Vaccination saves lives: How do patients with chronic diseases and severe COVID-19 fare? Analysis from India’s National Clinical registry for COVID-19 (preprint)

Objectives This study aims to describe the demographic and clinical profile and ascertain the determinants of outcome among hospitalised COVID-19 adult patients enrolled in the National Clinical Registry for COVID-19 (NCRC). Methods NCRC is an on-going data collection platform operational in 42 hospitals across India. Data of hospitalized COVID-19 patients enrolled in NCRC between 1 st September 2020 to 26 th October 2021 were examined. Results Analysis of 29,509 hospitalised, adult COVID-19 patients [mean (SD) age: 51.1 (16.2) year; male: 18752 (63.6%)] showed that 15678 (53.1%) had at least one comorbidity. Among 25715 (87.1%) symptomatic patients, fever was the commonest symptom (72.3%) followed by shortness of breath (48.9%) and dry cough (45.5%). In-hospital mortality was 14.5% (n=3957). Adjusted odds of dying were significantly higher in age-group ≥60 years, males, with diabetes, chronic kidney diseases, chronic liver disease, malignancy, and tuberculosis, presenting with dyspnea and neurological symptoms. WHO ordinal scale 4 or above at admission carried the highest odds of dying [5.6 (95% CI: 4.6, 7.0)]. Patients receiving one [OR: 0.5 (95% CI: 0.4, 0.7)] or two doses of anti-SARS CoV-2 vaccine [OR: 0.4 (95% CI: 0.3, 0.7)] were protected from in-hospital mortality. Conclusions WHO ordinal scale at admission is the most important independent predictor for in-hospital death in COVID-19 patients. Anti-SARS-CoV2 vaccination provides significant protection against mortality.

Analysis of predictors and outcomes of COVID-19 patients requiring ICU admission from COVID 19 (preprint)

BackgroundSevere Corona virus disease (COVID-19) is associated with high mortality. Although single centre intensive care units (ICU) have reported clinical characteristics and outcomes, no large scale multicentric study from India has been published. The present retrospective, multi-centre study was aimed to describe the predictors and outcomes of COVID-19 patients requiring ICU admission from COVID-19 Registry of Indian council of Medical Research (ICMR), India.MethodsProspectively collected data from multiple participating institutions was entered in the electronic National Clinical Registry of COVID 19. We enrolled patients aged>18 years with COVID-19 pneumonia requiring ICU admission between March 2020 and August 2021. Exclusion criteria were negative RT PCR, death within 24 hours of ICU admission, or patients with incomplete data in the registry Their demographic characteristics, laboratory variables, ICU severity indices, treatment strategies and outcomes were analysed.ResultsA total of 5865 patients, with mean age 56±15 years, with 3840/5865 (65.4%) men, were enrolled in the ICMR registry.. Overall mortality was 2535/5865 (43.5%). Non-survivors were older than survivors (58.2±15.4 years vs 53.6 ±14.7 years; P=0.001). Non-survivors had multiple comorbidities (n=1951, 52.9%) with hypertension (47.2%) and diabetes (45.6%) being the most common, higher creatinine (1.6 ± P=0.001, high D-dimer (1.56 vs 1.37, P=0.001), higher CT severity index (16.8±5.2 vs 13.5 ±5.47 ) compared to  survivors. Non survivors had longer hospital and ICU stay (P=0.001). On multivariate regression analysis, high NLR (HR 1.017, 95% CI 1.005- 1.029, P=0.001), high CRP (HR 1.008, 95% CI 1.006- 1.010, P=0.001), high D dimer ((HR 1.089, 95% CI 1.065- 1.113, P=0.001) were associated with mechanical ventilation while younger age, (HR 0.974, CI 0.965-0.983, p=0.001), high D dimer (HR-1.014, CI 1.001-1.027, P=0.035) and use of prophylactic LMWH (HR 0.647, CI 0.527-0.794, p=0.001) were independently associated with mortality. ConclusionIn this large retrospective study of 5865 critically ill COVID 19 patients admitted to ICU, overall mortality was 2535/5865 (43.5%). Age, high D dimer, CT Severity score and use of prophylactic LMWH were independently associated with mortality. 

