SARS-CoV-2 genomics: An Indian perspective on sequencing viral variants

Development of multiplex allele-specific RT-qPCR assays for differentiation of SARS-CoV-2 Omicron subvariants

Quick differentiation of current circulating variants and the emerging recombinant variants of SARS-CoV-2 is essential to monitor their transmissions. However, the widely applied gene sequencing method is time-consuming and costly especially when facing recombinant variants, because a large part or whole genome sequencing is required. Allele-specific reverse transcriptase real time RT-PCR (RT-qPCR) represents a quick and cost-effective method for SNP (single nucleotide polymorphism) genotyping and has been successfully applied for SARS-CoV-2 variant screening. In the present study, we developed a panel of 5 multiplex allele-specific RT-qPCR assays targeting 20 key mutations for quick differentiation of the Omicron subvariants (BA.1 to BA.5 and their descendants) and the recombinant variants (XBB.1 and XBB.1.5). Two parallel multiplex RT-qPCR reactions were designed to separately target the prototype allele and the mutated allele of each mutation in the allele-specific RT-qPCR assay. Optimal annealing temperatures, primer and probe dosage, and time for annealing/extension for each reaction were determined by multi-factor and multi-level orthogonal test. The variation of Cp (crossing point) values (ΔCp) between the two multiplex RT-qPCR reactions was applied to determine if a mutation occurs or not. SARS-CoV-2 subvariants and related recombinant variants were differentiated by their unique mutation patterns. The developed multiplex allele-specific RT-qPCR assays exhibited excellent analytical sensitivities (with limits of detection (LoDs) of 1.47-18.52 copies per reaction), wide linear detection ranges (109-100 copies per reaction), good amplification efficiencies (88.25 to 110.68%), excellent reproducibility (coefficient of variations (CVs) < 5% in both intra-assay and inter-assay tests), and good clinical performances (99.5-100% consistencies with Sanger sequencing). The developed multiplex allele-specific RT-qPCR assays in the present study provide an alternative tool for quick differentiation of the SARS-CoV-2 Omicron subvariants and their recombinant variants. KEY POINTS: • A panel of five multiplex allele-specific RT-qPCR assays for quick differentiation of 11 SARS-CoV-2 Omicron subvariants (BA.1, BA.2, BA.4, BA.5, and their descendants) and 2 recombinant variants (XBB.1 and XBB.1.5). • The developed assays exhibited good analytical sensitivities and reproducibility, wide linear detection ranges, and good clinical performances, providing an alternative tool for quick differentiation of the SARS-CoV-2 Omicron subvariants and their recombinant variants.

Genomic characterization of SARS-CoV-2 in Guinea, West Africa

SARS-CoV-2 has claimed several million lives since its emergence in late 2019. The ongoing evolution of the virus has resulted in the periodic emergence of new viral variants with distinct fitness advantages, including enhanced transmission and immune escape. While several SARS-CoV-2 variants of concern trace their origins back to the African continent-including Beta, Eta, and Omicron-most countries in Africa remain under-sampled in global genomic surveillance efforts. In an effort to begin filling these knowledge gaps, we conducted retrospective viral genomic surveillance in Guinea from October 2020 to August 2021. We found that SARS-CoV-2 clades 20A, 20B, and 20C dominated throughout 2020 until the coincident emergence of the Alpha and Eta variants of concern in January 2021. The Alpha variant remained dominant throughout early 2021 until the arrival of the Delta variant in July. Surprisingly, despite the small sample size of our study, we also found the persistence of the early SARS-CoV-2 clade 19B as late as April 2021. Together, these data help fill in our understanding of the SARS-CoV-2 population dynamics in West Africa early in the COVID-19 pandemic.

Severe acute respiratory syndrome Coronavirus-2 GenoAnalyzer and mutagenic anomaly detector using FCMFI and NSCE

In order to deepen our understanding of the virus and help guide the creation of efficient therapies, this study uses artificial intelligence tools to thoroughly explore the genetic sequences of the SARS-CoV-2 virus. The process starts by using the Fuzzy Closure Miner for Frequent Itemsets (FCMFI) on a large corpus of SARS-CoV-2 genomic sequences to reveal hidden patterns, including nucleotides base sequences, repeating motifs, and corresponding interchanges. Then, using the Nucleotide Sequence Comprehension Engine (NSCE) technique, we were able to precisely define the genomic areas for mutation analysis. Structured and unstructured proteins are both strongly impacted by virus mutations, with spike proteins that are linked to the severity of COVID-19 pneumonia being particularly affected. Notably, the Mutagenic Anomaly Detector shows a 65 % efficiency boost in computing genome mutation rates compared to conventional point mutation analysis, while GenoAnalyzer offers a remarkable 93.33 % improvement over existing approaches in recognizing common genomic sequence patterns. These results highlight the potential of FCMFI to reveal complex genomic patterns and significant insights in COVID-19 genetic sequences when combined with mutation analysis. The Mutagenic Anomaly Detector and GenoAnalyzer show promise for revealing hidden genomic patterns and precisely estimating the SARS-CoV-2 mutation rate.

Early warning of statewide COVID-19 Omicron wave by sentineled urbanized sewer network monitoring using digital PCR in a province capital city, of Gujarat, India

Wastewater-based epidemiology (WBE) has been implemented globally. However, there remains confusion about the number and frequency of samples to be collected, as well as which types of treatment systems can provide reliable specific details about the virus prevalence in specific areas or communities, enabling prompt management and intervention measures. More research is necessary to fully comprehend the possibility of deploying sentinel locations in sewer networks in larger geographic areas. The present study introduces the first report on wastewater-based surveillance in Gandhinagar City using digital PCR (d-PCR) as a SARS-Cov-2 quantification tool, which describes the viral load from five pumping stations in Gandhinagar from October 2021 to March 2022. Raw wastewater samples (n = 119) were received and analyzed weekly to detect SARS-CoV-2 RNA, 109 of which were positive for N1 or N2 genes. The monthly variation analysis in viral genome copies depicted the highest concentrations in January 2022 and February 2022 (p < 0.05; Wilcoxon signed rank test) coincided with the Omicron wave, which contributed mainly from Vavol and Jaspur pumping stations. Cross-correlation analysis indicated that WBE from five stations in Gandhinagar, i.e., capital city sewer networks, provided two-week lead times to the citywide and statewide active cases (time-series cross-correlation function [CCF]; 0.666 and 0.648, respectively), mainly from individual contributions of the urbanized Kudasan and Vavol stations (CCF; 0.729 and 0.647, respectively). These findings suggest that sewer pumping stations in urbanized neighborhoods can be used as sentinel sites for statewide clinical surveillance and that WBE surveillance using digital PCR can be an efficient monitoring and management tool.

Genomic Surveillance of SARS-CoV-2 in México: Three Years since Wuhan, China's First Reported Case

OBJECTIVE

The aim of this work was to analyze the metadata of the SARS-CoV-2 sequences obtained from samples collected in Mexico from 2020 to 2022.

MATERIALS AND METHODS

Metadata of SARS-CoV-2 sequences from samples collected in Mexico up to 31 December 2022 was retrieved from GISAID and manually cured for interpretation.

RESULTS

As of December 2022, Mexican health authorities and the scientific community have sequenced up to 81,983 SARS-CoV-2 viral genomes deposited in GISAID, representing 1.1% of confirmed cases. The number of sequences obtained per state corresponded to the gross domestic product (GDP) of each state for the first (Mexico City) and the last (Tlaxcala). Approximately 25% of the sequences were obtained from CoViGen-Mex, an interdisciplinary initiative of health and scientific institutions to collect and sequence samples nationwide. The metadata showed a clear dominance of sequences retrieved by women. A similar variant distribution over time was found in Mexico and overseas, with the Omicron variant predominating. Finally, the age group with the highest representation in the sequences was adults aged 21 to 50 years, accounting for more than 50% of the total.

CONCLUSIONS

Mexico presents diverse sociodemographic and economic characteristics. The COVID-19 pandemic has been and continues to be a challenge for collaboration across the country and around the world.

In vivo efficacy of 2% povidone iodine, chlorhexidine gluconate, and herbal extract mouthwash on SARS-CoV-2 viral load in saliva: A randomized clinical trial

Background

One of the major techniques to reduce the transmission rate of COVID-19 would be to decrease the viral titers of SARS-CoV-2 in the saliva of infected patients and it is particularly useful in a dental setting. The present study evaluated the change in salivary viral load of COVID-19 patients using povidone iodine (PI), chlorhexidine (CHX), and an herbal extract (RightSure®) oral antiviral herbal mouthwash (HM) at clinically recommended duration and concentrations.

Materials and Methods

Thirty individuals with SARS-CoV-2 were randomly allocated to three groups: (1) Group 1, PI mouthwash; (2) Group 2, CHX mouthwash; and (3) Group 3, HM mouthwash. A baseline salivary throat sample was collected from all the participants who were later instructed to rinse with their respective mouthwash for 30 s. A second salivary sample was collected 30 min after rinsing. The SARS-CoV-2 viral load was analyzed using real-time reverse-transcription polymerase chain reaction wherein the cyclic threshold (Ct) values were evaluated.

