well plate. Both individual RNA (ID) and pooled RNA RT-qPCR for the screening E gene were done in the same plate and the positivity for the E gene was seen. Results: The present study demonstrated that pool testing with 8 RNA samples can easily detect even up to a single positive sample with Ct value as high as 38. The present study also showed that the results of pool testing is not affected by number of positive samples in a pool. Conclusion: Pooling of 8 RNA samples can reduce the time and expense by one eighth, and can help expand diagnostic capabilities, especially during constrained supply of reagents and PCR kits for the diagnosis of SARS-CoV-2 infection.