UVA radiation could be a significant contributor to sunlight inactivation of SARS-CoV-2 (preprint)

Past experiments demonstrated SARS-CoV-2 inactivation by simulated sunlight; models have considered exclusively mechanisms involving UVB acting directly on RNA. However, UVA inactivation has been demonstrated for other enveloped RNA viruses, through indirect mechanisms involving the suspension medium. We propose a model combining UVB and UVA inactivation for SARS-CoV-2, which improves predictions by accounting for effects associated with the medium. UVA sensitivities deduced for SARS-CoV-2 are consistent with data for SARS-CoV-1 under UVA only. This analysis calls for experiments to separately assess effects of UVA and UVB in different media, and for including UVA in inactivation models. Key words: SARS-CoV-2, COVID-19, environmental persistence, sunlight, UVA, UVB, modeling, inactivation methods, photobiology

Analysis of SARS-CoV-2 genomes from across Africa reveals potentially clinically relevant mutations. (preprint)

SARS-CoV-2 is a betacoronavirus, the etiologic agent of the novel Coronavirus disease 2019 (COVID-19). In December 2019, an outbreak of COVID-19 began in Wuhan province of the Hubei district in China and rapidly spread across the globe. On March 11th, 2020, the World Health Organization officially designated COVID-19 as a pandemic. Across the continents and specifically in Africa, all index cases were travel related. Thus, it is crucial to compare COVID-19 genome sequences from the African continent with sequences from COVID-19 hotspots (including China, Brazil, Italy, United State of America and the United Kingdom). To identify if there are distinguishing mutations in the African SARS-CoV-2 genomes compared to genomes from other countries, including disease hotspots, we conducted in silico analyses and comparisons. Complete African SARS-CoV-2 genomes deposited in GISAID and NCBI databases as of June 2020 were downloaded and aligned with genomes from Wuhan, China and other SARS-CoV-2 hotspots. Using phylogenetic analysis and amino acid sequence alignments of the spike and replicase (NSP12) proteins, we searched for possible targets for vaccine coverage or potential therapeutic agents. Our results showed a similarity between the African SARS-CoV-2 genomes and genomes in countries including China, Brazil, France, the United Kingdom, Italy, France and the United States of America. This study shows for the first time, an in-depth analysis of the SARS-CoV-2 landscape across Africa and will potentially provide insights into specific mutations to relevant proteins in the SARS-CoV-2 genomes in African populations.

A prefusion SARS-CoV-2 spike RNA vaccine is highly immunogenic and prevents lung infection in non-human primates (preprint)

To contain the coronavirus disease 2019 (COVID-19) pandemic, a safe and effective vaccine against the new severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is urgently needed in quantities sufficient to immunise large populations. In this study, we report the design, preclinical development, immunogenicity and anti-viral protective effect in rhesus macaques of the BNT162b2 vaccine candidate. BNT162b2 contains an LNP-formulated nucleoside-modified mRNA that encodes the spike glycoprotein captured in its prefusion conformation. After expression of the BNT162b2 coding sequence in cells, approximately 20% of the spike molecules are in the one-RBD up, two-RBD down state. Immunisation of mice with a single dose of BNT162b2 induced dose level-dependent increases in pseudovirus neutralisation titers. Prime-boost vaccination of rhesus macaques elicited authentic SARS-CoV-2 neutralising geometric mean titers 10.2 to 18.0 times that of a SARS-CoV-2 convalescent human serum panel. BNT162b2 generated strong TH1 type CD4+ and IFNy+ CD8+ T-cell responses in mice and rhesus macaques. The BNT162b2 vaccine candidate fully protected the lungs of immunised rhesus macaques from infectious SARS-CoV-2 challenge. BNT162b2 is currently being evaluated in a global, pivotal Phase 2/3 trial (NCT04368728).

In vitro study of BromAc on SARS-CoV-2 spike and envelope proteins shows synergy and disintegration at modest concentrations (preprint)

Objectives: SARS-CoV-2 infection is the cause of a worldwide pandemic, currently with limited therapeutic options. It is characterised by being highly contagious and nasal mucosa appears to be the primary site with subsequent spread to the lungs and elsewhere. BromAc (Bromelain & Acetylcysteine) has been described to disrupt glycoproteins by the synchronous breakage of glycosidic linkages and disulphide bonds. The spike protein of SARS-CoV-2 is an attractive target as it is essential for binding to the ACE2 receptor in host cells and is formed of glycoprotein and disulphide bridges for stabilisation. Hence, we sought to determine whether BromAc has activity on the spike and envelope protein specific to SARS-CoV-2 virus. Design: Gel electrophoresis analysis was carried out on recombinant spike and envelope proteins that were treated with a range of concentrations of single agents and BromAc. For UV analysis of disulfide bonds reduction, both spike and envelope protein were treated with Acetylcysteine with the determination of loss of disulfide bonds. Results: Recombinant spike and envelope SARS-CoV-2 protein were fragmented by BromAc whilst single agents had minimal effect. Spike and envelope proteins disulphide bonds were reduced by Acetylcysteine. Conclusion: BromAc disintegrates the spike and envelope protein from SARS-CoV-2 and may render it non-infective. In vitro tests on live virus have been encouraging and clinical testing through nasal administration in patients with early SARS-CoV-2 infection is imminent.

