SARS-CoV-2 Omicron subvariant spike N405 unlikely to rapidly deamidate.

The RGD motif on the SARS-CoV-2 spike protein has been suggested to interact with RGD-binding integrins αVß3 and α5ß1 to enhance viral cell entry and alter downstream signaling cascades. The D405N mutation on the Omicron subvariant spike proteins, resulting in an RGN motif, has recently been shown to inhibit binding to integrin αVß3. Deamidation of asparagines in protein ligand RGN motifs has been demonstrated to generate RGD and RGisoD motifs that permit binding to RGD-binding integrins. Two asparagines, N481 and N501, on the Wild-type spike receptor-binding domain have been previously shown to have deamidation half-lives of 16.5 and 123 days, respectively, which may occur during the viral life cycle. Deamidation of Omicron subvariant N405 may recover the ability to interact with RGD-binding integrins. Thus, herein, all-atom molecular dynamics simulations of the Wild-type and Omicron subvariant spike protein receptor-binding domains were conducted to investigate the potential for asparagines, the Omicron subvariant N405 in particular, to assume the optimized geometry for deamidation to occur. In summary, the Omicron subvariant N405 was primarily found to be stabilized in a state unfavourable for deamidation after hydrogen bonding with downstream E406. Nevertheless, a small number of RGD or RGisoD motifs on the Omicron subvariant spike proteins may restore the ability to interact with RGD-binding integrins. The simulations also provided structural clarification regarding the deamidation rates of Wild-type N481 and N501 and highlighted the utility of tertiary structure dynamics information in predicting asparagine deamidation. Further work is needed to characterize the effects of deamidation on spike-integrin interactions.

Analysis of daily COVID-19 death bulletin data during the first two waves of the COVID-19 pandemic in Thiruvananthapuram district, Kerala, India.

Context: Coronavirus disease 2019 (COVID-19) mortality trends can help discern the pattern of outbreak evolution and systemic responses. Aim: This study aimed to explore patterns of COVID-19 deaths in Thiruvananthapuram district from 31 March 2020 to 31 December 2021. Setting and Design: Secondary data analysis of COVID-19 deaths in Thiruvananthapuram district was performed. Materials and Methods: Mortality data were obtained from the district COVID-19 control room, and deaths in the first and second waves of COVID-19 were compared. Statistical Analysis: We summarised data as proportions and medians with the inter-quartile range (IQR) and performed Chi-square tests to make comparisons wherever applicable. Results: As on 31 December 2021, 4587 COVID-19 deaths were reported in Thiruvananthapuram district, with a case fatality rate of 0.91%. We observed high mortality among older persons (66.7%) and men (56.6%). The leading cause of death was bronchopneumonia (60.6%). The majority (88.5%) had co-morbidities, commonly diabetes mellitus (54.9%). The median interval from diagnosis to hospitalisation was 4 days (IQR 2-7), and that from hospitalisation to death was 2 days (IQR 0-6). The deaths reported during the second wave were four times higher than those of the first wave with a higher proportion of deaths in the absence of co-morbidities (p < 0.001). The majority of the deceased were unvaccinated. Ecological analysis with vaccine coverage data indicated 5.4 times higher mortality among unvaccinated than those who received two vaccine doses. Conclusions: The presence of co-morbidities, an unvaccinated status, and delay in hospitalisation were important reasons for COVID-19 deaths. Primary level health providers can potentially help sustaining vaccination, expeditious referral, and monitoring of COVID-19 patients.

Migrants and the Inclusive Policy Framework: Has Kerala Set the Precedent for Others to Emulate?

Migrants are subjects that are often left out in the policy discourse, even though India has one of the largest floating populations in the world. At times when the migrant communities are facing scornful events at different quarters of their lives, the State of Kerala has addressed similar concerns through policy deliberations framed with the utmost care and importance, thus emerging as the pro-migrant State in the country. The article incorporates a discussion on the various policy initiatives adopted by the State machinery for the welfare and betterment of inter-state migrant workers employed in the State. Expanding the scope, the study deals with the different policy interventions adopted by the State machinery to address the vulnerabilities of in-migrants which emerged during the ongoing COVID-19 pandemic. An evaluation of the State's existing migrant related policy framework points to the extent of its effectiveness in sensitising and improving the lives of inter-state migrants. Through these efforts, the Government of Kerala sends a strong message on the inevitability of having an inclusive and unified approach in identifying and addressing the needs of the migrant community by transcending the trivial human-made distinctions while keeping human beings and humanity at the centre of all actions.

