Evolution of SARS-CoV-2: BA.4/BA.5 Variants Continues to Pose New Challenges.

The acquisition of a high number of mutations, notably, the gain of two mutations L452R and F486V in RBD, and the ability to evade vaccine/natural infection-induced immunity suggests that Omicron is continuing to use "immune-escape potential" as an evolutionary space to maintain a selection advantage within the population. Despite the low hospitalizations and lower death rate, the surges by these variants may offset public health measures and disrupt health care facilities as seen recently in Portugal and the USA. Interestingly these BA.4/BA.5 variants have been found to be more severe than the earlier-emerged Omicron variants. We believe that aggressive COVID-19 surveillance using affordable testing strategies might actually help understand the evolution and transmission pattern of new variants. The sudden dip in reporting of new cases in some of the low- and middle-income countries is an alarming situation and needs to be addressed as this could lead to undetected transmission of future variants of interest/concern of SARS-CoV-2 in large population settings, including advent of a 'super' virus. It would be interesting to examine the possible role/influence, if any, of the two different kinds of vaccines, the spike protein-based versus the inactivated whole virus, in the evolution of BA.4/BA.5.

Energetics of Spike Protein Opening of SARS-CoV-1 and SARS-CoV-2 and Its Variants of Concern: Implications in Host Receptor Scanning and Transmission.

The receptor binding domain(s) (RBD) of spike (S) proteins of SARS-CoV-1 and SARS-CoV-2 (severe acute respiratory syndrome coronavirus) undergoes closed to open transition to engage with host ACE2 receptors. In this study, using multi atomistic (equilibrium) and targeted (non-equilibrium) molecular dynamics simulations, we have compared energetics of RBD opening pathways in full-length (modeled from cryo-EM structures) S proteins of SARS-CoV-1 and SARS-CoV-2. Our data indicate that amino acid variations at the RBD interaction interface can culminate into distinct free energy landscapes of RBD opening in these S proteins. We further report that mutations in the S protein of SARS-CoV-2 variants of concern can reduce the protein-protein interaction affinity of RBD(s) with its neighboring domains and could favor its opening to access ACE2 receptors. The findings can also aid in predicting the impact of future mutations on the rate of S protein opening for rapid host receptor scanning.

A single-center experience in use of tocilizumab in COVID-19 pneumonia in India.

BACKGROUND: IL-6 receptor antagonist tocilizumab (TCZ) has been used in several reported studies in the treatment of COVID-19 pneumonia and pieces of evidence are still emerging. METHODS: All patients with COVID-19 pneumonia showing features of hyperinflammatory syndrome receiving TCZ at a tertiary care center in India were included in the study and a retrospective descriptive analysis was done. RESULTS: Between May 2020 to August 2020, 21 patients received TCZ out of which 13 survived and 8 died. All non-survivors had longer duration (median 12 days, minimum 9, maximum 15 days compared to median 6 days, minimum 3 and maximum 14 days in survivors) of symptoms and severe disease requiring mechanical ventilation at the time of TCZ administration. Among survivors, 8 patients had severe disease, 3 had moderate disease, and 2 patients had mild disease. Six out of 8 (75%) among non-survivors and 8 out of 13 (62%) among survivors had preexisting medical comorbidities. The non-survivors had higher baseline neutrophil-to-leukocyte ratio (10.5 vs 8.8), serum ferritin (960 ng/ml vs 611 ng/ml), lactate dehydrogenase (795 IU/L vs 954 IU/L), and D-dimer (5900 µg/ml vs 1485 mg/ml) levels. No drug-related serious adverse effect was noted among the patients. CONCLUSION: In a scenario of emerging evidence for the role of TCZ in the management of severe COVID-19, our study provides useful data on its use in the Indian scenario. Deliberate patient selection and timing initiation of TCZ at a crucial stage of the disease may be beneficial in COVID-19 pneumonia with good safety returns.

Role of multiple factors likely contributing to severity-mortality of COVID-19.

