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Background: According to Norwegian registries, 91% of individuals ≥ 16 years had received ≥ 1 dose of COVID-19 vaccine by mid-July 2022, whereas less than 2% of children < 12 years were vaccinated. Confirmed COVID-19 was reported for 27% of the population, but relaxation of testing lead to substantial underreporting. We have characterized the humoral immunity to SARS-CoV-2 in Norway in the late summer of 2022 by estimating the seroprevalence and identifying antibody profiles based on reactivity to Wuhan or Omicron-like viruses in a nationwide cross-sectional collection of residual sera, and validated our findings using cohort sera. Methods: 1,914 anonymized convenience sera and 243 NorFlu-cohort sera previously collected from the Oslo-area with reported infection and vaccination status were analyzed for antibodies against spike, the receptor-binding domain (RBD) of the ancestral Wuhan strain and Omicron BA.2 RBD, and nucleocapsid (N). Samples were also tested for antibodies inhibiting RBD-ACE2 interaction. Neutralization assays were performed on subsets of residual sera against B.1, BA.2, XBB.1.5 and BQ.1.1. Results: The national seroprevalence estimate from vaccination and/or infection was 99.1% (95% CrI 97.0-100.0%) based on Wuhan (spike_W and RBD_W) and RBD_BA2 antibodies. Sera from children < 12 years had 2.2 times higher levels of antibodies against RBD_BA2 than RBD_W and their seroprevalence estimate showed a 14.4 percentage points increase when also including anti-RBD_BA2 antibodies compared to Wuhan-antibodies alone. 50.3% (95% CI 45.0-55.5%) of residual sera from children and 38.1% (95% CI 36.0-40.4%) of all residual sera were positive for anti-N-antibodies. By combining measurements of binding- and ACE2-RBD-interaction-inhibiting antibodies, reactivity profiles indicative of infection and vaccination history were identified and validated using cohort sera. Residual sera with a profile indicative of hybrid immunity were able to neutralize newer Omicron variants XBB.1.5 and BQ.1.1. Conclusions: By late summer of 2022, most of the Norwegian population had antibodies to SARS-CoV-2, and almost all children had been infected. Antibody profiles indicated that children mostly had experienced a primary Omicron infection, while hybrid immunity was common among adults. The finding that sera displaying hybrid immunity could neutralize newer Omicron variants indicates that Wuhan-like priming of the immune response did not have a harmful imprinting effect and that infections induce cross-reacting antibodies against future variants. [ABSTRACT FROM AUTHOR]

At the end of 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China. On 11 March 2020, the World Health Organization declared COVID-19 a pandemic. This virus affects many organs, including the eye, and can manifest through various clinical manifestations. Multiple neuro-ophthalmological manifestations have been reported in association with COVID-19, including, Optic Neuritis, cranial nerve palsies, eye movement abnormalities, and visual field defects. In this article, we report a case of bilateral neuroretinitis in association with (SARS-CoV-2). [ABSTRACT FROM AUTHOR]

Background: The primary causative agent of the COVID-19 pandemic is the newly identified severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). After being identified in the Chinese city of Wuhan, SARS-CoV-2 quickly spread to every country worldwide. The highly mutated SARS-CoV-2 variant B.1.1.529 (Omicron) has the ability to evade the neutralizing antibodies produced by vaccines. This is because the immune response generated by the vaccines is focused on a specific group of receptor-binding domain (RBD) epitopes. The objective of this work is to establish a systematic protocol for isolating, cultivating, and inactivating the SARS-CoV-2 Omicron variant in cell lines without causing any genetic alterations. This is done to develop an inactivated vaccine and make it ready for future pre-clinical trials in animal models. Material and methods: This investigation involves the collection of nasopharyngeal swabs (n = 40) from individuals who are suspected to have COVID-19. The molecular identification of SARS-CoV-2 was achieved by Real-Time Quantitative Reverse Transcription PCR (RT-qPCR). Whole genome sequencing (WGS) has been performed for all collected samples (n = 40). The determination of clade assignment, Pangolin lineages, mutation calling, and phylogenetic placement was performed. We selected only one sample for our candidate vaccine, which has the lowest Ct value and represents the most common strain among all the collected samples. The selected virus sample was cultured on the Vero cell line for 7 continuous passages. The confirmation of SARS CoV-2 propagation was based on the data obtained from both RT-qPCR and the observation of cytopathic effect (CPE). The tissue culture infective dose 50% (TCID50) was determined to examine the growth kinetics for each passage in the tissue culture. The genetic stability of our selected sample for the vaccine candidate was investigated by performing whole genome sequencing (WGS) of the propagated virus. Furthermore, SARS-CoV-2 was fully inactivated by chemical means utilizing beta-propiolactone (βPL), and the overall protein content was assessed. Result: Finally, we will possess a genetically consistent, inactivated form of the SARS CoV-2 Omicron variant, specifically clade 22B and Pango lineage BA.5.2. Conclusion: This inactivated variant will have a known titer and total protein content, making it suitable for further examination in a pre-clinical study aimed at creating an inactivated vaccine for the SARS CoV-2 Omicron variant that was isolated in Egypt. [ABSTRACT FROM AUTHOR]

Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) can infect a broad range of animal species and has been associated with severe disease in some taxa. Few studies have evaluated optimal strategies to mitigate the risk to susceptible zoo animals. This study evaluated the safety and immunogenicity of a protein‐based veterinary SARS‐CoV‐2 vaccine (SpikeVet™) in zoo animals. Two to three doses of SpikeVet™ were administered intramuscularly or subcutaneously 3–4 weeks apart to 354 zoo animals representing 38 species. SpikeVet™ was very well tolerated across all species. Minor adverse effects were observed in 1.69% of animals vaccinated, or 1.04% of vaccine doses administered. Preliminary immunogenicity analyses in representative carnivores (meerkats, lions) and an artiodactylid (domestic goat) showed SpikeVet™‐immunized animals developed serum antibodies able to neutralize a range of SARS‐CoV‐2 variants, including the vaccine‐homologous Wuhan and Mu variants, as well as vaccine‐heterologous Omicron BA.2 and XBB.1 strains. Prior to vaccination, all eight lions were seropositive for Wuhan strain by surrogate viral neutralization testing, suggesting past infection with SARS‐CoV‐2 or cross‐reactive antibodies generated by another closely related coronavirus. These results from a range of zoo species support the ongoing development of SpikeVet™ as a safe and effective veterinary SARS‐CoV‐2 vaccine. [ABSTRACT FROM AUTHOR]

The reoccurrence of successive waves of SARS-CoV-2 variants suggests the exploration of more vaccine alternatives is imperative. Modified vaccinia virus Ankara (MVA) is a virus vector exhibiting excellent safety as well as efficacy for vaccine development. Here, a series of recombinant MVAs (rMVAs) expressing monomerized or trimerized S proteins from different SARS-CoV-2 variants are engineered. Trimerized S expressed from rMVAs is found predominantly as trimers on the surface of infected cells. Remarkably, immunization of mice with rMVAs demonstrates that S expressed in trimer elicits higher levels of binding IgG and IgA, as well as neutralizing antibodies for matched and mismatched S proteins than S in the monomer. In addition, trimerized S expressed by rMVA induces enhanced cytotoxic T-cell responses than S in the monomer. Importantly, the rMVA vaccines expressing trimerized S exhibit superior protection against a lethal SARS-CoV-2 challenge as the immunized animals all survive without displaying any pathological conditions. This study suggests that opting for trimerized S may represent a more effective approach and highlights that the MVA platform serves as an ideal foundation to continuously advance SARS-CoV-2 vaccine development. IMPORTANCE MVA is a promising vaccine vector and has been approved as a vaccine for smallpox and mpox. Our analyses suggested that recombinant MVA expressing S in trimer (rMVA-ST) elicited robust cellular and humoral immunity and was more effective than MVA-S-monomer. Importantly, the rMVA-ST vaccine was able to stimulate decent cross-reactive neutralization against pseudoviruses packaged using S from different sublineages, including Wuhan, Delta, and Omicron. Remarkably, mice immunized with rMVA-ST were completely protected from a lethal challenge of SARS-CoV-2 without displaying any pathological conditions. Our results demonstrated that an MVA vectored vaccine expressing trimerized S is a promising vaccine candidate for SARS-CoV-2 and the strategy might be adapted for future vaccine development for coronaviruses. [ABSTRACT FROM AUTHOR]