In silico analysis of mutations near S1/S2 cleavage site in SARS-CoV-2 spike protein reveals increased propensity of glycosylation in Omicron strain.

Cleavage of the severe respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein has been demonstrated to contribute to viral-cell fusion and syncytia formation. Studies have shown that variants of concern (VOC) and variants of interest (VOI) show differing membrane fusion capacity. Mutations near cleavage motifs, such as the S1/S2 and S2' sites, may alter interactions with host proteases and, thus, the potential for fusion. The biochemical basis for the differences in interactions with host proteases for the VOC/VOI spike proteins has not yet been explored. Using sequence and structure-based bioinformatics, mutations near the VOC/VOI spike protein cleavage sites were inspected for their structural effects. All mutations found at the S1/S2 sites were predicted to increase affinity to the furin protease but not TMPRSS2. Mutations at the spike residue P681 in several strains, such P681R in the Delta strain, resulted in the disruption of a proline-directed kinase phosphorylation motif at the S1/S2 site, which may lessen the impact of phosphorylation for these variants. However, the unique N679K mutation in the Omicron strain was found to increase the propensity for O-linked glycosylation at the S1/S2 cleavage site, which may prevent recognition by proteases. Such glycosylation in the Omicron strain may hinder entry at the cell surface and, thus, decrease syncytia formation and induce cell entry through the endocytic pathway as has been shown in previous studies. Further experimental work is needed to confirm the effect of mutations and posttranslational modifications on SARS-CoV-2 spike protein cleavage sites.

Secretory autophagy maintains proteostasis upon lysosome inhibition.

The endolysosome system plays central roles in both autophagic degradation and secretory pathways, including the release of extracellular vesicles and particles (EVPs). Although previous work reveals important interconnections between autophagy and EVP-mediated secretion, our understanding of these secretory events during endolysosome inhibition remains incomplete. Here, we delineate a secretory autophagy pathway upregulated in response to endolysosomal inhibition, which mediates EVP-associated release of autophagic cargo receptors, including p62/SQSTM1. This secretion is highly regulated and dependent on multiple ATGs required for autophagosome formation, as well as the small GTPase Rab27a. Furthermore, disrupting autophagosome maturation, either via genetic inhibition of autophagosome-to-autolysosome fusion or expression of SARS-CoV-2 ORF3a, is sufficient to induce EVP secretion of autophagy cargo receptors. Finally, ATG-dependent EVP secretion buffers against the intracellular accumulation of autophagy cargo receptors when classical autophagic degradation is impaired. Thus, we propose secretory autophagy via EVPs functions as an alternate route to clear sequestered material and maintain proteostasis during endolysosomal dysfunction or impaired autophagosome maturation.

Effect of the COVID-19 Pandemic on Sports-Related Injuries Evaluated in US Emergency Departments.

BACKGROUND: Organized athletics are undergoing a gradual resumption after a prolonged hiatus in 2020 because of the coronavirus disease 2019 (COVID-19) pandemic. PURPOSE/HYPOTHESIS: The purpose of this study was to evaluate the effect of the 2020 COVID-19 period on emergency department (ED) visits for sports-related injuries in the United States. It was hypothesized that such visits decreased in response to the pandemic conditions. STUDY DESIGN: Descriptive epidemiology study. METHODS: A selection of sports (baseball, basketball, softball, soccer, American football, weightlifting, track and field, martial arts, boxing, golf, personal fitness, cycling, tennis, and ice hockey) were classified as being an organized team, organized individual, or nonorganized sport. The National Electronic Injury Surveillance System database was then queried for ED visits for sports-related injuries between January 1, 2018, and December 31, 2020, and we compared weighted national injury estimates and injury characteristics from athletes presenting to EDs in 2018 and 2019 versus those from the 2020 COVID-19 pandemic period and between March 1 and May 31, 2020 (government-imposed lockdown period). Bivariate comparisons between variables were conducted using chi-square analysis, with strength of association assessed using odds ratios. RESULTS: The 164,151 unweighted cases obtained from the query resulted in a weighted national estimate of 5,664,795 sports-related injuries during the study period. Overall, there was a 34.6% decrease in sports-related ED visits in 2020 compared with the yearly average between 2018 and 2019 (baseline). The number of ED visits in 2020 decreased by 53.9% versus baseline for injuries incurred by participation in an organized team sport and by 34.9% for injuries incurred by participation in an organized individual sport. The number of ED visits during the 2020 lockdown period decreased by 76.9% versus baseline for injuries incurred by participation in an organized team sport and by 65.8% for injuries incurred by participation in an organized individual sport. Injuries sustained while participating in a nonorganized sport remained relatively unaffected and decreased by only 8.1% in 2020. CONCLUSION: ED visits in the United States for injuries sustained while participating in an organized team or individual sport underwent a decrease after the beginning of the COVID-19 pandemic in 2020, especially during the lockdown period.