COVID-19 stalled the world in 2020 and continues to be the greatest health crisis of this generation. While the apparent case fatality rates across fluctuates around ~2% globally, associated mortality/death rate (deaths per million population) varies distinctly across regions from the global average of ~600 per million population. Heterogeneous factors have been linked with COVID-19 associated mortalities and these include age, share of geriatric population, comorbidities, trained immunity and climatic conditions. Apart from direct or indirect role of endemic diseases, dietary factors and host immunity in regulating COVID-19 severity, human behaviour will inevitably control outcome of this pandemic. Comprehensive understanding of these factors will have a bearing on management of future health crises.

Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity.

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) outbreak in December 2019 has caused a global pandemic. The rapid mutation rate in the virus has created alarming situations worldwide and is being attributed to the false negativity in RT-PCR tests. It has also increased the chances of reinfection and immune escape. Recently various lineages namely, B.1.1.7 (Alpha), B.1.617.1 (Kappa), B.1.617.2 (Delta) and B.1.617.3 have caused rapid infection around the globe. To understand the biophysical perspective, we have performed molecular dynamic simulations of four different spikes (receptor binding domain)-hACE2 complexes, namely wildtype (WT), Alpha variant (N501Y spike mutant), Kappa (L452R, E484Q) and Delta (L452R, T478K), and compared their dynamics, binding energy and molecular interactions. Our results show that mutation has caused significant increase in the binding energy between the spike and hACE2 in Alpha and Kappa variants. In the case of Kappa and Delta variants, the mutations at L452R, T478K and E484Q increased the stability and intra-chain interactions in the spike protein, which may change the interaction ability of neutralizing antibodies to these spike variants. Further, we found that the Alpha variant had increased hydrogen interaction with Lys353 of hACE2 and more binding affinity in comparison to WT. The current study provides the biophysical basis for understanding the molecular mechanism and rationale behind the increase in the transmissivity and infectivity of the mutants compared to wild-type SARS-CoV-2.

Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications.

SARS-CoV-2 (Severe Acute Respiratory Syndrome-Coronavirus 2) has accumulated multiple mutations during its global circulation. Recently, three SARS-CoV-2 lineages, B.1.1.7 (501Y.V1), B.1.351 (501Y.V2) and B.1.1.28.1 (P.1), have emerged in the United Kingdom, South Africa and Brazil, respectively. Here, we have presented global viewpoint on implications of emerging SARS-CoV-2 variants based on structural-function impact of crucial mutations occurring in its spike (S), ORF8 and nucleocapsid (N) proteins. While the N501Y mutation was observed in all three lineages, the 501Y.V1 and P.1 accumulated a different set of mutations in the S protein. The missense mutational effects were predicted through a COVID-19 dedicated resource followed by atomistic molecular dynamics simulations. Current findings indicate that some mutations in the S protein might lead to higher affinity with host receptors and resistance against antibodies, but not all are due to different antibody binding (epitope) regions. Mutations may, however, result in diagnostic tests failures and possible interference with binding of newly identified anti-viral candidates against SARS-CoV-2, likely necessitating roll out of recurring "flu-like shots" annually for tackling COVID-19. The functional relevance of these mutations has been described in terms of modulation of host tropism, antibody resistance, diagnostic sensitivity and therapeutic candidates. Besides global economic losses, post-vaccine reinfections with emerging variants can have significant clinical, therapeutic and public health impacts.

Diabetes Mellitus and Hypertension Increase Risk of Death in Novel Corona Virus Patients Irrespective of Age: a Prospective Observational Study of Co-morbidities and COVID-19 from India.

Elderly people and people with co-morbidities have emerged as the most vulnerable group at risk of developing complications and succumbing to novel coronavirus (COVID-19) infection. We recorded the baseline demographic profile, baseline clinical and laboratory parameters, and prevalence of various co-morbidities and their effect on the prognosis of COVID-19 cases. We conducted a prospective observational study and analyzed baseline clinical and laboratory parameters and co-morbidities and their effect on severity and mortality in 710 COVID-19 cases. Seven hundred ten patients with laboratory-confirmed COVID-19 were recruited from the 28th of March to the 31st of August 2020. The mean age was 48.4 ± 16.4years. A total of 530 (74.6%) patients were male. Overall, the mean length of hospital stay was 12.7 days. In total, 645 patients(90.8%) were mild to moderate cases and did not require initial ICU care. Sixty-five (9.2%) cases required initial intensive care unit care. Fifty (7%) admitted patients succumbed to the illness. Diabetes mellitus and hypertension increased the risk of death in COVID-19 patients irrespective of age. Increasing age and co-morbidities adversely affect the prognosis of patients of COVID-19. Diabetes mellitus and hypertension increase the risk of death in COVID-19 patients and negate the incremental effect of age on death in these patients.