Results

Independent t-test analysis reported a statistically significant difference concerning the PI group (before-after comparison) (P < 0.05). The rest of the two study groups failed to report any significant difference in the nucleocapsid gene and open reading frame 1a gene levels.

Conclusion

While all three types of mouthwash increased the Ct values, a statistically significant difference was observed with PI mouthwash, indicating that it might potentially reduce the spread of the SARS-CoV-2 virus, especially via aerosol but further studies with larger sample size and longer follow-up periods are required to investigate this relationship.

Some common deleterious mutations are shared in SARS-CoV-2 genomes from deceased COVID-19 patients across continents

The identification of deleterious mutations in different variants of SARS-CoV-2 and their roles in the morbidity of COVID-19 patients has yet to be thoroughly investigated. To unravel the spectrum of mutations and their effects within SARS-CoV-2 genomes, we analyzed 5,724 complete genomes from deceased COVID-19 patients sourced from the GISAID database. This analysis was conducted using the Nextstrain platform, applying a generalized time-reversible model for evolutionary phylogeny. These genomes were compared to the reference strain (hCoV-19/Wuhan/WIV04/2019) using MAFFT v7.470. Our findings revealed that SARS-CoV-2 genomes from deceased individuals belonged to 21 Nextstrain clades, with clade 20I (Alpha variant) being the most predominant, followed by clade 20H (Beta variant) and clade 20J (Gamma variant). The majority of SARS-CoV-2 genomes from deceased patients (33.4%) were sequenced in North America, while the lowest percentage (0.98%) came from Africa. The 'G' clade was dominant in the SARS-CoV-2 genomes of Asian, African, and North American regions, while the 'GRY' clade prevailed in Europe. In our analysis, we identified 35,799 nucleotide (NT) mutations throughout the genome, with the highest frequency (11,402 occurrences) found in the spike protein. Notably, we observed 4150 point-specific amino acid (AA) mutations in SARS-CoV-2 genomes, with D614G (20%) and N501Y (14%) identified as the top two deleterious mutations in the spike protein on a global scale. Furthermore, we detected five common deleterious AA mutations, including G18V, W45S, I33T, P30L, and Q418H, which play a key role in defining each clade of SARS-CoV-2. Our novel findings hold potential value for genomic surveillance, enabling the monitoring of the evolving pattern of SARS-CoV-2 infection, its emerging variants, and their impact on the development of effective vaccination and control strategies.

Evolution of Sequence and Structure of SARS-CoV-2 Spike Protein: A Dynamic Perspective

Novel coronavirus (SARS-CoV-2) enters its host cell through a surface spike protein. The viral spike protein has undergone several modifications/mutations at the genomic level, through which it modulated its structure-function and passed through several variants of concern. Recent advances in high-resolution structure determination and multiscale imaging techniques, cost-effective next-generation sequencing, and development of new computational methods (including information theory, statistical methods, machine learning, and many other artificial intelligence-based techniques) have hugely contributed to the characterization of sequence, structure, function of spike proteins, and its different variants to understand viral pathogenesis, evolutions, and transmission. Laying on the foundation of the sequence-structure-function paradigm, this review summarizes not only the important findings on structure/function but also the structural dynamics of different spike components, highlighting the effects of mutations on them. As dynamic fluctuations of three-dimensional spike structure often provide important clues for functional modulation, quantifying time-dependent fluctuations of mutational events over spike structure and its genetic/amino acidic sequence helps identify alarming functional transitions having implications for enhanced fusogenicity and pathogenicity of the virus. Although these dynamic events are more difficult to capture than quantifying a static, average property, this review encompasses those challenging aspects of characterizing the evolutionary dynamics of spike sequence and structure and their implications for functions.

Diagnostics and analysis of SARS-CoV-2: current status, recent advances, challenges and perspectives

The disastrous spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has induced severe public healthcare issues and weakened the global economy significantly. Although SARS-CoV-2 infection is not as fatal as the initial outbreak, many infected victims suffer from long COVID. Therefore, rapid and large-scale testing is critical in managing patients and alleviating its transmission. Herein, we review the recent advances in techniques to detect SARS-CoV-2. The sensing principles are detailed together with their application domains and analytical performances. In addition, the advantages and limits of each method are discussed and analyzed. Besides molecular diagnostics and antigen and antibody tests, we also review neutralizing antibodies and emerging SARS-CoV-2 variants. Further, the characteristics of the mutational locations in the different variants with epidemiological features are summarized. Finally, the challenges and possible strategies are prospected to develop new assays to meet different diagnostic needs. Thus, this comprehensive and systematic review of SARS-CoV-2 detection technologies may provide insightful guidance and direction for developing tools for the diagnosis and analysis of SARS-CoV-2 to support public healthcare and effective long-term pandemic management and control.

Investigating the mediating effect of anxiety and fear of a third wave of COVID-19 among students in South India

The COVID-19 pandemic, which is a global health emergency, has potentiality had a serious impact on students' mental health. An online cross-sectional survey design that included 534 senior year college students from South India revealed a significant and direct positive effect of the fear of a third wave of COVID-19 on academic anxiety which in turn showed a significant and direct positive effect on COVID-19 burnout. Academic anxiety was also found to mediate the relationship between the fear of a third wave of COVID-19 and subsequent cases of burnout. The study suggested measures to be taken by policy makers for the broader interest and wellbeing of student communities. Managerial implications, limitations and future studies were also examined in the paper.

An Automated Strategy to Handle Antigenic Variability in Immunisation Protocols, Part I: Nanopore Sequencing of Infectious Agent Variants

Infectious agents often challenge therapeutics, from antibiotics resistance to antigenic variability affecting inoculation measures. Over the last decades, genome sequencing arose as an important ally to address such challenges. In bacterial infection, whole-genome-sequencing (WGS) supports tracking pathogenic alterations affecting the human microbiome. In viral infection, the analysis of the relevant sequence of nucleotides helps with determining historical variants of a virus and elucidates details about infection clusters and their distribution. Additionally, genome sequencing is now an important step in inoculation protocols, isolating target genes to design more robust immunisation assays. Ultimately, genetic engineering has empowered repurposing at scale, allowing long-lasting repeating clinical trials to be automated within a much shorter time-frame, by adjusting existing protocols. This is particularly important during sanitary emergencies as the ones caused by the 2014 West African Ebola outbreak, the Zika virus rapid spread in both South and North America in 2015, followed by Asia in 2016, and the pandemic caused by the SARS-CoV-2, which has infected more than 187 million people and caused more than 4 million deaths, worldwide, as per July 2021 statistics. In this scenery, this chapter presents a novel fully automated strategy to handle antigenic variability in immunisation protocols. The methodology comprises of two major steps (1) nanopore sequencing of infectious agent variants - the focus is on the SARS-CoV-2 and its variants; followed by (2) mRNA vector design for immunotherapy. This chapter presents the nanopore sequencing step and Chapter 17 introduces a protocol for mRNA vector design.

Non-uniform aspects of the SARS-CoV-2 intraspecies evolution reopen question of its origin

Several hypotheses have been presented on the origin of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) from its identification as the agent causing the current coronavirus disease 19 (COVID-19) pandemic. So far, no solid evidence has been found to support any hypothesis on the origin of this virus, and the issue continue to resurface over and over again. Here we have unfolded a pattern of distribution of several mutations in the SARS-CoV-2 proteins in 24 geo-locations across different continents. The results showed an evenly uneven distribution of the unique protein variants, distinct mutations, unique frequency of common conserved residues, and mutational residues across these 24 geo-locations. Furthermore, ample mutations were identified in the evolutionarily conserved invariant regions in the SARS-CoV-2 proteins across almost all geo-locations studied. This pattern of mutations potentially breaches the law of evolutionary conserved functional units of the beta-coronavirus genus. These mutations may lead to several novel SARS-CoV-2 variants with a high degree of transmissibility and virulence. A thorough investigation on the origin and characteristics of SARS-CoV-2 needs to be conducted in the interest of science and for the preparation of meeting the challenges of potential future pandemics.

Whole-genome sequence analysis reveals the circulation of multiple SARS-CoV-2 variants of concern in Nairobi and neighboring counties, Kenya between March and July 2021

The emergence and rapid spread of SARS-CoV-2 variants of concern (VOC) have been linked to new waves of COVID-19 epidemics occurring in different regions of the world. The VOC have acquired adaptive mutations that have enhanced virus transmissibility, increased virulence, and reduced response to neutralizing antibodies. Kenya has experienced six waves of COVID-19 epidemics. In this study, we analyzed 64 genome sequences of SARS-CoV-2 strains that circulated in Nairobi and neighboring counties, Kenya between March 2021 and July 2021. Viral RNA was extracted from RT-PCR confirmed COVID-19 cases, followed by sequencing using the ARTIC network protocol and Oxford Nanopore Technologies. Analysis of the sequence data was performed using different bioinformatics methods. Our analyses revealed that during the study period, three SARS-CoV-2 variants of concern (VOC) circulated in Nairobi and nearby counties in Kenya. The Alpha (B.1.1.7) lineage predominated (62.7%), followed by Delta (B.1.617.2, 35.8%) and Beta (B.1.351, 1.5%). Notably, the Alpha (B.1.1.7) VOC were most frequent from March 2021 to May 2021, while the Delta (B.1.617.2) dominated beginning June 2021 through July 2021. Sequence comparisons revealed that all the Kenyan viruses were genetically similar to those that circulated in other regions. Although the majority of Kenyan viruses clustered together in their respective phylogenetic lineages/clades, a significant number were interspersed among foreign strains. Between March and July 2021, our study's findings indicate the prevalence of multiple lineages of SAR-CoV-2 VOC in Nairobi and nearby counties in Kenya. The data suggest that the recent increase in SARS-CoV-2 infection, particularly in Nairobi and Kenya as a whole, is attributable to the introduction and community transmission of SARS-CoV-2 VOC among the populace. In conclusion, the findings provide a snapshot of the SARS-CoV-2 variants that circulated in Kenya during the study period.