Anxiety and depression in the elderly due to COVID-19 pandemic: a pilot study

Background: The elderly are a vulnerable section of the population who are prone to physical, mental, social, and economic deprivation. The effect of COVID-19 had a worldwide impact on all age groups, with a particularly higher mortality and morbidity rate among the elderly population. The present study was undertaken to know about the psychological morbidity in the geriatric population during the period of the COVID-19 pandemic. The study was cross-sectional and was done through a telephonic survey. Eligible elderly subjects were contacted telephonically, and the Geriatric Anxiety Scale and the Geriatric Depression Scale were administered. To evaluate the functional ability of elderly subjects, the Everyday Abilities Scale for India (EASI) scale was administered. For the telephonic survey, verbal consent was sought. Results: A total of 92 elderly subjects were included. Male outnumbered the females with a ratio of 1.8:1. Spouse and children were primary caregivers in 83.7% of the subjects. 90.2% were married, and 66.3% had earned a graduate/professional level of education. Chronic illness was present in 50% of subjects. The most common co-morbidities were hypertension (27.2%) and diabetes (21.7%). The proportion of elderly with anxiety and depression was 8.7% and 15.2% respectively. Conclusion: The elderly showed lower levels of anxiety and depression. Higher resilience among the elderly and good family support may be the reasons for such an unexpected finding. However, more studies are required to validate the findings of the current study. © 2021, The Author(s).

PCN206 Evaluating Patient Experiences in Follicular Lymphoma (FL) through Social Media Listening (SML) Research from Five Countries in North America and Europe

Objective: To understand patient experiences with FL disease and treatment through SML. Method: Social media data were extracted between February 2019 and July 2020 using “Follicular Lymphoma” and related keywords via Social Studio®, an online aggregator tool for social media posts. English as well as local language posts were extracted from five countries including United States (US), Canada, United Kingdom (UK), Germany and France. Patient conversations were identified, synthesized, mapped, and analyzed to understand different concerns. Results: 487 patient posts discussing 1324 topics of conversation were identified. In most countries, top discussed topics included patient concerns such as quality of life (QoL) changes, and disease and/or treatment management. Multiple patient concerns (n=554) were observed across all geographies: impact on QoL (198), curability (73), fear of relapse/progression (64), disease/treatment information need (50), lack of emotional support (43), FL transformation to diffuse large B-cell lymphoma (42), and cost of treatment (30) were notable concerns. To assess QoL impact, patient conversations (198) were mapped to the statements in the Functional Assessment of Cancer Therapy – Lymphoma questionnaire (FACT-Lym). Pain and lack of energy (57), swollen nodes/lumps (47), and side effects of treatment (31) had impacted physical wellbeing, while support from family/friends (41) helped patients cope emotionally. A few patients (18) said that they were able to return to work after treatment. As for inter-country differences, conversations were mostly from the US (43%) and UK (20%);male patients in Germany were more active social media participants than female patients, which was different from other four countries;only patients in the UK had expressed concerns about COVID-19 impact. Conclusion: Insights from international SML research indicated concerns related to disease- and/or treatment-related impact on QoL and interest about potential cure for the disease.

The InterPro protein families and domains database: 20 years on.

The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites. InterProScan is the underlying software that allows protein and nucleic acid sequences to be searched against InterPro's signatures. Signatures are predictive models which describe protein families, domains or sites, and are provided by multiple databases. InterPro combines signatures representing equivalent families, domains or sites, and provides additional information such as descriptions, literature references and Gene Ontology (GO) terms, to produce a comprehensive resource for protein classification. Founded in 1999, InterPro has become one of the most widely used resources for protein family annotation. Here, we report the status of InterPro (version 81.0) in its 20th year of operation, and its associated software, including updates to database content, the release of a new website and REST API, and performance improvements in InterProScan.

A two-tiered system of analysis to tackle rice fraud: The Indian Basmati study.