Purpose: After the identification of a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at Wuhan, China, a pandemic was widely spread worldwide. In Italy, about 240,000 people were infected because of this virus including 34,721 deaths until the end of June 2020. To control this new pandemic, epidemiologists recommend the enforcement of serious mitigation measures like country lockdown, contact tracing or testing, social distancing and self-isolation. Design/methodology/approach: This paper presents the most popular epidemic model of susceptible (S), exposed (E), infected (I) and recovered (R) collectively called SEIR to understand the virus spreading among the Italian population. Findings: Developed SEIR model explains the infection growth across Italy and presents epidemic rates after and before country lockdown. The results demonstrated that follow-up of strict measures such that country lockdown along with high testing is making Italy practically a pandemic-free country. Originality/value: These models largely help to estimate and understand how an infectious agent spreads in a particular country and how individual factors can affect the dynamics. Further studies like classical SEIR modeling can improve the quality of data and implementation of this modeling could represent a novelty of epidemic models. [ABSTRACT FROM AUTHOR]

Pregnant women represent a high‐risk population for Severe Acute Respiratory Syndrome Coronavirus‐2 (SARS‐CoV‐2) infection. The presence of SARS‐CoV‐2 has been reported in placenta from infected pregnant women, but whether the virus influences placenta immune response remains unclear. We investigated the properties of maternal–fetal interface macrophages (MFMs) in a cohort of unvaccinated women who contracted coronavirus disease 2019 (COVID‐19) during their pregnancy. We reported an infiltration of CD163+ macrophages in placenta from COVID‐19 women 19 whereas lymphoid compartment was not affected. Isolated MFMs exhibited nonpolarized activated signature (NOS2, IDO1, IFNG, TNF, TGFB) mainly in women infected during the second trimester of pregnancy. COVID‐19 during pregnancy primed MFM to produce type I and III interferon response to SARS‐CoV‐2 (Wuhan and δ strains), that were unable to elicit this in MFMs from healthy pregnant women. COVID‐19 also primed SARS‐CoV‐2 internalization by MFM in an angiotensin‐converting enzyme 2‐dependent manner. Activation and recall responses of MFMs were influenced by fetal sex. Collectively, these findings support a role for MFMs in the local immune response to SARS‐CoV‐2 infection, provide a basis for protective placental immunity in COVID‐19, and highlight the interest of vaccination in pregnant women. [ABSTRACT FROM AUTHOR]

With the continuous emergence of coronavirus disease 2019 (COVID-19) waves, the scientific community has developed a vaccine that offers broad-spectrum protection at virus-targeted organs for inhibiting the transmission and protection of disease development. In the present study, a bivalent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine containing receptor-binding domain (RBD) protein of spike from Wuhan-1 and omicron BA.1 loaded in nanoparticles, bivalent RBD NPs, was developed. The immunogenicity and protective efficacy of this vaccine candidate were evaluated using an in vivo model. Results showed that mice that received intranasal cGAMP-adjuvanted bivalent RBD-NPs vaccine elicited robust and durable antibody responses. The stimulated antibody broadly neutralized the ancestral strain and variants of concerns (delta and omicron BA.1) in the upper and lower respiratory tracts. Furthermore, the immunized mice developed T-cell response in their lung tissue. Importantly, intranasal immunization with this vaccine candidate efficiently protected mice from nasal infection caused by both Wuhan-1 and BA.1 viruses. Immunized mice that remained susceptible to nasal infection did not develop any symptoms. This is because activated responses in the nasal cavity significantly suppressed virus production. Another word is this nasal vaccine completely protected the mice from disease development and mortality. Therefore, the bivalent RBD vaccine platform has potential to be developed into an anti-SARS-CoV-2 universal vaccine. [ABSTRACT FROM AUTHOR]

Human infection with the coronavirus disease 2019 (COVID-19) is mediated by the binding of the spike protein of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to the human angiotensin-converting enzyme 2 (ACE2). The frequent mutations in the receptor-binding domain (RBD) of the spike protein induced the emergence of variants with increased contagion and can hinder vaccine efficiency. Hence, it is crucial to better understand the binding mechanisms of variant RBDs to human ACE2 and develop efficient methods to characterize this interaction. In this work, we present an approach that uses machine learning to analyze the molecular dynamics simulations of RBD variant trajectories bound to ACE2. Along with the binding free energy calculation, this method was used to characterize the major differences in ACE2-binding capacity of three SARS-CoV-2 RBD variants—namely the original Wuhan strain, Omicron BA.1, and the more recent Omicron BA.5 sublineages. Our analyses assessed the differences in binding free energy and shed light on how it affects the infectious rates of different variants. Furthermore, this approach successfully characterized key binding interactions and could be deployed as an efficient tool to predict different binding inhibitors to pave the way for new preventive and therapeutic strategies. [ABSTRACT FROM AUTHOR]

Background: In early infected or severe coronavirus disease 2019 (COVID-19) patients, circulating NK cells are consistently reduced, despite being highly activated or exhausted. The aim of this paper was to establish whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein (SP) may directly trigger NK cells and through which receptor(s). Methods: SP-stimulated human NK cells have been evaluated for the expression of activation markers, cytokine release, and cytotoxic activity, as well as for gene expression profiles and NF-κB phosphorylation, and they have been silenced with specific small interfering RNAs. Results: SPs from the Wuhan strain and other variants of concern (VOCs) directly bind and stimulate purified NK cells by increasing activation marker expression, cytokine release, and cytolytic activity, prevalently in the CD56brightNK cell subset. VOC-SPs differ in their ability to activate NK cells, G614, and Delta-Plus strains providing the strongest activity in the majority of donors. While VOC-SPs do not trigger ACE2, which is not expressed on NK cells, or other activating receptors, they directly and variably bind to both Toll-like receptor 2 (TLR2) and TLR4. Moreover, SP-driven NK cell functions are inhibited upon masking such receptors or silencing the relative genes. Lastly, VOC-SPs upregulate CD56dimNK cell functions in COVID-19 recovered, but not in non-infected, individuals. Conclusions: TLR2 and TLR4 are novel activating receptors for SP in NK cells, suggesting a new role of these cells in orchestrating the pathophysiology of SARS-CoV-2 infection. The pathogenic relevance of this finding is highlighted by the fact that free SP providing NK cell activation is frequently detected in a SARS-CoV-2 inflamed environment and in plasma of infected and long-COVID-19 subjects. [ABSTRACT FROM AUTHOR]