Potential medicinal plants involved in inhibiting 3CLpro activity: A practical alternate approach to combating COVID-19

At present, a variety of vaccines have been approved, and existing antiviral drugs are being tested to find an effective treatment for coronavirus disease 2019 (COVID-19). However, no standardized treatment has yet been approved by the World Health Organization. The virally encoded chymotrypsin-like protease (3CL^pro) from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which facilitates the replication of SARS-CoV in the host cells, is one potential pharmacological target for the development of anti-SARS drugs. Online search engines, such as Web of Science, Google Scholar, Scopus and PubMed, were used to retrieve data on the traditional uses of medicinal plants and their inhibitory effects against the SARS-CoV 3CL^pro. Various pure compounds, including polyphenols, terpenoids, chalcones, alkaloids, biflavonoids, flavanones, anthraquinones and glycosides, have shown potent inhibition of SARS-CoV-2 3CL^pro activity with 50% inhibitory concentration (IC₅₀) values ranging from 2-44 µg/mL. Interestingly, most of these active compounds, including xanthoangelol E (isolated from Angelica keiskei), dieckol 1 (isolated from Ecklonia cava), amentoflavone (isolated from Torreya nucifera), celastrol, pristimerin, tingenone and iguesterin (isolated from Tripterygium regelii), tannic acid (isolated from Camellia sinensis), and theaflavin-3,3'-digallate, 3-isotheaflav1in-3 gallate and dihydrotanshinone I (isolated from Salvia miltiorrhiza), had IC₅₀ values of less than 15 µg/mL. Kinetic mechanistic studies of several active compounds revealed that their mode of inhibition was dose-dependent and competitive, with K_i values ranging from 2.4-43.8 μmol/L. Given the significance of plant-based compounds and the many promising results obtained, there is still need to explore the phytochemical and mechanistic potentials of plants and their products. These medicinal plants could serve as an effective inexpensive nutraceutical for the general public to help manage COVID-19.

Recombination in sarbecovirus lineage and mutations/insertions in spike protein are linked to the emergence and adaptation of SARS-CoV-2

The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan city, China in December 2019 and thereafter its spillover across the world has created a global pandemic and public health crisis. Right after, there has been intense interest in understanding how the SARS-CoV-2 originated and evolved. This paper also aims to shed light on the origin and evolution of SARS-CoV- 2. A consensus result based on whole genome phylogeny, gene tree analysis, and genetic similarity study revealed that SARS-CoV-2 evolved from Bat-CoV-RaTG13. Furthermore, recombination analysis indicated that probable origin of SARS-CoV-2 is the results of ancestral intra-species recombination events between bat coronaviruses belonging to Sarbecovirus sub-genus. Multiple sequence alignment (MSA) revealed the insertion of four amino acid residues "PRRA" (Proline-Arginine-Arginine-Alanine) to the S1/S2 site in the spike protein of SARS-CoV-2, and structural modeling of spike protein of bat-CoV-RaTG13 also shows a high number of mutations at one of the receptor binding domains (RBD). Acquisition of the furin cleavage sites ("PRRA") along with high number of mutations at one of its RBD is probably responsible for the adaptation of SARS-CoV-2 into human systems. Furthermore, the codon adaptation index (CAI) was used to quantify the magnitude of adaptive efficacy of SARS-CoV-2 in human host in comparison with SARS-CoV. The CAI result showed a relatively less adaptive efficacy of the newly emerged SARS-CoV-2 to the human systems, which might be an indication of its mild clinical severity and progression compared to SARS-CoVs.

The Spike Mutants Website: A Worldwide Used Resource against SARS-CoV-2

A large number of SARS-CoV-2 mutations in a short period of time has driven scientific research related to vaccines, new drugs, and antibodies to combat the new variants of the virus. Herein, we present a web portal containing the structural information, the tridimensional coordinates, and the molecular dynamics trajectories of the SARS-CoV-2 spike protein and its main variants. The Spike Mutants website can serve as a rapid online tool for investigating the impact of novel mutations on virus fitness. Taking into account the high variability of SARS-CoV-2, this application can help the scientific community when prioritizing molecules for experimental assays, thus, accelerating the identification of promising drug candidates for COVID-19 treatment. Below we describe the main features of the platform and illustrate the possible applications for speeding up the drug discovery process and hypothesize new effective strategies to overcome the recurrent mutations in SARS-CoV-2 genome.

SARS-CoV-2 variants of concern: a review

The virus that causes severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) belongs to the genus Beta coronavirus and the family Coronaviridae. The SARS-CoV-2 virus is a positive sense, non-segmented single-strand RNA virus that causes coronavirus disease 2019 (COVID-19), which was first reported in December 2019 in Wuhan, China. COVID-19 is now a worldwide pandemic. Globally, several newer variants have been identified; however, only a few of them are of concern (VOCs). VOCs differ in terms of infectivity, transmissibility, disease severity, drug efficacy, and neutralization efficacy by monoclonal antibodies, convalescent sera, or vaccines. VOCs reported from various parts of the world include B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617/B.1.617.2 (Delta), P.1 (Gamma), and B.1.1.529 (Omicron). These VOCs are the result of mutations, with some based on spike proteins. Mutations may also cause molecular diagnostic tests to fail to detect the few VOCs, leading to a delayed diagnosis, increased community spread, and delayed treatment. We searched PubMed, EMBASE, Covariant, Stanford variants database, and CINAHL from December 2019 to February 2022 using the following search terms: Variant of Concern, SARS-CoV-2, Omicron, etc. All types of research were chosen. All research methods were considered. This review discusses the various VOCs, as well as their mutations, infectivity, transmissibility, and neutralization efficacy.

Quantifying Mutational Response to Track the Evolution of SARS-CoV-2 Spike Variants: Introducing a Statistical-Mechanics-Guided Machine Learning Method

The emergence of SARS-CoV-2 and its variants that critically affect global public health requires characterization of mutations and their evolutionary pattern from specific Variants of Interest (VOIs) to Variants of Concern (VOCs). Leveraging the concept of equilibrium statistical mechanics, we introduce a new responsive quantity defined as "Mutational Response Function (MRF)" aptly quantifying domain-wise average entropy-fluctuation in the spike glycoprotein sequence of SARS-CoV-2 based on its evolutionary database. As the evolution transits from a specific variant to VOC, we find that the evolutionary crossover is accompanied by a dramatic change in MRF, upholding the characteristic of a dynamic phase transition. With this entropic information, we have developed an ancestral-based machine learning method that helps predict future domain-specific mutations. The feedforward binary classification model pinpoints possible residues prone to future mutations that have implications for enhanced fusogenicity and pathogenicity of the virus. We believe such MRF analyses followed by a statistical mechanics augmented ML approach could help track different evolutionary stages of such species and identify a critical evolutionary transition that is alarming.

Immunology to Immunotherapeutics of SARS-CoV-2: Identification of Immunogenic Epitopes for Vaccine Development

The emergence of COVID19 pandemic caused by SARS-CoV-2 virus has created a global public health and socio-economic crisis. Immunoinformatics-based approaches to investigate the potential antigens is the fastest way to move towards a multiepitope-based vaccine development. This review encompasses the underlying mechanisms of pathogenesis, innate and adaptive immune signaling along with evasion pathways of SARS-CoV-2. Furthermore, it compiles the promiscuous peptides from in silico studies which are subjected to prediction of cytokine milieu using web-based servers. Out of the 434 peptides retrieved from all studies, we have identified 33 most promising T cell vaccine candidates. This review presents a list of the most potential epitopes from several proteins of the virus based on their immunogenicity, homology, conservancy and population coverage studies. These epitopes can form a basis of second generation of vaccine development as the first generation vaccines in various stages of trials mostly focus only on Spike protein. We therefore, propose them as most potential candidates which can be taken up immediately for confirmation by experimental studies.