Reinfection or Reactivation of Coronavirus-19 in Patients with Hematologic Malignancies: Case Report Series.

Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been relentless. We are into the 10th month of the pandemic, and we are still getting surprised every day. Although neutralizing antibodies are generated in response to coronavirus disease-19 (COVID-19), these antibodies do not appear to confer lifelong immunity, as lately there have been reports from various parts of the world of reinfection with the virus, starting from Hong Kong, Belgium, and the USA. The Indian Council of Medical Research (ICMR) has been on-record claiming three cases of reinfection in India. Herein, we report three patients of hematologic malignancy who most probably had reinfection with SARS-CoV-2, after complete documented recovery from first infection. All three patients were immunocompromised owing to their primary hematologic malignancy coupled with ongoing therapy, and the second infection was documented to be severe in all the three cases from the first episode.

Clinical Triaging in Cough Clinic Alleviates COVID-19 Overload in Emergency Department in India.

The importance of this study is the efficacy of "symptoms only" approach at a screening clinic for coronavirus disease 2019 (COVID-19) diagnosis in low- and middle-income countries (LMIC) setting. The objective of this study was to assess how efficiently primary care physicians at the screening clinic were able to predict whether a patient had COVID-19 or not, based on their symptom-based assessment alone. The current study is a cross-sectional retrospective observational study. This study was conducted at a single-center, tertiary care setting with a dedicated COVID-19 facility in a metropolitan city in eastern India. Participants are all suspected COVID-19 patients who presented themselves to this center during the outbreak from 1 August 2020 to 30 August 2020. Patients were referred to the Cough Clinic from the various outpatient departments of the hospital or from smaller satellite centers located in different parts of the city and other dependent geographical areas. The main outcome(s) and measure(s) is to study whether outcome of confirmatory test results can be predicted accurately by history taking alone. From 01 August 2020 to 30 Aug 2020, 511 patients with at least one symptom suggestive of COVID-19 reported to screening clinic. Out of these, 65.4% were males and 34.6% were females. Median age was 45 years with range being 01 to 92 years. Fever was seen in 70.4% while cough was present in 22% of cases. Overall positivity for SARS-CoV-2 during this period in this group was 54.21%. At 50% pre-test probability, the sensitivity of trained doctors working at the clinic, in predicting positive cases based on symptoms alone, was approximately 74.7%, and specificity for the same was 58.12%. The positive predictive value of the doctors' assessment was 67.87%, and the negative predictive value was 66.02%. Rapid triaging for confirmatory diagnosis of COVID-19 is feasible at screening clinic based on history taking alone by training of primary care physicians. This is particularly relevant in LMIC with scarce healthcare resources to overcome COVID-19 pandemic.

Emerging genetic diversity among clinical isolates of SARS-CoV-2: Lessons for today.

Considering the current pandemic of COVID-19, it is imperative to gauge the role of molecular divergence in SARS-CoV-2 with time, due to clinical and epidemiological concerns. Our analyses involving molecular phylogenetics is a step toward understanding the transmission clusters that can be correlated to pathophysiology of the disease to gain insight into virulence mechanism. As the infections are increasing rapidly, more divergence is expected followed possibly by viral adaptation. We could identify mutational hotspots which appear to be major drivers of diversity among strains, with RBD of spike protein emerging as the key region involved in interaction with ACE2 and consequently a major determinant of infection outcome. We believe that such molecular analyses correlated with clinical characteristics and host predisposition need to be evaluated at the earliest to understand viral adaptability, disease prognosis, and transmission dynamics.