Background: Estimation of the SARS-CoV-2 incubation time distribution is hampered by incomplete data about infection. We discuss two biases that may result from incorrect handling of such data. Notified cases may recall recent exposures more precisely (differential recall). This creates bias if the analysis is restricted to observations with well-defined exposures, as longer incubation times are more likely to be excluded. Another bias occurred in the initial estimates based on data concerning travellers from Wuhan. Only individuals who developed symptoms after their departure were included, leading to under-representation of cases with shorter incubation times (left truncation). This issue was not addressed in the analyses performed in the literature. Methods: We performed simulations and provide a literature review to investigate the amount of bias in estimated percentiles of the SARS-CoV-2 incubation time distribution. Results: Depending on the rate of differential recall, restricting the analysis to a subset of narrow exposure windows resulted in underestimation in the median and even more in the 95th percentile. Failing to account for left truncation led to an overestimation of multiple days in both the median and the 95th percentile. Conclusion: We examined two overlooked sources of bias concerning exposure information that the researcher engaged in incubation time estimation needs to be aware of. [ABSTRACT FROM AUTHOR]

Introduction: Convalescent plasma (CP) emerged as potential treatment for COVID-19 early in the pandemic. While efficacy in hospitalised patients has been lacklustre, CP may be beneficial at the first stages of disease. Despite multiple new variants emerging, no trials have involved analyses on variant-specific antibody titres of CP. Methods: We recruited hospitalised COVID-19 patients within 10 days of symptom onset and, employing a double-blinded approach, randomised them to receive 200 ml convalescent plasma with high (HCP) or low (LCP) neutralising antibody (NAb) titre against the ancestral strain (Wuhan-like variant) or placebo in 1:1:1 ratio. Primary endpoints comprised intubation, corticosteroids for symptom aggravation, and safety assessed as serious adverse events. For a pre-planned ad hoc analysis, the patients were regrouped by infused CP’s NAb titers to variants infecting the recipients i.e. by titres of homologous HCP (hHCP) or LCP (hLCP). Results: Of the 57 patients, 18 received HCP, 19 LCP and 20 placebo, all groups smaller than planned. No significant differences were found for primary endpoints. In ad hoc analysis, hHCPrecipients needed significantly less respiratory support, and appeared to be given corticosteroids less frequently (1/14; 7.1%) than those receiving hLCP (9/23; 39.1%) or placebo (8/20; 40%), (p = 0.077). Discussion: Our double-blinded, placebo-controlled CP therapy trial remained underpowered and does not allow any firm conclusions for early-stage hospitalised COVID-19 patients. Interestingly, however, regrouping by homologous – recipients’ variant-specific – CP titres suggested benefits for hHCP. We encourage similar re-analysis of ongoing/previous larger CP studies. [ABSTRACT FROM AUTHOR]

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a positive-sense, single-stranded RNA genome-containing virus which has infected millions of people all over the world. The virus has been mutating rapidly enough, resulting in the emergence of new variants and sub-variants which have reportedly been spread from Wuhan city in China, the epicenter of the virus, to the rest of China and all over the world. The occurrence of mutations in the viral genome, especially in the viral spike protein region, has resulted in the evolution of multiple variants and sub-variants which gives the virus the benefit of host immune evasion and thus renders modern-day vaccines and therapeutics ineffective. Therefore, there is a continuous need to study the genetic characteristics and evolutionary dynamics of the SARS-CoV-2 variants. Hence, in this study, a total of 832 complete genomes of SARS-CoV-2 variants from the cities of Taiyuan and Wuhan in China was genetically characterized and their phylogenetic and evolutionary dynamics studied using phylogenetics, genetic similarity, and phylogenetic network analyses. This study shows that the four most prevalent lineages in Taiyuan and Wuhan are as follows: the Omicron lineages EG.5.1.1, followed by HK.3, FY.3, and XBB.1.16 (Pangolin classification), and clades 23F (EG.5.1), followed by 23H (HK.3), 22F (XBB), and 23D (XBB.1.9) (Nextclade classification), and lineage B followed by the Omicron FY.3, lineage A, and Omicron FL.2.3 (Pangolin classification), and the clades 19A, followed by 22F (XBB), 23F (EG.5.1), and 23H (HK.3) (Nextclade classification), respectively. Furthermore, our genetic similarity analysis show that the SARS-CoV-2 clade 19A-B.4 from Wuhan (name starting with 412981) has the least genetic similarity of about 95.5% in the spike region of the genome as compared to the query sequence of Omicron XBB.2.3.2 from Taiyuan (name starting with 18495234), followed by the Omicron FR.1.4 from Taiyuan (name starting with 18495199) with ~97.2% similarity and Omicron DY.3 (name starting with 17485740) with ~97.9% similarity. The rest of the variants showed ≥98% similarity with the query sequence of Omicron XBB.2.3.2 from Taiyuan (name starting with 18495234). In addition, our recombination analysis results show that the SARS-CoV-2 variants have three statistically significant recombinant events which could have possibly resulted in the emergence of Omicron XBB.1.16 (recombination event 3), FY.3 (recombination event 5), and FL.2.4 (recombination event 7), suggesting some very important information regarding viral evolution. Also, our phylogenetic tree and network analyses show that there are a total of 14 clusters and more than 10,000 mutations which may have probably resulted in the emergence of cluster-I, followed by 47 mutations resulting in the emergence of cluster-II and so on. The clustering of the viral variants of both cities reveals significant information regarding the phylodynamics of the virus among them. The results of our temporal phylogenetic analysis suggest that the variants of Taiyuan have likely emerged as independent variants separate from the variants of Wuhan. This study, to the best of our knowledge, is the first ever genetic comparative study between Taiyuan and Wuhan cities in China. This study will help us better understand the virus and cope with the emergence and spread of new variants at a local as well as an international level, and keep the public health authorities informed for them to make better decisions in designing new viral vaccines and therapeutics. It will also help the outbreak investigators to better examine any future outbreak. [ABSTRACT FROM AUTHOR]

COVID-19 is a systemic disease caused by the etiologic agent SARS-CoV-2, first reported in Hubei Province in Wuhan, China, in late 2019. The SARS-CoV-2 virus has evolved over time with distinct transmissibility subvariants from ancestral lineages. The clinical manifestations of the disease vary according to their severity and can range from asymptomatic to severe. Due to the rapid evolution to a pandemic, epidemiological studies have become essential to understand and effectively combat COVID-19, as the incidence and mortality of this disease vary between territories and populations. This study correlated epidemiological data on the incidence and mortality of COVID-19 with frequencies of important SNPs in GWAS studies associated with the susceptibility and mortality of this disease in different populations. Our results indicated significant correlations for 11 genetic variants (rs117169628, rs2547438, rs2271616, rs12610495, rs12046291, rs35705950, rs2176724, rs10774671, rs1073165, rs4804803 and rs7528026). Of these 11 variants, 7 (rs12046291, rs117169628, rs1073165, rs2547438, rs2271616, rs12610495 and rs35705950) were positively correlated with the incidence rate, these variants were more frequent in EUR populations, suggesting that this population is more susceptible to COVID-19. The rs2176724 variant was inversely related to incidence rates; therefore, the higher the frequency of the allele is, the lower the incidence rate. This variant was more frequent in the AFR population, which suggests a protective factor against SARS-CoV-2 infection in this population. The variants rs10774671, rs4804803, and rs7528026 showed a significant relationship with mortality rates. SNPs rs10774671 and rs4804803 were inversely related to mortality rates and are more frequently present in the AFR population. The rs7528026 variant, which is more frequent in the AMR population, was positively related to mortality rates. The study has the potential to identify and correlate the genetic profile with epidemiological data, identify populations that are more susceptible to severe forms of COVID-19, and relate them to incidence and mortality. [ABSTRACT FROM AUTHOR]