Transmission Dynamics and Genomic Epidemiology of Emerging Variants of SARS-CoV-2 in Bangladesh

With the progression of the global SARS-CoV-2 pandemic, the new variants have become more infectious and continue spreading at a higher rate than pre-existing ones. Thus, we conducted a study to explore the epidemiology of emerging variants of SARS-CoV-2 that circulated in Bangladesh from December 2020 to September 2021, representing the 2nd and 3rd waves. We collected new cases and deaths per million daily data with the reproduction rate. We retrieved 928 SARS-CoV-2 sequences from GISAID and performed phylogenetic tree construction and mutation analysis. Case counts were lower initially at the end of 2020, during January-February and April-May 2021, whereas the death toll reached the highest value of 1.587 per million on the first week of August and then started to decline. All the variants (α, β, δ, η) were prevalent in the capital city, Dhaka, with dispersion to large cities, such as Sylhet and Chattogram. The B.1.1.25 lineage was prevalent during December 2020, but the B.1.617.2/δ variant was later followed by the B.1.351/β variant. The phylogeny revealed that the various strains found in Bangladesh could be from numerous countries. The intra-cluster and inter-cluster communication began in Bangladesh soon after the virus arrived. The prominent amino acid substitution was D614G from December 2020 to July 2021 (93.5 to 100%). From February-April, one of the VOC's important mutations, N501Y substitution, was also estimated at 51.8%, 76.1%, and 65.1% for the α, β and γ variants, respectively. The γ variant's unique mutation K417T was detected only at 1.8% in February. Another frequent mutation was P681R, a salient feature of the δ variant, detected in June (88.2%) and July (100%). Furthermore, only one γ variant was detected during the entire second and third wave, whereas no η variant was observed in this period. This rapid growth in the number of variants identified across Bangladesh shows virus adaptation and a lack of strict quarantine, prompting periodic genomic surveillance to foresee the spread of new variants, if any, and to take preventive measures as soon as possible.

SARS-CoV-2 Delta spike protein enhances the viral fusogenicity and inflammatory cytokine production

The Delta variant had spread globally in 2021 and caused more serious disease than the original virus and Omicron variant. In this study, we investigated several virological features of Delta spike protein (SP_Delta), including protein maturation, its impact on viral entry of pseudovirus and cell-cell fusion, and its induction of inflammatory cytokine production in human macrophages and dendritic cells. The results showed that SPΔC_Delta exhibited enhanced S1/S2 cleavage in cells and pseudotyped virus-like particles (PVLPs). Further, SPΔC_Delta elevated pseudovirus entry in human lung cell lines and significantly enhanced syncytia formation. Furthermore, we revealed that SPΔC_Delta-PVLPs had stronger effects on stimulating NF-κB and AP-1 signaling in human monocytic THP1 cells and induced significantly higher levels of proinflammatory cytokine, such as TNF-α, IL-1β, and IL-6, released from human macrophages and dendritic cells. Overall, these studies provide evidence to support the important role of SPΔC_Delta during virus infection, transmission, and pathogenesis.

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SARS-CoV-2 Delta-SP exhibits enhanced cleavage and more efficient pseudovirus entry

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Delta-SP enhances syncytia formation in A549 cells expressing ACE2

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Delta-SP stimulates higher NF-κB and AP1 signaling pathway activities

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Delta-SP stimulates higher proinflammatory cytokine production in MDMs and MDDCs

Development of a panel of three multiplex allele-specific qRT-PCR assays for quick differentiation of recombinant variants and Omicron subvariants of SARS-CoV-2

Quick differentiation of the circulating variants and the emerging recombinant variants of SARS-CoV-2 is essential to monitor their transmission. However, the widely used gene sequencing method is time-consuming and costly when facing the viral recombinant variants, because partial or whole genome sequencing is required. Allele-specific real time RT-PCR (qRT-PCR) represents a quick and cost-effective method in SNP genotyping and has been successfully applied for SARS-CoV-2 variant screening. In the present study, we developed a panel of 3 multiplex allele-specific qRT-PCR assays targeting 12 key differential mutations for quick differentiation of SARS-CoV-2 recombinant variants (XD and XE) and Omicron subvariants (BA.1 and BA.2). Two parallel multiplex qRT-PCR reactions were designed to separately target the protype allele and the mutated allele of the four mutations in each allele-specific qRT-PCR assay. The variation of Cp values (ΔCp) between the two multiplex qRT-PCR reactions was applied for mutation determination. The developed multiplex allele-specific qRT-PCR assays exhibited outstanding analytical sensitivities (with limits of detection [LoDs] of 2.97-27.43 copies per reaction), wide linear detection ranges (10⁷-10⁰ copies per reaction), good amplification efficiencies (82% to 95%), good reproducibility (Coefficient of Variations (CVs) < 5% in both intra-assay and inter-assay tests) and clinical performances (99.5%-100% consistency with Sanger sequencing). The developed multiplex allele-specific qRT-PCR assays in this study provide an alternative tool for quick differentiation of SARS-CoV-2 recombinant variants (XD and XE) and Omicron subvariants (BA.1 and BA.2).

Virtual screening reveals liquiritigenin as a broad-spectrum inhibitor of SARS-CoV-2 variants of concern: an in silico study

The SARS-CoV-2 has severely impacted the lives of people worldwide. Global concern is on the rise due to a large number of unexpected mutations in the viral genome, resulting in new variants. Nature-based bioactive phytochemicals hold great promise as inhibitors against pathogenic viruses. The current study was aimed at evaluating some bioactive antiviral phytochemicals against SARS-CoV-2 variants of concern. A total of 46 phytochemicals were screened against the pathogenic spike protein of Alpha, Beta, Delta, Gamma, and Omicron variants. In addition to molecular docking, screening for favorable pharmacokinetic and pharmacodynamic properties such as absorption, distribution, metabolism, excretion, and toxicity was undertaken. For each of the aforementioned five SARS-CoV-2 variants of concern, a 100 ns molecular dynamics simulation was run to assess the stability of the complexes between their respective spike protein receptor-binding domain and the best-selected compound. From our current investigation, the natural compound liquiritigenin turned out to be the most promising potential lead compound against almost all the variants. These findings could pave the way for the development of effective medications against SARS-CoV-2 variants. However, in vivo trials in future studies are necessary for further validation of our results.Communicated by Ramaswamy H. Sarma.

Natural selection plays a significant role in governing the codon usage bias in the novel SARS-CoV-2 variants of concern (VOC)

The ongoing prevailing COVID-19 pandemic caused by SARS-CoV-2 is becoming one of the major global health concerns worldwide. The SARS-CoV-2 genome encodes spike (S) glycoprotein that plays a very crucial role in viral entry into the host cell via binding of its receptor binding domain (RBD) to the host angiotensin converting enzyme 2 (ACE2) receptor. The continuously evolving SARS-CoV-2 genome results in more severe and transmissible variants characterized by the emergence of novel mutations called 'variants of concern' (VOC). The currently designated alpha, beta, gamma, delta and omicron VOC are the focus of this study due to their high transmissibility, increased virulence, and concerns for decreased effectiveness of the available vaccines. In VOC, the spike (S) gene and other non-structural protein mutations may affect the efficacies of the approved COVID-19 vaccines. To understand the diversity of SARS-CoV-2, several studies have been performed on a limited number of sequences. However, only a few studies have focused on codon usage bias (CUBs) pattern analysis of all the VOC strains. Therefore, to evaluate the evolutionary divergence of all VOC S-genes, we performed CUBs analysis on 300,354 sequences to understand the evolutionary relationship with its adaptation in different hosts, i.e., humans, bats, and pangolins. Base composition and RSCU analysis revealed the presence of 20 preferred AU-ended and 10 under-preferred GC-ended codons. In addition, CpG was found to be depleted, which may be attributable to the adaptive response by viruses to escape from the host defense process. Moreover, the ENC values revealed a higher bias in codon usage in the VOC S-gene. Further, the neutrality plot analysis demonstrated that S-genes analyzed in this study are under 83.93% influence of natural selection, suggesting its pivotal role in shaping the CUBs. The CUBs pattern of S-genes was found to be very similar among all the VOC strains. Interestingly, we observed that VOC strains followed a trend of antagonistic codon usage with respect to the human host. The identified CUBs divergence would help to understand the virus evolution and its host adaptation, thus help design novel vaccine strategies against the emerging VOC strains. To the best of our knowledge, this is the first report for identifying the evolution of CUBs pattern in all the currently identified VOC.

Immune Response to SARS-CoV-2 Vaccines

COVID-19 vaccines have been developed to confer immunity against the SARS-CoV-2 infection. Prior to the pandemic of COVID-19 which started in March 2020, there was a well-established understanding about the structure and pathogenesis of previously known Coronaviruses from the SARS and MERS outbreaks. In addition to this, vaccines for various Coronaviruses were available for veterinary use. This knowledge supported the creation of various vaccine platforms for SARS-CoV-2. Before COVID-19 there are no reports of a vaccine being developed in under a year and no vaccine for preventing coronavirus infection in humans had ever been developed. Approximately nine different technologies are being researched and developed at various levels in order to design an effective COVID-19 vaccine. As the spike protein of SARS-CoV-2 is responsible for generating substantial adaptive immune response, mostly all the vaccine candidates have been targeting the whole spike protein or epitopes of spike protein as a vaccine candidate. In this review, we have compiled the immune response to SARS-CoV-2 infection and followed by the mechanism of action of various vaccine platforms such as mRNA vaccines, Adenoviral vectored vaccine, inactivated virus vaccines and subunit vaccines in the market. In the end we have also summarized the various adjuvants used in the COVID-19 vaccine formulation.

