Epidemiology, clinical presentation and management of COVID-19 associated Mucormycosis: A single center experience from Pune, Western India. (preprint)

BackgroundThe second COVID-19 wave in India, triggered by the Delta variant,has been associated with an unprecedented increase in cases of COVID-19 associated Mucormycosis(CAM), mainly Rhino-orbito-cerebral mucormycosis(ROCM).The primary reason appears to be an unusual alignment of multiple risk factors in patients like prevalence of hypoxia, uncontrolled diabetes mellitus, indiscriminate use of steroids, high iron levels and immune dysfunction. MethodsThis retrospective cohort study was conducted at Noble hospital and Research Centre (NHRC), Pune, Western India between 1st April 2020 and 1st August 2021 to identify patients admitted with CAM. The primary endpoint was incidence of all cause mortality due to CAM. Secondary outcomes studied were need for mechanical ventilation and intensive care unit(ICU) admission. Baseline and time dependent risk factors significantly associated with death due to CAM were identified by Relative risk estimation. Results59 patients were diagnosed with Mucormycosis at NHRC (58 ROCM, 1 Renal (disseminated) mucormycosis). Median age of the cohort was 52(IQR: 41,61) years and it included 20.3% females. Median duration from first positive COVID-19 RT PCR test to diagnosis of Mucormycosis was 17(IQR: 12,22) days. 90% patients were diabetic with 30% being newly diagnosed at the time of COVID-19 admission and 89% having uncontrolled sugar level (HbA1c > 7%). All patients were prescribed steroids during treatment for COVID-19. 56% patients were prescribed steroids for non-hypoxemic, mild COVID (irrational steroid therapy) while in 9%, steroids were indicated but were prescribed in inappropriately high dose. Majority of the patients were treated with a combination of surgical debridement(94%), intravenous Amphotericin B(91%) and concomitant oral Posoconazole therapy(95.4%). 74.6% patients were discharged after clinical and radiologic recovery while 25.4% (15 patients) died. On Relative risk analysis, CT severity score during COVID-19 admission [≥]18 (p=0.017), presence of orbital symptoms(p=0.002), presence of diabetic ketoacidosis(p=0.011) and cerebral involvement by Mucor(p=0.0004) were associated with increased risk of death. Duration of Amphotericin B therapy of [≥] 21 days was associated with statistically significant reduction in mortality(p=0.002). ConclusionsCAM is an uncommon, rapidly progressive, angioinvasive, opportunistic fungal infection which is fatal if left untreated. Combination of surgical debridement and antifungal therapy leads to clinical and radiologic improvement in majority of cases.

Evolution of enhanced innate immune evasion by the SARS-CoV-2 B.1.1.7 UK variant (preprint)

Emergence of SARS-CoV-2 variants, including the globally successful B.1.1.7 lineage, suggests viral adaptations to host selective pressures resulting in more efficient transmission. Although much effort has focused on Spike adaptation for viral entry and adaptive immune escape, B.1.1.7 mutations outside Spike likely contribute to enhance transmission. Here we used unbiased abundance proteomics, phosphoproteomics, mRNA sequencing and viral replication assays to show that B.1.1.7 isolates more effectively suppress host innate immune responses in airway epithelial cells. We found that B.1.1.7 isolates have dramatically increased subgenomic RNA and protein levels of Orf9b and Orf6, both known innate immune antagonists. Expression of Orf9b alone suppressed the innate immune response through interaction with TOM70, a mitochondrial protein required for RNA sensing adaptor MAVS activation, and Orf9b binding and activity was regulated via phosphorylation. We conclude that B.1.1.7 has evolved beyond the Spike coding region to more effectively antagonise host innate immune responses through upregulation of specific subgenomic RNA synthesis and increased protein expression of key innate immune antagonists. We propose that more effective innate immune antagonism increases the likelihood of successful B.1.1.7 transmission, and may increase in vivo replication and duration of infection.

Combination therapy of Tocilizumab and steroid for management of COVID-19 associated cytokine release syndrome: A single center experience from Pune, Western India (preprint)

Background: Cytokine release syndrome (CRS) or cytokine storm is thought to be the cause of inflammatory lung damage, worsening pneumonia and death in patients with COVID-19. Steroids (Methylprednisolone or Dexamethasone) and Tocilizumab (TCZ), an interleukin-6 receptor antagonist, are approved for the treatment of CRS in India. The aim of this study was to evaluate the efficacy and safety of combination therapy of TCZ and steroids in COVID-19 associated CRS. Methods: This retrospective cohort study was conducted at a tertiary level private hospital in Pune, India between 2nd April and 2nd November 2020. All patients administered TCZ and steroids for treatment of CRS were included. The primary endpoint was the incidence of all-cause mortality. Secondary outcomes studied were the need for mechanical ventilation and incidence of infectious complications. Baseline and time-dependent risk factors significantly associated with death were identified by Relative risk estimation. Results: Out of 2831 admitted patients, 515 (24.3% females) were administered TCZ and steroids. Median age of the cohort was 57 (IQR: 46.5, 66) years. Almost 72 % patients had preexisting co-morbidities. Median time to TCZ administration since onset of symptoms was 9 days (IQR: 7, 11). 63% patients needed intensive care unit (ICU) admission. Mechanical ventilation was required in 242 (47%) patients. Of these, 44.2% (107/242) recovered and were weaned off the ventilator. There were 135 deaths (26.2%), while 380 patients (73.8%) had clinical improvement. Infectious complications like hospital acquired pneumonia, bloodstream bacterial and fungal infections were observed in 2.13 %, 2.13 % and 0.06 % patients respectively. Age [≥] 60 years (p=0.014), presence of co-morbidities like hypertension (p = 0.011), IL-6 [≥] 100 pg/ml (p = 0.002), D-dimer [≥] 1000 ng/ml (p < 0.0001), CT severity index [≥] 18 (p < 0.0001) and systemic complications like lung fibrosis (p = 0.019), cardiac arrhythmia (p < 0.0001), hypotension (p < 0.0001) and encephalopathy (p < 0.0001) were associated with increased risk of death. Conclusions: Combination therapy of TCZ and Steroids is likely to be safe and effective in the management of COVID-19 associated cytokine release syndrome. Efficacy of this anti-inflammatory combination therapy needs to be validated in randomized controlled clinical trials.

A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing (preprint)

An outbreak of the novel coronavirus SARS-CoV-2, the causative agent of COVID-19 respiratory disease, has infected over 290,000 people since the end of 2019, killed over 12,000, and caused worldwide social and economic disruption1,2. There are currently no antiviral drugs with proven efficacy nor are there vaccines for its prevention. Unfortunately, the scientific community has little knowledge of the molecular details of SARS-CoV-2 infection. To illuminate this, we cloned, tagged and expressed 26 of the 29 viral proteins in human cells and identified the human proteins physically associated with each using affinity-purification mass spectrometry (AP-MS), which identified 332 high confidence SARS-CoV-2-human protein-protein interactions (PPIs). Among these, we identify 66 druggable human proteins or host factors targeted by 69 existing FDA-approved drugs, drugs in clinical trials and/or preclinical compounds, that we are currently evaluating for efficacy in live SARS-CoV-2 infection assays. The identification of host dependency factors mediating virus infection may provide key insights into effective molecular targets for developing broadly acting antiviral therapeutics against SARS-CoV-2 and other deadly coronavirus strains.