The Omicron BA.5 variant of SARS-CoV-2 is known for its high transmissibility and its capacity to evade immunity provided by vaccine protection against the (original) Wuhan strain. In our prior research, we successfully produced the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein in an E. coli expression system. Extensive biophysical characterization indicated that, even without glycosylation, the RBD maintained native-like conformational and biophysical properties. The current study explores the immunogenicity and neutralization capacity of the E. coli-expressed Omicron BA.5 RBD using a mouse model. Administration of three doses of the RBD without any adjuvant elicited high titer antisera of up to 7.3 × 105 and up to 1.6 × 106 after a booster shot. Immunization with RBD notably enhanced the population of CD44+CD62L+ T cells, indicating the generation of T cell memory. The in vitro assays demonstrated the antisera's protective efficacy through significant inhibition of the interaction between SARS-CoV-2 and its human receptor, ACE2, and through potent neutralization of a pseudovirus. These findings underscore the potential of our E. coli-expressed RBD as a viable vaccine candidate against the Omicron variant of SARS-CoV-2. [ABSTRACT FROM AUTHOR]

Since the first discovery of the first case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019 in Wuhan, China, the virus quickly spread throughout the world and became a pandemic. The virus has continued to pose challenges, with new variants emerging and evolving, necessitating ongoing adaptation and response from governments, healthcare systems, and communities worldwide. Various drug regimens were introduced with immediate implementation and there is a need for the study of Review of Quality Control aspects of drugs employed in COVID-19 treatment is critical for ensuring their safety, efficacy, and reliability. With the proliferation of pharmaceutical interventions aimed at combating the pandemic, such as antiviral, immunomodulators, and repurposed medications, a thorough review is essential. Harnessing immune modulators, monoclonal antibodies, and antiviral agents like the ritonavir (RTN)/nirmatrelvir (NTV) combination, molnupiravir (MLP), and favipiravir (FVP) presents a multifaceted approach to combating COVID-19. These pharmaceutical interventions offer diverse mechanisms of action aimed at suppressing viral replication, mitigating immune responses, and enhancing the body's ability to combat the virus Improving analytical methods to achieve precise and sensitive quantification of these drugs is paramount for advancing quality control measures. The study delved into a variety of analytical techniques for assessing the concentrations of antiviral drugs utilized in COVID-19 treatment. The techniques covered by these methods include Ultra High-Performance Liquid Chromatography (UHPLC-MS/MS) or Ultraviolet detectors (HPLC-UV), High-Performance Thin Layer Chromatography (HPTLC), Reversed Phase-High Performance Liquid Chromatography (RP-HPLC), High-Performance Liquid Chromatography Tandem Mass Spectrometry (HPLCMS/MS) or Ultraviolet detectors (TLC-UV), and Micellar Liquid Chromatography (MLC). With regard to sensitivity, selectivity, and efficiency in measuring drug concentrations, each of these methods has special benefits. The TLC and HPTLC techniques offer reasonably easy sample preparation at a reasonable price, whereas the RP-HPLC, HPLC-MS/MS, UHPLC-MS/MS, and UPLC-UV techniques offer more sensitivity and precision, especially in complex sample types. Furthermore, precise identification and quantification of pharmacological molecules at low concentrations are made possible by the application of UV and mass spectrometric detection. The purpose of the study is to assess the effectiveness of the RP-HPLC method and validate the chosen medications. The results of the study will be further examined, and the development of a novel RP-HPLC method will be optimized. These analytical techniques can be refined to satisfy legal specifications and guarantee accurate anti-COVID-19 medication quantification. Here, we focus on clarifying modern, straightforward, fast, accurate, and eco-friendly analytical techniques that demonstrate great sensitivity, selectivity, and accuracy for the analysis of anti-COVID-19 medications. [ABSTRACT FROM AUTHOR]

SARS-CoV-2 swiftly spread in Wuhan, China, leading to a pandemic crisis worldwide. Genome sequence analysis of this virus revealed a close analogy with its closely related strains, SARS-COV and MERS-COV. In the case of SARS-CoV-2, Nonstructural protein 13 (NSP13), also known as helicase, has been identified as a target for reducing the severity of infection due to its high sequence conservation and essential role in viral replication. NSP13 helicase structure in SARS-CoV-2 differs only by one amino acid from the SARS-CoV helicase structure. Targeting NSP13 with natural compounds holds significant potential for developing safe and effective antiviral therapies utilizing advanced computational approaches. The properties of 8 different natural compounds, i.e. Imidazole, Pyrrole, Tropolone, Benzotriazole, Imidazodiazepine, Phenothiazine, Acridone and Bananin were screened by applying Lipinski's rule of five, ADME (absorption, distribution, metabolism, and excretion) properties, and Radar plots to discover their drug efficacy at a target site, safety, and absorption. Docking studies confirmed Bananin with a binding affinity of -7 kcal/mol as a potential inhibitor of NSP13 of SARS-CoV-2 with better pharmacokinetics, drug likeliness, and oral bioavailability. Based on the in silico study, it is suggested that Bananin shows promising effects against NSP13 protein, forming a maximum number of hydrogen bonds exhibiting higher binding affinity. This stronger affinity indicates a stronger interaction between the compound and its target, potentially leading to enhanced biological activity and therapeutic efficacy. This novel study has unlocked the door for a prospective SARS-CoV-2 inhibition strategy and developing antiviral interventions targeting NSP13 based on molecular docking. [ABSTRACT FROM AUTHOR]

Coronavirus disease 2019 (COVID‐19) caused by the severe acute respiratory syndrome coronavirus 2n first appeared in Wuhan, China in 2019. Soon after, it was declared a pandemic by the World Health Organization. The health crisis imposed by a new virus and its rapid spread worldwide prompted the fast development of vaccines. For the first time in human history, two vaccines based on recombinant genetic material technology were approved for human use. These mRNA vaccines were applied in massive immunization programs around the world, followed by other vaccines based on more traditional approaches. Even though all vaccines were tested in clinical trials prior to their general administration, serious adverse events, usually of very low incidence, were mostly identified after application of millions of doses. Establishing a direct correlation (the cause‐effect paradigm) between vaccination and the appearance of adverse effects has proven challenging. This review focuses on the main adverse effects observed after vaccination, including anaphylaxis, myocarditis, vaccine‐induced thrombotic thrombocytopenia, Guillain–Barré syndrome, and transverse myelitis reported in the context of COVID‐19 vaccination. We highlight the symptoms, laboratory tests required for an adequate diagnosis, and briefly outline the recommended treatments for these adverse effects. The aim of this work is to increase awareness among healthcare personnel about the serious adverse events that may arise post‐vaccination. Regardless of the ongoing discussion about the safety of COVID‐19 vaccination, these adverse effects must be identified promptly and treated effectively to reduce the risk of complications. [ABSTRACT FROM AUTHOR]

Background: Since severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) was first reported in Wuhan, China, in December 2019, it has spread rapidly, and many coronavirus disease (COVID‐19) cases have occurred in Gwangju, South Korea. Viral mutations following the COVID‐19 epidemic have increased interest in the characteristics of epidemics in this region, and pathogen genetic analysis is required for infection control and prevention. Methods: In this study, SARS‐CoV‐2 whole‐genome analysis was performed on samples from patients with COVID‐19 in Gwangju from 2020 to 2022 to identify the trends in COVID‐19 prevalence and to analyze the phylogenetic relationships of dominant variants. B.41 and B.1.497 prevailed in 2020, the early stage of the COVID‐19 outbreak; then, B.1.619.1 mainly occurred until June 2021. B.1.617.2, classified as sublineages AY.69 and AY.122, occurred continuously from July to December 2021. Since strict measures to strengthen national quarantine management had been implemented in South Korea until this time, the analysis of mutations was also able to infer the epidemiological relationship between infection transmission routes. Since the first identification of the Omicron variant in late December 2021, the spread of infection has been very rapid, and weekly whole‐genome analysis of specimens has enabled us to monitor new Omicron sublineages occurring in Gwangju. Conclusions: Our study suggests that conducting regional surveillance in addition to nation‐level genomic surveillance will enable more rapid and detailed variant surveillance, which will be helpful in the overall prevention and management of infectious diseases. [ABSTRACT FROM AUTHOR]