Facing the wrath of enigmatic mutations: a review on the emergence of severe acute respiratory syndrome coronavirus 2 variants amid coronavirus disease-19 pandemic

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging respiratory virus responsible for the ongoing coronavirus disease 19 (COVID-19) pandemic. More than a year into this pandemic, the COVID-19 fatigue is still escalating and takes hold of the entire world population. Driven by the ongoing geographical expansion and upcoming mutations, the COVID-19 pandemic has taken a new shape in the form of emerging SARS-CoV-2 variants. These mutations in the viral spike (S) protein enhance the virulence of SARS-CoV-2 variants by improving viral infectivity, transmissibility and immune evasion abilities. Such variants have resulted in cluster outbreaks and fresh infection waves in various parts of the world with increased disease severity and poor clinical outcomes. Hence, the variants of SARS-CoV-2 pose a threat to human health and public safety. This review enlists the most recent updates regarding the presently characterized variants of SARS-CoV-2 recognized by the global regulatory health authorities (WHO, CDC). Based on the slender literature on SARS-CoV-2 variants, we collate information on the biological implications of these mutations on virus pathology. We also shed light on the efficacy of therapeutics and COVID-19 vaccines against the emerging SARS-CoV-2 variants.

The effect of various compounds on the COVID mechanisms, from chemical to molecular aspects

The novel coronavirus that caused COVID-19 pandemic is SARS-CoV-2. Although various vaccines are currently being used to prevent the disease's severe consequences, there is still a need for medications for those who become infected. The SARS-CoV-2 has a variety of proteins that have been studied extensively since the virus's advent. In this review article, we looked at chemical to molecular aspects of the various structures studied that have pharmaceutical activity and attempted to find a link between drug activity and compound structure. For example, designing of the compounds which bind to the allosteric site and modify hydrogen bonds or the salt bridges can disrupt SARS-CoV2 RBD–ACE2 complex. It seems that quaternary ammonium moiety and quinolin-1-ium structure could act as a negative allosteric modulator to reduce the tendency between spike-ACE2. Pharmaceutical structures with amino heads and hydrophobic tails can block envelope protein to prevent making mature SARS-CoV-2. Also, structures based on naphthalene pharmacophores or isosteres can form a strong bond with the PLpro and form a π-π and the Mpro's active site can be occupied by octapeptide compounds or linear compounds with a similar fitting ability to octapeptide compounds. And for protein RdRp, it is critical to consider pH and pKa so that pKa regulation of compounds to comply with patients is very effective, thus, the presence of tetrazole, phenylpyrazole groups, and analogs of pyrophosphate in the designed drugs increase the likelihood of the RdRp active site inhibition. Finally, it can be deduced that designing hybrid drug molecules along with considering the aforementioned characteristics would be a suitable approach for developing medicines in order to accurate targeting and complete inhibition this virus.

Genomic Surveillance of COVID-19 Variants With Language Models and Machine Learning

The global efforts to control COVID-19 are threatened by the rapid emergence of novel SARS-CoV-2 variants that may display undesirable characteristics such as immune escape, increased transmissibility or pathogenicity. Early prediction for emergence of new strains with these features is critical for pandemic preparedness. We present Strainflow, a supervised and causally predictive model using unsupervised latent space features of SARS-CoV-2 genome sequences. Strainflow was trained and validated on 0.9 million sequences for the period December, 2019 to June, 2021 and the frozen model was prospectively validated from July, 2021 to December, 2021. Strainflow captured the rise in cases 2 months ahead of the Delta and Omicron surges in most countries including the prediction of a surge in India as early as beginning of November, 2021. Entropy analysis of Strainflow unsupervised embeddings clearly reveals the explore-exploit cycles in genomic feature-space, thus adding interpretability to the deep learning based model. We also conducted codon-level analysis of our model for interpretability and biological validity of our unsupervised features. Strainflow application is openly available as an interactive web-application for prospective genomic surveillance of COVID-19 across the globe.

Knowledge, attitude and practice survey towards COVID-19 vaccination: A mediation analysis

BACKGROUND AND AIM

The COVID-19 pandemic has significantly impacted human lives across the world. In a country like India, with the second highest population in the world, impact of COVID-19 has been diverse and multidimensional. Under such circumstances, vaccination against COVID-19 infection is claimed to be one of the major solutions to contain the pandemic. Understanding of Knowledge, Attitude and Practice (KAP) measures are essential prerequisites to design suitable intervention programs. This paper examines the different KAP factors in Indians towards their decision of vaccine uptake.

METHOD

An online questionnaire was administered to Indian respondents. (Pilot study: n = 100, Main study: n = 221) to assess their existing knowledge on COVID-19 infections and vaccination, attitude and intentions towards COVID-19 vaccines and their decision towards COVID-19 vaccine uptake.

RESULT

The findings highlighted that existing knowledge on COVID-19 infections and vaccination directly impacted their attitude and intention towards vaccination. The attitude and intention towards COVID-19 vaccines directly impacted their practice of undergoing COVID-19 vaccination. Further, there was a statistically significant and considerably large indirect effect of existing knowledge on COVID-19 infections and vaccination on the practice of undergoing COVID-19 vaccination through attitude and intention towards the vaccine. There was no direct effect of Knowledge (existing knowledge on COVID-19 infections and vaccination) on Practice (decision to undergo COVID-19 vaccination). Therefore, Attitude and intention towards COVID-19 vaccine is the primary mediator between Knowledge (existing knowledge on COVID-19 infections and vaccination) and Practice (decision to undergo COVID-19 vaccination).

CONCLUSION

Participants decision towards COVID-19 vaccination decisions are strongly related to their attitude and intentions that confirms the strong role of attitude towards success of COVID-19 vaccination programme. Therefore, 'person-centric' attitude based positive intervention strategies that links their prior knowledge on COVID-19 infections and vaccination must be designed for greater vaccine acceptance amongst Indians.

Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka

Background: As the coronavirus disease 2019 (COVID-19) pandemic continues, the selection of genomic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) associated with higher transmission, more severe disease, re-infection, and immune escape are a cause for concern. Such variants have been reported from the UK (B.1.1.7), South Africa (B.1.351) and, Brazil (P.1/B.1.1.28). We performed this study to track the importation, spread, and emergence of variants locally. Methods: We sequenced whole genomes of SARS-CoV-2 from international travellers (n=75) entering Karnataka, South India, between Dec 22, 2020 and Jan 31, 2021, and from positive cases in the city of Bengaluru (n=108), between Nov 22, 2020- Jan 22, 2021, as well as a local outbreak. We present the lineage distribution and analysis of these sequences. Results: Genomes from the study group into 34 lineages. Variant B.1.1.7 was introduced by international travel (24/73, 32.9%). Lineage B.1.36 and B.1 formed a major fraction of both imported (B.1.36: 20/73, 27.4%; B.1: 14/73, 19.2%), and circulating viruses (B.1.36: 45/103; 43.7%,. B.1: 26/103; 25.2%). The lineage B.1.36 was also associated with a local outbreak. We detected nine amino acid changes, previously associated with immune escape, spread across multiple lineages. The N440K change was detected in 45/162 (27.7%) of the sequences, 37 of these were in the B.1.36 lineage (37/65, 56.92%) Conclusions: Our data support the idea that variants of concern spread by travel. Viruses with amino acid replacements associated with immune escape are already circulating. It is critical to check transmission and monitor changes in SARS-CoV-2 locally.

SARS-CoV-2 Omicron variant replication in human bronchus and lung ex vivo

The emergence of SARS-CoV-2 variants of concern with progressively increased transmissibility between humans is a threat to global public health. The Omicron variant of SARS-CoV-2 also evades immunity from natural infection or vaccines¹, but it is unclear whether its exceptional transmissibility is due to immune evasion or intrinsic virological properties. Here we compared the replication competence and cellular tropism of the wild-type virus and the D614G, Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2) and Omicron (B.1.1.529) variants in ex vivo explant cultures of human bronchi and lungs. We also evaluated the dependence on TMPRSS2 and cathepsins for infection. We show that Omicron replicates faster than all other SARS-CoV-2 variants studied in the bronchi but less efficiently in the lung parenchyma. All variants of concern have similar cellular tropism compared to the wild type. Omicron is more dependent on cathepsins than the other variants of concern tested, suggesting that the Omicron variant enters cells through a different route compared with the other variants. The lower replication competence of Omicron in the human lungs may explain the reduced severity of Omicron that is now being reported in epidemiological studies, although determinants of severity are multifactorial. These findings provide important biological correlates to previous epidemiological observations.