Convalescent plasma in the management of moderate COVID-19 in India: An open-label parallel-arm phase II multicentre randomized controlled trial (PLACID Trial) (preprint)

ObjectivesConvalescent plasma (CP) as a passive source of neutralizing antibodies and immunomodulators is a century-old therapeutic option used for the management of viral diseases. We investigated its effectiveness for the treatment of COVID-19. DesignOpen-label, parallel-arm, phase II, multicentre, randomized controlled trial. SettingThirty-nine public and private hospitals across India. ParticipantsHospitalized, moderately ill confirmed COVID-19 patients (PaO2/FiO2: 200-300 or respiratory rate > 24/min and SpO2 [≤] 93% on room air). InterventionParticipants were randomized to either control (best standard of care (BSC)) or intervention (CP + BSC) arm. Two doses of 200 mL CP was transfused 24 hours apart in the intervention arm. Main Outcome MeasureComposite of progression to severe disease (PaO2/FiO2< 100) or all-cause mortality at 28 days post-enrolment. ResultsBetween 22nd April to 14th July 2020, 464 participants were enrolled; 235 and 229 in intervention and control arm, respectively. Composite primary outcome was achieved in 44 (18.7%) participants in the intervention arm and 41 (17.9%) in the control arm [aOR: 1.09; 95% CI: 0.67, 1.77]. Mortality was documented in 34 (13.6%) and 31 (14.6%) participants in intervention and control arm, respectively [aOR) 1.06 95% CI: -0.61 to 1.83]. InterpretationCP was not associated with reduction in mortality or progression to severe COVID-19. This trial has high generalizability and approximates real-life setting of CP therapy in settings with limited laboratory capacity. A priori measurement of neutralizing antibody titres in donors and participants may further clarify the role of CP in management of COVID-19. Trial registrationThe trial was registered with Clinical Trial Registry of India (CTRI); CTRI/2020/04/024775.

Antibody binding to SARS-CoV-2 S glycoprotein correlates with, but does not predict neutralization (preprint)

Convalescent plasma from SARS-CoV-2 infected individuals and monoclonal antibodies were shown to potently neutralize viral and pseudoviral particles carrying the S glycoprotein. However, a non-negligent proportion of plasma samples from infected individuals as well as S-specific monoclonal antibodies were reported to be non-neutralizing despite efficient interaction with the S glycoprotein in different biochemical assays using soluble recombinant forms of S or when expressed at the cell surface. How neutralization relates to binding of S glycoprotein in the context of viral particles remains to be established. Here we developed a pseudovirus capture assay (VCA) to measure the capacity of plasma samples or antibodies immobilized on ELISA plates to bind to membrane-bound S glycoproteins from SARS-CoV-2 expressed at the surface of lentiviral particles. By performing VCA and neutralization assays we observed a strong correlation between these two parameters. However, while we found that plasma samples unable to capture viral particles did not neutralize, capture did not guarantee neutralization, indicating that the capacity of antibodies to bind to the S glycoprotein at the surface of viral particles is required but not sufficient to mediate neutralization. Altogether, our results highlights the importance of better understanding the inactivation of S by plasma and neutralizing antibodies.

Interaction of human ACE2 to membrane-bound SARS-CoV-1 and SARS-CoV-2 S glycoproteins (preprint)

A novel severe acute respiratory (SARS)-like coronavirus (SARS-CoV-2) is responsible for the current global coronavirus disease 2019 (COVID-19) pandemic, infecting millions of people and causing hundreds of thousands of deaths. The viral entry of SARS-CoV-2 depends on an interaction between the receptor binding domain of its trimeric Spike glycoprotein and the human angiotensin converting enzyme 2 (ACE2) receptor. A better understanding of the Spike/ACE2 interaction is still required to design anti-SARS-CoV-2 therapeutics. Here, we investigated the degree of cooperativity of ACE2 within both the SARS-CoV-2 and the closely related SARS-CoV-1 membrane-bound S glycoproteins. We show that there exist differential inter-protomer conformational transitions between both Spike trimers. Interestingly, the SARS-CoV-2 spike exhibits a positive cooperativity for monomeric soluble ACE2 binding when compared to the SARS-CoV-1 spike, which might have more structural restrains. Our findings can be of importance in the development of therapeutics that block the Spike/ACE2 interaction.