Immunocompromised individuals are at significantly elevated risk for severe courses of coronavirus disease 2019 (COVID‐19). In addition to vaccination, severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) neutralizing antibodies (nAbs) have been applied throughout the pandemic, with time of treatment onset and potency against the currently prevailing virus variant identified as relevant factors for medical benefit. Using data from the European Society for Immunodeficiencies (ESID) registry, the present study evaluated COVID‐19 cases in three groups of patients with inborn errors of immunity (IEI; 981 agammaglobulinemia patients on immunoglobulin replacement therapy (IGRT); 8960 non‐agammaglobulinemia patients on IGRT; 14 428 patients without IGRT), and the neutralizing capacity of 1100 immunoglobulin lots against SARS‐CoV‐2 ("Wuhan" and Omicron strains), throughout 3 years. From the first (2020/2021) to the second (2021/2022) cold season, i.e., during the virus drift to the more contagious Omicron variants, an increase in case numbers was recorded that was comparable (~2‐ to 3‐fold) for all three study groups. During the same period, immunoglobulin lots showed a profound nAb increase against the archetypal SARS‐CoV‐2 strain, yet only low levels of Omicron nAbs. Notably, shortly before the third (2022/2023) cold season, Omicron‐neutralizing capacity of released immunoglobulin lots had plateaued at high levels. From the second to the third cold season, COVID‐19 cases dropped markedly. While a ~6‐fold case reduction was recorded for the groups of non‐agammaglobulinemia patients on IGRT and IEI patients not receiving IGRT, the decline was ~30‐fold for the group of agammaglobulinemia patients on IGRT. These findings suggest a substantial COVID‐19‐protective effect of IGRT, at least for distinct groups of antibody‐deficient patients. [ABSTRACT FROM AUTHOR]

We determined neutralizing antibody levels to the ancestral Wuhan SARS-CoV-2 strain and three Omicron variants, namely BA.5, XBB.1.5, and EG.5, in a heavily vaccinated cohort of 178 adults 15–19 months after the initial vaccine series and prospectively after 4 months. Although all participants had detectable neutralizing antibodies to Wuhan, the proportion with detectable neutralizing antibodies to the Omicron variants was decreased, and the levels were lower. Individuals with hybrid immunity at the baseline visit and those receiving the Original/Omicron bivalent vaccine between the two sampling times demonstrated increased neutralizing antibodies to all strains. Both a higher baseline neutralizing antibody titer to Omicron BA.5 and hybrid immunity were associated with protection against a breakthrough SARS-CoV-2 infection during a 4-month period of follow up during the Omicron BA.5 wave. Neither were associated with protection from a breakthrough infection at 10 months follow up. Receipt of an Original/Omicron BA.4/5 vaccine was associated with protection from a breakthrough infection at both 4 and 10 months follow up. This work demonstrates neutralizing antibody escape with the emerging Omicron variants and supports the use of additional vaccine doses with components that match circulating SARS-CoV-2 variants. A threshold value for neutralizing antibodies for protection against reinfection cannot be determined. [ABSTRACT FROM AUTHOR]

Background. In late 2019, several medical institutions in Wuhan, Hubei Province, China, reported cases of unexplained pneumonia. A novel coronavirus was isolated from human airway epithelial cells causing coronavirus disease-2019 (COVID-19). In recent years, many nonpharmaceutical interventions (NPIs) have been implemented to stop COVID-19 epidemic. This study aimed to explore the effect of NPIs on the circulation of avian influenza virus (AIV) in Wuhan. Materials and Methods. External environmental samples were collected and subjected to viral RNA extraction. Real-time quantitative polymerase chain reaction was used to detect the H5, H7, and H9 subtypes of AIV. Statistical analyses were performed using the chi-square test and binary logistic regression in SPSS 20.0 software. Results. A total of 2,451 external environmental samples were collected from seven districts from 2018 to 2022 in Wuhan, comprising 1,041 samples collected before COVID-19 and 1,410 samples after COVID-19. After COVID-19, the positive rate of AIV decreased significantly with the implementation of NPIs. The dominant subtype was the H9 subtype, followed by the H5 subtype. The positive rates of AIV in live poultry markets and poultry free-range sites were reduced significantly through the implementation of NPIs. Among the different sample types, higher positive rates of AIV were found in chopping boards, sewage, and cages. The positive rate of AIV was higher in trafficked source samples than that in autotrophic source samples. Conclusions. This study identified the characteristics of AIV in terms of different districts, surveillance sites, sample types, and bird sources in Wuhan. This study conducted a multifactorial analysis of the factors affecting AIV infection and provided a theoretical basis and guidance for the future prevention and control of AIV in Wuhan. [ABSTRACT FROM AUTHOR]

The complexity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and its variants in lung cells can truly be characterized only at the tissue and protein levels among unique cell subtypes. However, in vivo data are limited due to lack of accessible human tissues. Using a transgenic mouse model of SARS-CoV-2 infection and flow cytometry, we provide in vivo novel insight at the protein level that the differential impact of SARS-CoV-2 (Wuhan strain) and its B.1.617.2 (Delta) and BA.1 (Omicron) variants on lung may be attributed to differential patterns of viral protein levels among ciliated airway cells, alveolar types 1 and 2 cells, immune cells, and endothelial lung cells. [ABSTRACT FROM AUTHOR]

Novel respiratory viruses can cause a pandemic and then evolve to coexist with humans. The Omicron strain of severe acute respiratory syndrome coronavirus 2 has spread worldwide since its emergence in late 2021, and its sub-lineages are now established in human society. Compared to previous strains, Omicron is markedly less invasive in the lungs and causes less severe disease. One reason for this is that humans are acquiring immunity through previous infection and vaccination, but the nature of the virus itself is also changing. Using our newly established low-volume inoculation system, which reflects natural human infection, we show that the Omicron strain spreads less efficiently into the lungs of hamsters compared with an earlier Wuhan strain. Furthermore, by characterizing chimeric viruses with the Omicron gene in the Wuhan strain genetic background and vice versa, we found that viral genes downstream of ORF3a, but not the S gene, were responsible for the limited spread of the Omicron strain in the lower airways of the virus-infected hamsters. Moreover, molecular evolutionary analysis of SARS-CoV-2 revealed a positive selection of genes downstream of ORF3a (M and E genes). Our findings provide insight into the adaptive evolution of the virus in humans during the pandemic convergence phase. [ABSTRACT FROM AUTHOR]

The emergence of the novel coronavirus in Wuhan, China since 2019, has put the world in an exotic state of emergency and affected millions of lives. It is five times more deadly than Influenza and causes significant morbidity and mortality. COVID-19 mainly affects the pulmonary system leading to respiratory disorders. However, earlier studies indicated that COVID-19 infection may cause cardiovascular diseases, which can be detected using an electrocardiogram (ECG). This work introduces an advanced deep learning architecture for the automatic detection of COVID-19 and heart diseases from ECG images. In particular, a hybrid combination of the EfficientNet-B0 CNN model and Vision Transformer is adopted in the proposed architecture. To our knowledge, this study is the first research endeavor to investigate the potential of the vision transformer model to identify COVID-19 in ECG data. We carry out two classification schemes, a binary classification to identify COVID-19 cases, and a multi-class classification, to differentiate COVID-19 cases from normal cases and other cardiovascular diseases. The proposed method surpasses existing state-of-the-art approaches, demonstrating an accuracy of 100% and 95.10% for binary and multiclass levels, respectively. These results prove that artificial intelligence can potentially be used to detect cardiovascular anomalies caused by COVID-19, which may help clinicians overcome the limitations of traditional diagnosis. [ABSTRACT FROM AUTHOR]