Learning From Biological and Computational Machines: Importance of SARS-CoV-2 Genomic Surveillance, Mutations and Risk Stratification

The global coronavirus disease 2019 (COVID-19) pandemic has demonstrated the range of disease severity and pathogen genomic diversity emanating from a singular virus (severe acute respiratory syndrome coronavirus 2, SARS-CoV-2). This diversity in disease manifestations and genomic mutations has challenged healthcare management and resource allocation during the pandemic, especially for countries such as India with a bigger population base. Here, we undertake a combinatorial approach toward scrutinizing the diagnostic and genomic diversity to extract meaningful information from the chaos of COVID-19 in the Indian context. Using methods of statistical correlation, machine learning (ML), and genomic sequencing on a clinically comprehensive patient dataset with corresponding with/without respiratory support samples, we highlight specific significant diagnostic parameters and ML models for assessing the risk of developing severe COVID-19. This information is further contextualized in the backdrop of SARS-CoV-2 genomic features in the cohort for pathogen genomic evolution monitoring. Analysis of the patient demographic features and symptoms revealed that age, breathlessness, and cough were significantly associated with severe disease; at the same time, we found no severe patient reporting absence of physical symptoms. Observing the trends in biochemical/biophysical diagnostic parameters, we noted that the respiratory rate, total leukocyte count (TLC), blood urea levels, and C-reactive protein (CRP) levels were directly correlated with the probability of developing severe disease. Out of five different ML algorithms tested to predict patient severity, the multi-layer perceptron-based model performed the best, with a receiver operating characteristic (ROC) score of 0.96 and an F1 score of 0.791. The SARS-CoV-2 genomic analysis highlighted a set of mutations with global frequency flips and future inculcation into variants of concern (VOCs) and variants of interest (VOIs), which can be further monitored and annotated for functional significance. In summary, our findings highlight the importance of SARS-CoV-2 genomic surveillance and statistical analysis of clinical data to develop a risk assessment ML model.

Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India

COVID-19 pandemic 2nd wave catastrophic effect in the state of Chhattisgarh, India, from where no exclusive genomic data yet published, has prompted us to undertake this study to unearth the causative variant. Whole-genome sequencing of SARS-CoV-2 isolated from COVID-19 infected nine vaccinated healthcare workers (HCW), thirty mild/moderate, seventeen severe, and twenty-seven deceased patients, was performed. The significant predominance of the SARS-CoV-2 variant of concern (VOC), Delta (lineage B.1.617.2) identified in sixty-four (77.1%) cases in contrast to B.1 and its sublineage in eleven (13.2%), variant under monitoring (VUM), Kappa (lineage B.1.617.1) in five (6.0%) and another VOC Alpha (lineage B.1.1.7) in three (3.6%) cases respectively (p < 0.05, χ² = 162.49). 88.8% vaccine breakthrough, 60% mild/moderate, 94.4% severe and 81.5% dead patients were infected by Delta. Kappa presents exclusively in mild/moderate, Alpha in vaccine breakthrough, mild/moderate, and dead patient and B.1 and its sublineages in mild, severe, and dead patient categories. Delta variant spike mutation of T19R, G142D, E156G, L452R, and deletion (F157 and R158) helps in escaping antibody response, T478K and D614G enhance viral affinity with ACE2 receptor while P681R and D950N result in higher replication and transmissibility by cleaving S1/S2 at furin site. We conclude that Delta variant predominant role along with co-occurrence of Kappa, Alpha, and B.1 variant during COVID-19 2nd wave pandemic in Chhattisgarh may pose a potential threat of future outbreak through hybrid variant evolution. Thus, intensive genomic surveillance for monitoring variant evolution and a more efficacious vaccine against the Delta and Alpha variants are required.

Understanding the dynamics of IgM & IgG antibodies in COVID-19-positive patients

Background & objectives

The pandemic caused by the SARS-CoV-2 has been a threat to humankind due to the rapid spread of infection and appearance of multiple new variants. In the present study, we report the dynamics and persistence of immunoglobulin G (IgG) and immunoglobulin M (IgM) antibodies in asymptomatic and symptomatic COVID-19 patients by chemiluminescent assay.

Methods

A total of 463 serum samples from 218 SARS-CoV-2 PCR-positive patients were collected over a period of 124 days post-onset of disease (POD). Antibody levels were measured by chemiluminescence bioanalyzer. Neutralizing antibody titres were assessed by plaque reduction neutralization test (PRNT) for SARS-CoV-2.

Results

Both IgM and IgG started appearing from day five post-infection in symptomatic and asymptomatic patients. IgM antibody response peaked around day 35 POD and rapidly diminished thereafter, with the last IgM-positive sample observed at 90 days POD. IgG antibody response peaked around 45 days POD and persisted till 124 days. The chemiluminescence immunoassay (CLIA) results showed a moderate correlation (R=0.5846, P<0.001) compared with PRNT. Additional analysis indicated a neutralizing titre of 250 corresponded to 12.948 AU/ml of YHLO iFlash SARS-CoV-2 IgG units.

Interpretation & conclusions

Both symptomatic and asymptomatic COVID-19 patients seem to initiate production of antibody responses from day five of onset of disease. Although the CLIA gives high sensitivity and specificity and also its binding IgG antibody titres may correlate moderately with protective immunity, our results indicate that the values of binding antibody alone may not be a perfect guide to represent virus neutralization titre during donor selection for plasma therapy. However, IgM and IgG antibody detection may help in monitoring the status of disease progression and burden in the community.

Peptides and peptidomimetics as therapeutic agents for Covid-19

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Covid-19 pandemic has caused high morbidity and mortality rates worldwide. Virus entry into cells can be blocked using several strategies, including inhibition of protein-protein interactions (PPIs) between the viral spike glycoprotein and cellular receptors, as well as blocking of spike protein conformational changes that are required for cleavage/activation and fusogenicity. The spike-mediated viral attachment and entry into cells via fusion of the viral envelope with cellular membranes involve PPIs mediated by short peptide fragments exhibiting particular secondary structures. Thus, peptides that can inhibit these PPIs may be used as potential antiviral agents preventing virus entry and spread. This review is focused on peptides and peptidomimetics as PPI modulators and protease inhibitors against SARS-CoV-2.

Understanding the activating mechanism of the immune system against COVID-19 by Traditional Indian Medicine: Network pharmacology approach

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) transmissions are occurring rapidly; it is raising the alarm around the globe. Though vaccines are currently available, the evolution and mutations in the SARS-CoV-2 threaten available vaccines' significance. The drugs are still undergoing clinical trials, and certain medications are approved for “emergency use” or as an “off-label” drug during the pandemic. These drugs have been effective yet accommodating side effects, which also can be lethal. Complementary and alternative medicine is highly demanded since it embraces a holistic approach. Since ancient times, natural products have been used as drugs to treat various diseases in the medical field and are still widely practiced. Medicinal plants contain many active compounds that serve as the key to an effective drug design. The Kabasura kudineer and Nilavembu kudineer are the two most widely approved formulations to treat COVID-19. However, the mechanism of these formulations is not well known. The proposed study used a network pharmacology approach to understand the immune-boosting mechanism by the Kabasura kudineer, Nilavembu kudineer, and JACOM in treating COVID-19. The plants and phytochemical chemical compounds in the Kabasura kudineer, Nilavembu kudineer, and JACOM were obtained from the literature. The Swiss target prediction algorithm was used to predict the targets for these phytochemical compounds. The common genes for the COVID-19 infection and the drug targets were identified. The gene–gene interaction network was constructed to understand the interactions between these common genes and enrichment analyses to determine the biological process, molecular functions, cellular functions, pathways involved, etc. Finally, virtual screening and molecular docking studies were performed to identify the most potential targets and significant phytochemical compounds to treat the COVID-19. The present study identified potential targets as ACE, Cathepsin L, Cathepsin B, Cathepsin K, DPP4, EGFR, HDAC2, IL6, RIPK1, and VEGFA. Similarly, betulinic acid, 5″-(2⁗-Hydroxybenzyl) uvarinol, antofine, (S)-1′-methyloctyl caffeate, (Z)-3-phenyl-2-propenal, 7-oxo-10α-cucurbitadienol, and PLX-4720 collectively to be potential treatment agents for COVID-19.

An update on host immunity correlates and prospects of re-infection in COVID-19

Reinfection with SARS-CoV-2 is not frequent yet the incidence rate of it is increasing globally owing to the slow emergence of drift variants that pose a perpetual threat to vaccination strategies and have a greater propensity for disease reoccurrence. Long-term protection against SARS-CoV-2 reinfection relies on the induction of the innate as well as the adaptive immune response endowed with immune memory. However, a multitude of factors including the selection pressure, the waning immunity against SARS-CoV-2 over the first year after infection possibly favors evolution of more infectious immune escape variants, amplifying the risk of reinfection. Additionally, the correlates of immune protection, the novel SARS-CoV-2 variants of concern (VOC), the durability of the adaptive and mucosal immunity remain major challenges for the development of therapeutic and prophylactic interventions. Interestingly, a recent body of evidence indicated that the gastrointestinal (GI) tract is another important target organ for SARS-CoV-2 besides the respiratory system, potentially increasing the likelihood of reinfection by impacting the microbiome and the immune response via the gut-lung axis. In this review, we summarized the latest development in SARS-CoV-2 reinfection, and explored the untapped potential of trained immunity. We also highlighted the immune memory kinetics of the humoral and cell-mediated immune response, genetic drift of the emerging viral variants, and discussed the current challenges in vaccine development. Understanding the dynamics and the quality of immune response by unlocking the power of the innate, humoral and cell-mediated immunity during SARS-CoV-2 reinfection would open newer avenues for drug discovery and vaccine designs.