Demand for high quality Basmati rice has increased significantly in the last decade. This commodity is highly vulnerable to fraud, especially in the post COVID-19 era. A unique two-tiered analytical system comprised of rapid on-site screening of samples using handheld portable Near-infrared NIR and laboratory confirmatory technique using a Head space gas chromatography mass spectrometry (HS-GC-MS) strategy for untargeted analysis was developed. Chemometric models built using NIR data correctly predicted nearly 100% of Pusa 1121 and Taraori, two high value types of Basmati, from potential adulterants. Furthermore, rice VOC profile fingerprints showed very good classification (R2 >0.9, Q2 > 0.9, Accuracy > 0.99) for these high quality Basmati varieties from potential adulterant varieties with aldehydes identified as key VOC marker compounds. Using a two-tiered system of a rapid method for on-site screening of many samples alongside a laboratory-based confirmatory method can classify Basmati rice varieties, protecting the supply chain from fraud.

Engineered ACE2 receptor traps potently neutralize SARS-CoV-2.

An essential mechanism for severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection begins with the viral spike protein binding to the human receptor protein angiotensin-converting enzyme II (ACE2). Here, we describe a stepwise engineering approach to generate a set of affinity optimized, enzymatically inactivated ACE2 variants that potently block SARS-CoV-2 infection of cells. These optimized receptor traps tightly bind the receptor binding domain (RBD) of the viral spike protein and prevent entry into host cells. We first computationally designed the ACE2-RBD interface using a two-stage flexible protein backbone design process that improved affinity for the RBD by up to 12-fold. These designed receptor variants were affinity matured an additional 14-fold by random mutagenesis and selection using yeast surface display. The highest-affinity variant contained seven amino acid changes and bound to the RBD 170-fold more tightly than wild-type ACE2. With the addition of the natural ACE2 collectrin domain and fusion to a human immunoglobulin crystallizable fragment (Fc) domain for increased stabilization and avidity, the most optimal ACE2 receptor traps neutralized SARS-CoV-2-pseudotyped lentivirus and authentic SARS-CoV-2 virus with half-maximal inhibitory concentrations (IC50s) in the 10- to 100-ng/mL range. Engineered ACE2 receptor traps offer a promising route to fighting infections by SARS-CoV-2 and other ACE2-using coronaviruses, with the key advantage that viral resistance would also likely impair viral entry. Moreover, such traps can be predesigned for viruses with known entry receptors for faster therapeutic response without the need for neutralizing antibodies isolated from convalescent patients.

Unusual Pattern of Arterial Macrothrombosis Causing Stroke in a Young Adult Recovered from COVID-19.

Coronavirus disease-19 (COVID-19) pandemic continues to grow all over the world. Neurological manifestations related to COVID-19, including acute ischemic Stroke (AIS), have been reported in recent studies. In most of these, the patients are older, have multiple co-morbidities as risk factors for AIS and have developed a severe respiratory illness. Herein, we report a 36-year-old man with no significant past medical history who recently recovered from a mild COVID-19 infection and presented with unusual pattern of arterial macrothrombosis causing AIS. When the AIS happened, he had no COVID-19 related symptoms, had two negative screening tests for the infection and his chest CT was unremarkable.

Engineered ACE2 receptor traps potently neutralize SARS-CoV-2 (preprint)

An essential mechanism for SARS-CoV-1 and -2 infection begins with the viral spike protein binding to the human receptor protein angiotensin-converting enzyme II (ACE2). Here we describe a stepwise engineering approach to generate a set of affinity optimized, enzymatically inactivated ACE2 variants that potently block SARS-CoV-2 infection of cells. These optimized receptor traps tightly bind the receptor binding domain (RBD) of the viral spike protein and prevent entry into host cells. We first computationally designed the ACE2-RBD interface using a two-stage flexible protein backbone design process that improved affinity for the RBD by up to 12-fold. These designed receptor variants were affinity matured an additional 14-fold by random mutagenesis and selection using yeast surface display. The highest affinity variant contained seven amino acid changes and bound to the RBD 170-fold more tightly than wild-type ACE2. With the addition of the natural ACE2 collectrin domain and fusion to a human Fc domain for increased stabilization and avidity, the most optimal ACE2 receptor traps neutralized SARS-CoV-2 pseudotyped lentivirus and authentic SARS-CoV-2 virus with half-maximal inhibitory concentrations (IC50) in the tens of ng/ml range. Engineered ACE2 receptor traps offer a promising route to fighting infections by SARS-CoV-2 and other ACE2-utilizing coronaviruses, with the key advantage that viral resistance would also likely impair viral entry. Moreover, such traps can be pre-designed for viruses with known entry receptors for faster therapeutic response without the need for neutralizing antibodies isolated or generated from convalescent patients.