The devastating pandemic of SARS-CoV-2 (COVID-19) began in Wuhan, China, and spread rapidly through most parts of the world in the second half of 2020. The air droplet spread of SARS-CoV-2 is of great global health concern as it is potentially fatal. Various drugs and treatment modalities have been tried to date, but none have been found to be definitive. Tranexamic acid (TXA) is commonly used in pigmentary disorders in dermatology due to its ability to reduce melanocyte tyrosinase activity. It also possesses anti-fibrinolytic and anti-inflammatory properties, which have been observed to suppress the cytokine storm and modulate coagulopathy in patients suffering from COVID-19. TXA, when administered early, has been effective in decreasing the severity of symptoms in COVID-19 patients, but on the contrary, it has also been associated with life-threatening thrombosis when given as a single drug. [ABSTRACT FROM AUTHOR]

Background: In December 2019, a cluster of patients with pneumonia of undetermined etiology was recognized in Wuhan, Hubei, China. Subsequently, a novel coronavirus (Severe Acute Respiratory Distress Syndrome- related Coronavirus) (SARS-CoV-2) was identified from lower respiratory tract samples obtained from affected patients. The clinical manifestation of Coronavirus disease 2019 (COVID 19) is broad and ranges from asymptomatic and mild upper respiratory tract symptoms to severe illnesses with multi-organ failure and death. Furthermore, it is challenging to predict the clinical course or determine patients at risk of deterioration. Aim of the work: The aim of our study is to assess prevalence of gastrointestinal tract (GIT) symptoms in COVID 19 infected patients and to assess significance of rectal PCR in detecting COVID 19 patients with gastrointestinal symptoms. Patients and methods: This study was conducted on 100 adult COVID 19 patients recently diagnosed by polymerase chain reaction (PCR). All patients were submitted to clinical examination, laboratory testing for Erythrocyte Sedimentation Rate (ESR), C-Reactive Protein,(CRP), Complete Blood Count (CBC), and D-dimer. Radiological investigations in the form of Computed Tomography Chest were reported by radiologist for all patients (High resolution computed tomography). Nasopharyngeal, oropharyngeal and rectal swabs were collected for COVID-19 (PCR) test. All patients received COVID-19 treatment according to protocols of World Health Organization (WHO) and Ministry of Health and Population, Egypt. Results: We found that GI symptoms are prevalent among COVID-19 Egyptian patients (64%). The most common GIT symptoms were Nausea, vomiting and diarrhea. We observed that 25 patients (25%) had positive viral RiboNucleic Acid (RNA) in rectal swab. Nausea was manifested in 38 patients (38%), Vomiting was manifested in 24 patients (24%), diarrhea was manifested in 21 patients (21%), pain was manifested in 22 patients (22%), hematemesis was manifested in 3 patients (3%) and melena was manifested in 2 patients (2%). Conclusion: The results of current study demonstrated that GIT symptoms are prevalent among COVID-19 Egyptian patients (64%) with Nausea, vomiting and diarrhea to be most common symptoms. Rectal PCR was found in 25 patients, all of them had GIT symptoms but it was statistically non-significant result when compared to the overall number of COVID-19 infected patients. Severe COVID-19 was more frequent in older age. [ABSTRACT FROM AUTHOR]

Coronavirus disease of 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is an ongoing outbreak, disrupting human life worldwide. Vaccine development was prioritized to obtain a biological substance for combating the viral pathogen and lessening disease severity. In vaccine production, biological origin and relevant materials must be carefully examined for potential contaminants in conformity with good manufacturing practice. Due to fast mutation, several SARS-CoV-2 variants and sublineages have been identified. Currently, most of COVID-19 vaccines are developed based on the protein sequence of the Wuhan wild type strain. New vaccines specific for emerging SARS-CoV-2 strains are continuously needed to tackle the incessant evolution of the virus. Therefore, in vaccine development and production, a reliable method to identify the nature of subunit vaccines is required to avoid cross-contamination. In this study, liquid chromatography-mass spectrometry using quadrupole-time of flight along with tryptic digestion was developed for distinguishing protein materials derived from different SARS-CoV-2 strains. After analyzing the recombinantly produced receptor-binding domain (RBD) of the SARS-CoV-2 spike protein, nine characteristic peptides were identified with acceptable limits of detection. They can be used together to distinguish 14 SARS-CoV-2 strains, except Kappa and Epsilon. Plant-produced RBD-Fc protein derived from Omicron strains can be easily distinguished from the others with 4–5 unique peptides. Eventually, a peptide key was developed based on the nine peptides, offering a prompt and precise flowchart to facilitate SARS-CoV-2 strain identification in COVID-19 vaccine manufacturing. [ABSTRACT FROM AUTHOR]

After the outbreak of COVID-19 pandemic, devising an effective reverse logistics supply chain to clean up disaster medical waste is conducive to controlling and containing novel coronavirus transmission. Thus, the focus of this paper concentrates on multi-period multi-type disaster medical waste location-transportation integrated optimization problem with the concern of sustainability, which is formulated as a tri-objective mixed-integer programming model with the goals of maximizing total economic benefits, minimizing total carbon emissions and total potential social risks. Then, a real-world case from Wuhan using CPLEX solver is used to validate the developed model. Results indicate that constructing DMWTTSs with flexible capacity in different periods is encouraged to handle the sharply increasing disaster medical waste. The multi-period decision model outperforms the single-period one in disaster medical waste supply chains because the former has the capability of handling the uncertainties in the future periods. Increasingly, since the increase of budget doesn't always work well and social resources are limited, the estimation of minimum budget to obtain optimum overall performance is of great importance. [ABSTRACT FROM AUTHOR]

• Waning immunity and new variants necessitate next generation SARS-CoV-2 vaccines. • The M2SR platform has a clear safety and immunogenic profile in clinical testing. • Intranasal dual influenza/COVID-19 vaccine induces systemic and mucosal antibodies. • SARS-CoV-2 M2SR protects hamsters from SARS-CoV-2 infection and lung pathology. • Dual vaccine maintains immunogenicity to matched and drifted influenza strains. The COVID-19 pandemic has highlighted the need for mucosal vaccines as breakthrough infections, short-lived immune responses and emergence of new variants have challenged the efficacy provided by the first generation of vaccines against SARS-CoV-2 viruses. M2SR SARS-CoV-2, an M2-deleted single-replication influenza virus vector modified to encode the SARS-CoV-2 receptor binding domain, was evaluated following intranasal delivery in a hamster challenge model for protection against Wuhan SARS-CoV-2. An adjuvanted inactivated SARS-CoV-2 whole virus vaccine administered intramuscularly was also evaluated. The intranasal M2SR SARS-CoV-2 was more effective than the intramuscular adjuvanted inactivated whole virus vaccine in providing protection against SARS-CoV-2 challenge. M2SR SARS-CoV-2 elicited neutralizing serum antibodies against Wuhan and Omicron SARS-CoV-2 viruses in addition to cross-reactive mucosal antibodies. Furthermore, M2SR SARS-CoV-2 generated serum HAI and mucosal antibody responses against influenza similar to an H3N2 M2SR influenza vaccine. The intranasal dual influenza/COVID M2SR SARS-CoV-2 vaccine has the potential to provide protection against both influenza and COVID. [ABSTRACT FROM AUTHOR]