E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody

SARS-CoV2 mutants B.1.1.7, B.1.351, and P.1 contain a key mutation N501Y. B.1.135 and P.1 lineages have another mutation, E484K. Here, we decode the effect of these two mutations on the host receptor, ACE2, and neutralizing antibody (B38) recognition. The N501Y RBD mutant binds to ACE2 with higher affinity due to improved π-π stacking and π-cation interactions. The higher binding affinity of the E484K mutant is caused due to the formation of additional hydrogen bond and salt-bridge interactions with ACE2. Both the mutants bind to the B38 antibody with reduced affinity due to the loss of several hydrogen-bonding interactions. The insights obtained from the study are crucial to interpret the increased transmissibility and reduced neutralization efficacy of rapidly emerging SARS-CoV2 VOCs.

The Development of SARS-CoV-2 Variants: The Gene Makes the Disease

A novel coronavirus (SARS-CoV-2) emerged towards the end of 2019 that caused a severe respiratory disease in humans called COVID-19. It led to a pandemic with a high rate of morbidity and mortality that is ongoing and threatening humankind. Most of the mutations occurring in SARS-CoV-2 are synonymous or deleterious, but a few of them produce improved viral functions. The first known mutation associated with higher transmissibility, D614G, was detected in early 2020. Since then, the virus has evolved; new mutations have occurred, and many variants have been described. Depending on the genes affected and the location of the mutations, they could provide altered infectivity, transmissibility, or immune escape. To date, mutations that cause variations in the SARS-CoV-2 spike protein have been among the most studied because of the protein's role in the initial virus-cell contact and because it is the most variable region in the virus genome. Some concerning mutations associated with an impact on viral fitness have been described in the Spike protein, such as D614G, N501Y, E484K, K417N/T, L452R, and P681R, among others. To understand the impact of the infectivity and antigenicity of the virus, the mutation landscape of SARS-CoV-2 has been under constant global scrutiny. The virus variants are defined according to their origin, their genetic profile (some characteristic mutations prevalent in the lineage), and the severity of the disease they produce, which determines the level of concern. If they increase fitness, new variants can outcompete others in the population. The Alpha variant was more transmissible than previous versions and quickly spread globally. The Beta and Gamma variants accumulated mutations that partially escape the immune defenses and affect the effectiveness of vaccines. Nowadays, the Delta variant, identified around March 2021, has spread and displaced the other variants, becoming the most concerning of all lineages that have emerged. The Delta variant has a particular genetic profile, bearing unique mutations, such as T478K in the spike protein and M203R in the nucleocapsid. This review summarizes the current knowledge of the different mutations that have appeared in SARS-CoV-2, mainly on the spike protein. It analyzes their impact on the protein function and, subsequently, on the level of concern of different variants and their importance in the ongoing pandemic.

Structural and functional insights into the spike protein mutations of emerging SARS-CoV-2 variants

Since the emergence of the first case of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus (SARS-CoV-2), the viral genome has constantly undergone rapid mutations for better adaptation in the host system. These newer mutations have given rise to several lineages/ variants of the virus that have resulted in high transmission and virulence rates compared to the previously circulating variants. Owing to this, the overall caseload and related mortality have tremendously increased globally to > 233 million infections and > 4.7 million deaths as of Sept. 28th, 2021. SARS-CoV-2, Spike (S) protein binds to host cells by recognizing human angiotensin-converting enzyme 2 (hACE2) receptor. The viral S protein contains S1 and S2 domains that constitute the binding and fusion machinery, respectively. Structural analysis of viral S protein reveals that the virus undergoes conformational flexibility and dynamicity to interact with the hACE2 receptor. The SARS-CoV-2 variants and mutations might be associated with affecting the conformational plasticity of S protein, potentially linked to its altered affinity, infectivity, and immunogenicity. This review focuses on the current circulating variants of SARS-CoV-2 and the structure-function analysis of key S protein mutations linked with increased affinity, higher infectivity, enhanced transmission rates, and immune escape against this infection.

Coronavirus Diseases (COVID-19): Features, Epidemiology, Mutational variations and Treatments Across India

Coronaviruses are a group of enveloped viruses with a longer, undivided single-stranded RNA genome, which cause diseases in a variety of animals and humans. In addition to infecting other economically important animals (such as pigs or chickens), six coronaviruses are known to infect human hosts, causing respiratory illness. Severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) are highly pathogenic animal coronaviruses that have produced local, regional, and worldwide outbreaks. It is suspected that the current pandemic, caused by a similar coronavirus (SARS-CoVID-19). A new variant of B.1.617 lineage that causes worry about many countries has been identified first in the UK but it makes the worst scenario in India. This includes mutants with immune prolapse E484K and N501Y mutations. Some new variants recently discovered in India like double & triple mutation due to some specific climatic and environmental conditions. Because it creates a viral exodermis and contacts human cells due to mutations in peplomer proteins. The other type of protein is spike protein, are required to bind to receptors in human cells mutations. It can improve the affinity for human receptors and increase the virus, they can cause immune prolapse and reinfection. Moreover, these viruses are capable of adapting and mutating to the new environment. Our immune system is unable to distinguish them from previous infections due to changes in the structure of proteins. The rapid transmission of the COVID-19 around the world causing a severe mortality rate depends on mutation on their spike protein.

Research advances and prospects of legume lectins

Lectins are widely distributed proteins having ability of binding selectively and reversibly with carbohydrates moieties and glycoconjugates. Although lectins have been reported from different biological sources, the legume lectins are the best-characterized family of plant lectins. Legume lectins are a large family of homologous proteins with considerable similarity in amino acid sequence and their tertiary structures. Despite having strong sequence conservation, these lectins show remarkable variability in carbohydrate specificity and quaternary structures. The ability of legume lectins in recognizing glycans and glycoconjugates on cells and other intracellular structures make them a valuable research tool in glycomic research. Due to variability in binding with glycans, glycoconjugates and multiple biological functions, legume lectins are the subject of intense research for their diverse application in different fields such as glycobiology, biomedical research and crop improvement. The present review specially focuses on structural and functional characteristics of legume lectins along with their potential areas of application.

A structurally conserved RNA element within SARS-CoV-2 ORF1a RNA and S mRNA regulates translation in response to viral S protein-induced signaling in human lung cells

The positive-sense, single-stranded RNA genome SARS-CoV-2 harbors functionally important cis-acting elements governing critical aspects of viral gene expression. However, insights on how these elements sense various signals from the host cell and regulate viral protein synthesis are lacking. Here, we identified two novel cis-regulatory elements in SARS-CoV-2 ORF1a and S RNAs and describe their role in translational control of SARS-CoV-2. These elements are sequence-unrelated but form conserved hairpin structures (validated by NMR) resembling Gamma Activated Inhibitor of Translation (GAIT) elements that are found in a cohort of human mRNAs directing translational suppression in myeloid cells in response to IFN-γ. Our studies show that treatment of human lung cells with receptor-binding S1 subunit, S protein pseudotyped lentivirus, and S protein-containing virus-like particles triggers a signaling pathway involving DAP-kinase1 that leads to phosphorylation and release of the ribosomal protein L13a from the large ribosomal subunit. Released L13a forms a Virus Activated Inhibitor of Translation (VAIT) complex that binds to ORF1a and S VAIT elements, causing translational silencing. Translational silencing requires extracellular S protein (and its interaction with host ACE2 receptor), but not its intracellular synthesis. RNA-protein interaction analyses and in vitro translation experiments showed that GAIT and VAIT elements do not compete with each other, highlighting differences between the two pathways. Sequence alignments of SARS-CoV-2 genomes showed a high level of conservation of VAIT elements, suggesting their functional importance. This VAIT-mediated translational control mechanism of SARS-CoV-2 may provide novel targets for small molecule intervention and/or facilitate development of more effective mRNA vaccines. Importance Specific RNA elements in the genomes of RNA viruses play important roles in host-virus interaction. For SARS-CoV-2, the mechanistic insights on how these RNA elements could sense the signals from the host cell are lacking. Here we report a novel relationship between the GAIT-like SARS-CoV-2 RNA element (called VAITs) and the signal generated from the host cell. We show that for SARS-CoV-2, the interaction of spike protein with ACE2 not only serves the purpose for viral entry into the host cell, but also transduces signals that culminate into the phosphorylation and the release of L13a from the large ribosomal subunit. We also show that this event leads to the translational arrest of ORF1a and S mRNAs in a manner dependent on the structure of the RNA elements. Translational control of viral mRNA by a host-cell generated signal triggered by viral protein is a new paradigm in the host-virus relationship.

Epidemiological Analysis of SARS-CoV-2 Transmission Dynamics in the State of Odisha, India: A Yearlong Exploratory Data Analysis

COVID-19 remains a matter of global public health concern. Previous research suggested the association between local environmental factors and viral transmission. We present a multivariate observational analysis of SARS-CoV-2 transmission in the state of Odisha, India, hinting at a seasonal activity. We aim to investigate the demographic characteristics of COVID-19 in the Indian state of Odisha for two specific timelines in 2020 and 2021. For a comparative outlook, we chose similar datasets from the state of New York, USA. Further, we present a critical analysis pertaining to the effects of environmental factors and the emergence of variants on SARS-CoV-2 transmission and persistence. We assessed the datasets for confirmed cases, death, age, and gender for 29 February 2020 to 31 May 2020, and 1 March 2021 to 31 May 2021. We determined the case fatalities, crude death rates, sex ratio, and incidence rates for both states along with monthly average temperature analysis. A yearlong epi-curve analysis was conducted to depict the coronavirus infection spread pattern in the respective states. The Indian state of Odisha reported a massive 436,455 confirmed cases and 875 deaths during the 2021 timeline as compared to a mere 2223 cases and 7 deaths during the 2020 timeline. We further discuss the demographic and temperature association of SARS-CoV-2 transmission during early 2020 and additionally comment on the variant-associated massive rise in cases during 2021. Along with the rapid rise of variants, the high population density and population behavior seem to be leading causes for the 2021 pandemic, whereas factors such as age group, gender, and average local temperature were prominent during the 2020 spread. A seasonal occurrence of SARS-CoV-2 transmission is also observed from the yearlong epidemiological plot. The recent second wave of COVID-19 is a lesson that emphasizes the significance of continuous epidemiological surveillance to predict the relative risk of viral transmission for a specific region.

Molecular Analysis and Genome Sequencing of SARS-CoV-2 during Second Wave 2021 Revealed Variant Diversity in India

SARS-CoV-2 variants rapid emergence has posed critical challenge of higher transmission and immune escape causing serious threats to control the pandemic. The present study was carried out in confirmed cases of SARS-CoV-2 patients to elucidate the prevalence of SARS-CoV-2 variant strain. We performed RT-PCR using extracted RNA from the nasopharyngeal swabs of suspected Covid-19 patients. Confirmed positive cases with CT<25 were subjected to whole-genome sequencing to track the prevalence of the virus in the Malwa region of Punjab. The presence of B.1, B.1.1.7, B.1.351, B.1.617.1, B.1.617.2, AY.1 and other unidentified variants of SARS-CoV-2 was found in the studied population. Among all the variants, B.1.1.7 (UK variant) and B.1.617.2 (delta-Indian variant) was found to be the most dominant variant in the population and was found majorly in Patiala followed by Ludhiana, SBS Nagar, Mansa and Sangrur. In addition to this, sequencing results also observed that the dominant trait was more prevalent in male population and age group 21-40 years. The B.1.1.7 and B.1.617.2 variant of SARS-CoV-2 is replacing the wild type (Wuhan Strain) and emerging as the dominant variant in Punjab.

The D614G Virus Mutation Enhances Anosmia in COVID-19 Patients: Evidence from a Systematic Review and Meta-analysis of Studies from South Asia

The prevalence of chemosensory dysfunction in patients with COVID-19 varies greatly between populations. It is unclear whether such differences are due to factors at the level of the human host, or at the level of the coronavirus, or both. At the host level, the entry proteins which allow virus binding and entry have variants with distinct properties, and the frequency of such variants differs between ethnicities. At the level of the virus, the D614G mutation enhances virus entry to the host cell. Since the two virus strains (D614 and G614) coexisted in the first six months of the pandemic in most populations, it has been difficult to distinguish between contributions of the virus and contributions of the host for anosmia. To answer this question, we conducted a systematic review and meta-analysis of studies in South Asian populations when either the D614 or the G614 virus was dominant. We show that populations infected predominantly with the G614 virus had a much higher prevalence of anosmia (pooled prevalence of 31.8%) compared with the same ethnic populations infected mostly with the D614 virus strain (pooled anosmia prevalence of 5.3%). We conclude that the D614G mutation is a major contributing factor that increases the prevalence of anosmia in COVID-19, and that this enhanced effect on olfaction constitutes a previously unrecognized phenotype of the D614G mutation. The new virus strains that have additional mutations on the background of the D614G mutation can be expected to cause a similarly increased prevalence of chemosensory dysfunctions.

The COVID-19 pandemic: viral variants and vaccine efficacy

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has prompted the scientific community and the pharmaceutical companies to put maximum efforts into developing vaccines to contain the spread of this disease. Presently, many vaccines have been developed and authorized for use in human beings in different countries. In particular, in Europe to date, the Pfizer-BioNTech, Moderna, AstraZeneca and Janssen COVID-19 vaccines have been authorized. All of them are based on a version of the spike (S) glycoprotein characterized at the beginning of the pandemic. However, they differ by their level of efficacy against COVID-19. SARS-COV-2, like other RNA viruses, mutates continually. Genome sequencing analysis shows a nucleotide substitution rate of about 1 × 10^-3 substitutions per year that leads to the emergence of variants through point mutations, insertions, deletions and recombination. There is concern about the ability of the current vaccines to protect against emerging viral variants. Mutations in the S-glycoprotein may affect transmission dynamics and the risk of immune escape. In this review, we address the different technological platforms in use for developing COVID-19 vaccines, the impact of emerging viral variants on virus transmission, hospitalization, and response to current vaccines, as well as rare but important adverse reactions to them. Finally, different methods for measuring antibody response to the vaccines, including the importance of using the WHO International Standard to calibrate immunoassays accurately to an arbitrary unit, to reduce interlaboratory variation and to create a common language for reporting results, are reported.

Predicting mortality in SARS-COV-2 (COVID-19) positive patients in the inpatient setting using a novel deep neural network

BACKGROUND

The nextwave of COVID-19 pandemic is anticipated to be worse than the initial one and will strain the healthcare systems even more during the winter months. Our aim was to develop a novel machine learning-based model to predict mortality using the deep learning Neo-V framework. We hypothesized this novel machine learning approach could be applied to COVID-19 patients to predict mortality successfully with high accuracy.

METHODS

We collected clinical and laboratory data prospectively on all adult patients (≥18 years of age) that were admitted in the inpatient setting at Aga Khan University Hospital between February 2020 and September 2020 with a clinical diagnosis of COVID-19 infection. Only patients with a RT-PCR (reverse polymerase chain reaction) proven COVID-19 infection and complete medical records were included in this study. A Novel 3-phase machine learning framework was developed to predict mortality in the inpatients setting. Phase 1 included variable selection that was done using univariate and multivariate Cox-regression analysis; all variables that failed the regression analysis were excluded from the machine learning phase of the study. Phase 2 involved new-variables creation and selection. Phase 3 and final phase applied deep neural networks and other traditional machine learning models like Decision Tree Model, k-nearest neighbor models, etc. The accuracy of these models were evaluated using test-set accuracy, sensitivity, specificity, positive predictive values, negative predictive values and area under the receiver-operating curves.

RESULTS

After application of inclusion and exclusion criteria (n=)1214 patients were selected from a total of 1228 admitted patients. We observed that several clinical and laboratory-based variables were statistically significant for both univariate and multivariate analyses while others were not. With most significant being septic shock (hazard ratio [HR], 4.30; 95% confidence interval [CI], 2.91-6.37), supportive treatment (HR, 3.51; 95% CI, 2.01-6.14), abnormal international normalized ratio (INR) (HR, 3.24; 95% CI, 2.28-4.63), admission to the intensive care unit (ICU) (HR, 3.24; 95% CI, 2.22-4.74), treatment with invasive ventilation (HR, 3.21; 95% CI, 2.15-4.79) and laboratory lymphocytic derangement (HR, 2.79; 95% CI, 1.6-4.86). Machine learning results showed our deep neural network (DNN) (Neo-V) model outperformed all conventional machine learning models with test set accuracy of 99.53%, sensitivity of 89.87%, and specificity of 95.63%; positive predictive value, 50.00%; negative predictive value, 91.05%; and area under the receiver-operator curve of 88.5.

CONCLUSION

Our novel Deep-Neo-V model outperformed all other machine learning models. The model is easy to implement, user friendly and with high accuracy.

Emerging SARS-CoV-2 Variants of Concern (VOCs): An Impending Global Crisis

The worldwide battle against the SARS-CoV-2 virus rages on, with millions infected and many innocent lives lost. The causative organism, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a beta coronavirus that belongs to the Coronaviridae family. Many clinically significant variants have emerged, as the virus's genome is prone to various mutations, leading to antigenic drift and resulting in evasion of host immune recognition. The current variants of concern (VOCs) include B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617/B.1.617.2 (Delta), and P.1 (Gamma). The emerging variants contain various important mutations on the spike protein, leading to deleterious consequences, such as immune invasion and vaccine escape. These adverse effects result in increased transmissibility, morbidity, and mortality and the evasion of detection by existing or currently available diagnostic tests, potentially delaying diagnosis and treatment. This review discusses the key mutations present in the VOC strains and provides insights into how these mutations allow for greater transmissibility and immune evasion than the progenitor strain. Continuous monitoring and surveillance of VOC strains play a vital role in preventing and controlling the virus's spread.