Simple Summary: Coronaviruses are serious pathogens for both humans and animals. The name corona was designated because of the crown-like spikes on their surface. Currently, seven coronaviruses have been identified, such as 229E, NL63, OC43, HKU1, MERS-CoV, SARS-CoV, and SARS-CoV-2. Sometimes, animal coronaviruses infect humans and evolve due to genetic mutations, interspecies transmission, host adaptations, and favorable conditions. The main objective of this study was to analyze the genetic diversity and predict the emergence of new variants with novel properties. It has been reported that the spike protein gene plays an important role in host cell attachment and entry into host cells. The S gene has the highest mutation/deletion and is the most utilized target for vaccine/antiviral development. In this work, we discussed the genetic diversity, phylogenetic relationship, and recombination patterns of selected HCoVs with an emphasis on the newly emerged SARS-CoV-2 and MERS-CoV. The findings of this study showed that MERS-CoV and SARS-CoV-2 have significant sequence identities with the selected HCoVs. The phylogenetic and recombination results concluded that new variants may emerge in the future with novel properties that infect both humans and animals. This information will be helpful for global society to design and develop an effective vaccine and disease management strategy. Human coronaviruses (HCoVs) are seriously associated with respiratory diseases in humans and animals. The first human pathogenic SARS-CoV emerged in 2002–2003. The second was MERS-CoV, reported from Jeddah, the Kingdom of Saudi Arabia, in 2012, and the third one was SARS-CoV-2, identified from Wuhan City, China, in late December 2019. The HCoV-Spike (S) gene has the highest mutation/insertion/deletion rate and has been the most utilized target for vaccine/antiviral development. In this manuscript, we discuss the genetic diversity, phylogenetic relationships, and recombination patterns of selected HCoVs with emphasis on the S protein gene of MERS-CoV and SARS-CoV-2 to elucidate the possible emergence of new variants/strains of coronavirus in the near future. The findings showed that MERS-CoV and SARS-CoV-2 have significant sequence identity with the selected HCoVs. The phylogenetic tree analysis formed a separate cluster for each HCoV. The recombination pattern analysis showed that the HCoV-NL63-Japan was a probable recombinant. The HCoV-NL63-USA was identified as a major parent while the HCoV-NL63-Netherland was identified as a minor parent. The recombination breakpoints start in the viral genome at the 142 nucleotide position and end at the 1082 nucleotide position with a 99% CI and Bonferroni-corrected p-value of 0.05. The findings of this study provide insightful information about HCoV-S gene diversity, recombination, and evolutionary patterns. Based on these data, it can be concluded that the possible emergence of new strains/variants of HCoV is imminent. [ABSTRACT FROM AUTHOR]

People living with HIV (PLWH) could be at risk of blunted immune responses to COVID-19 vaccination. We investigated factors associated with neutralizing antibody (NAb) responses against SARS-CoV-2 and variants of concern (VOCs), following two-dose and third booster monovalent COVID-19 mRNA vaccination in Japanese PLWH. NAb titers were assessed in polyclonal IgG fractions by lentiviral-based pseudovirus assays. Overall, NAb titers against Wuhan, following two-dose vaccination, were assessed in 82 PLWH on treatment, whereby 17/82 (20.73%) were classified as low-NAb participants. Within the low-NAb participants, the third booster vaccination enhanced NAb titers against Wuhan and VOCs, albeit to a significantly lower magnitude than the rest. In the multivariate analysis, NAb titers against Wuhan after two-dose vaccination correlated with age and days since vaccination, but not with CD4+ count, CD4+/CD8+ ratio, and plasma high-sensitivity C-Reactive protein (hsCRP). Interestingly, an extended analysis within age subgroups revealed NAb titers to correlate positively with the CD4+ count and negatively with plasma hsCRP in younger, but not older, participants. In conclusion, a third booster vaccination substantially enhances NAb titers, but the benefit may be suboptimal in subpopulations of PLWH exhibiting low titers at baseline. Considering clinical and immune parameters could provide a nuanced understanding of factors associated with vaccine responses in PLWH. [ABSTRACT FROM AUTHOR]

Oropharyngeal microbiomes play a significant role in the susceptibility and severity of COVID-19, yet the role of these microbiomes play for the development of COVID-19 Omicron variant have not been reported. A total of 791 pharyngeal swab samples were prospectively included in this study, including 297 confirmed cases of Omicron variant (CCO), 222 confirmed case of Omicron who recovered (CCOR), 73 confirmed cases of original strain (CCOS) and 199 healthy controls (HC). All samples completed MiSeq sequencing. The results showed that compared with HC, conditional pathogens increased in CCO, while acid-producing bacteria decreased. Based on six optimal oropharyngeal operational taxonomy units (OTUs), we constructed a marker microbial classifier to distinguish between patients with Omicron variant and healthy people, and achieved high diagnostic efficiency in both the discovery queue and the verification queue. At same time, we introduced a group of cross-age infection verification cohort and Omicron variant subtype XBB.1.5 branch, which can be accurately distinguished by this diagnostic model. We also analyzed the characteristics of oropharyngeal microbiomes in two subgroups of Omicron disease group—severity of infection and vaccination times, and found that the change of oropharyngeal microbiomes may affect the severity of the disease and the efficacy of the vaccine. In addition, we found that some genera with significant differences gradually increased or decreased with the recovery of Omicron variant infection. The results of Spearman analysis showed that 27 oropharyngeal OTUs were closely related to 6 clinical indexes in CCO and HC. Finally, we found that the Omicron variant had different characterization of oropharyngeal microbiomes from the original strain. Our research characterizes oropharyngeal microbiomes of Omicron variant cases and rehabilitation cases, successfully constructed and verified the non-invasive diagnostic model of Omicron variant, described the correlation between microbial OTUs and clinical indexes. It was found that the infection of Omicron variant and the infection of original strain have different characteristics of oropharyngeal microbiomes. Author summary: COVID-19, caused by the SARS-CoV-2 virus, was first discovered in Wuhan, Hubei Province, China in December 2019, causing a huge impact around the world. In the past three years, novel coronavirus has successively appeared many varieties through gene mutation, among which Omicron strain is the most popular variety. Studies have shown that the imbalance of microflora is closely related to the progress of novel coronavirus infection and the severity of clinical symptoms. In the previous study, we build database of oral-intestinal microbial metagenomics, immunome and metabolome of novel coronavirus Original Strain with mild, medium and severe clinical symptoms and healthy subjects, reveal the role and mechanism of the oral and intestinal microbiome in Original Strain infection and exacerbation, and build the model of susceptibility, severe warning and prognosis of Original Strain pneumonia which based on the microbiome-immunity-metabolism. Our research characterizes oropharyngeal microbiomes of Omicron variant cases and rehabilitation cases, successfully constructed and verified the non-invasive diagnostic model of Omicron variant. We also analyzed the characteristics of oropharyngeal microbiomes in two subgroups of Omicron disease group—severity of infection and vaccination times, and found that the change of oropharyngeal microbiomes may affect the severity of the disease and the efficacy of the vaccine. And we described the correlation between microbial OTUs and clinical indexes. At last, it was found that the infection of Omicron variant and the infection of original strain have different characteristics of oropharyngeal microbiomes. [ABSTRACT FROM AUTHOR]

The immune mechanisms of long coronavirus disease 2019 (COVID) are not yet fully understood. We aimed to investigate the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)–specific memory immune responses in discharged COVID-19 patients with and without long COVID symptoms. In this cross-sectional study, we included 1041 hospitalized COVID-19 patients with the original virus strain in Wuhan (China) 12 months after initial infection. We simultaneously conducted a questionnaire survey and collected peripheral blood samples from the participants. Based on the presence or absence of long COVID symptoms during the follow-up period, we divided the patients into 2 groups: a long COVID group comprising 480 individuals and a convalescent group comprising 561 individuals. Both groups underwent virus-specific immunological analyses, including enzyme-linked immunosorbent assay, interferon-γ-enzyme-linked immune absorbent spot, and intracellular cytokine staining. At 12 months after infection, 98.5% (1026/1041) of the patients were found to be seropositive and 93.3% (70/75) had detectable SARS-CoV-2-specific memory T cells. The long COVID group had significantly higher levels of receptor binding domain (RBD)–immunoglobulin G (IgG) levels, presented as OD450 values, than the convalescent controls (0.40 ± 0.22 vs 0.37 ± 0.20; P =.022). The magnitude of SARS-CoV-2-specific T-cell responses did not differ significantly between groups, nor did the secretion function of the memory T cells. We did not observe a significant correlation between SARS-CoV-2-IgG and magnitude of memory T cells. This study revealed that long COVID patients had significantly higher levels of RBD-IgG antibodies when compared with convalescent controls. Nevertheless, we did not observe coordinated SARS-CoV-2-specific cellular immunity. As there may be multiple potential causes of long COVID, it is imperative to avoid adopting a "one-size-fits-all" approach to future treatment modalities. [ABSTRACT FROM AUTHOR]

Background: The infection that caused the pneumonia, the virus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the source of coronavirus disease 2019 (COVID-19) is the source of the global pandemic. The pneumonia cases began in Wuhan, China in December 2019 and had no apparent reason. Essential inflammatory mediators Chemokines are necessary for an immune response to eliminate pathogens. However, the fundamental cause of hyper inflammation is their excessive release. Chemokines may be directly responsible for the acute respiratory illness syndrome in the current COVID-19 outbreak. Objective: The current study aimed to estimate hematological changes with immunogenic markers CD177, GNLY, and CXCR4 gene expression in COVID-19 patients, and compare these parameters among patients and healthy individuals. Materials and Methods: the study was conducted at Al-Yarmouk Teaching Hospital and Medical Teaching Laboratories. Finally, to detect the immune markers level in samples of patients, by RT-PCR. Results: the results revealed the gene expression results in patients with COVID-19 means Ct difference of CD177 (24.70) fold more than (10.5) elevated when compared with the mean of Ct control healthy group is (28.21) fold of gene expression is 1.00 of CD177 when our study showed increased gene expression the mean of GNLY Ct receptor was reached to (28.70 ng/L) with fold more than 15.0 in COVID-19 patients, while mean Ct in healthy control was (32.61 ng/L) with fold 1.00, the current study found mean CT of CXCR4 gene expression (31.2) with fold (1.1) compared with healthy control CT(31.3) fold of gene expression was (1.0). Conclusion: It was concluded that COVID-19 caused significant changes in many immunological parameters and found the titer of immune markers was higher in infection compared with control. [ABSTRACT FROM AUTHOR]

The global spread of the SARS-CoV-2 pandemic, originating in Wuhan, China, has had profound consequences on both health and the economy. Traditional alignment-based phylogenetic tree methods for tracking epidemic dynamics demand substantial computational power due to the growing number of sequenced strains. Consequently, there is a pressing need for an alignment-free approach to characterize these strains and monitor the dynamics of various variants. In this work, we introduce a swift and straightforward tool named GenoSig, implemented in C++. The tool exploits the Di and Tri nucleotide frequency signatures to delineate the taxonomic lineages of SARS-CoV-2 by employing diverse machine learning (ML) and deep learning (DL) models. Our approach achieved a tenfold cross-validation accuracy of 87.88% (± 0.013) for DL and 86.37% (± 0.0009) for Random Forest (RF) model, surpassing the performance of other ML models. Validation using an additional unexposed dataset yielded comparable results. Despite variations in architectures between DL and RF, it was observed that later clades, specifically GRA, GRY, and GK, exhibited superior performance compared to earlier clades G and GH. As for the continental origin of the virus, both DL and RF models exhibited lower performance than in predicting clades. However, both models demonstrated relatively higher accuracy for Europe, North America, and South America compared to other continents, with DL outperforming RF. Both models consistently demonstrated a preference for cytosine and guanine over adenine and thymine in both clade and continental analyses, in both Di and Tri nucleotide frequencies signatures. Our findings suggest that GenoSig provides a straightforward approach to address taxonomic, epidemiological, and biological inquiries, utilizing a reductive method applicable not only to SARS-CoV-2 but also to similar research questions in an alignment-free context. [ABSTRACT FROM AUTHOR]

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection is the cause of coronavirus disease 2019 (COVID-19); a severe respiratory distress that has emerged from the city of Wuhan, Hubei province, China during December 2019. COVID-19 is currently the major global health problem and the disease has now spread to most countries in the world. COVID-19 has profoundly impacted human health and activities worldwide. Genetic mutation is one of the essential characteristics of viruses. They do so to adapt to their host or to move to another one. Viral genetic mutations have a high potentiality to impact human health as these mutations grant viruses unique unpredicted characteristics. The difficulty in predicting viral genetic mutations is a significant obstacle in the field. Evidence indicates that SARS-CoV-2 has a variety of genetic mutations and genomic diversity with obvious clinical consequences and implications. In this review, we comprehensively summarized and discussed the currently available knowledge regarding SARS-CoV-2 outbreaks with a fundamental focus on the role of the viral proteins and their mutations in viral infection and COVID-19 progression. We also summarized the clinical implications of SARS-CoV-2 variants and how they affect the disease severity and hinder vaccine development. Finally, we provided a massive phylogenetic analysis of the spike gene of 214 SARS-CoV-2 isolates from different geographical regions all over the world and their associated clinical implications. [ABSTRACT FROM AUTHOR]

Understanding adaptive immunity against SARS-CoV-2 is a major requisite for the development of effective vaccines and treatments for COVID-19. CD4+ T cells play an integral role in this process primarily by generating antiviral cytokines and providing help to antibody-producing B cells. To empower detailed studies of SARS-CoV-2-specific CD4+ T cell responses in mouse models, we comprehensively mapped I-Ab-restricted epitopes for the spike and nucleocapsid proteins of the BA.1 variant of concern via IFNγ ELISpot assay. This was followed by the generation of corresponding peptide:MHCII tetramer reagents to directly stain epitope-specific T cells. Using this rigorous validation strategy, we identified 6 immunogenic epitopes in spike and 3 in nucleocapsid, all of which are conserved in the ancestral Wuhan strain. We also validated a previously identified epitope from Wuhan that is absent in BA.1. These epitopes and tetramers will be invaluable tools for SARS-CoV-2 antigen-specific CD4+ T cell studies in mice. [ABSTRACT FROM AUTHOR]

Background: The emergence of new SARS-CoV-2 variants and the waning of immunity raise concerns about vaccine effectiveness and protection against COVID-19. While antibody response has been shown to correlate with the risk of infection with the original variant and earlier variants of concern, the effectiveness of antibody-mediated protection against Omicron and the factors associated with protection remain uncertain. Methods: We evaluated antibody responses to SARS-CoV-2 spike (S) and nucleocapsid (N) antigens from Wuhan and variants of concern by Luminex and their role in preventing breakthrough infections 1 year after a third dose of mRNA vaccination, in a cohort of health care workers followed since the pandemic onset in Spain (N = 393). Data were analyzed in relation to COVID-19 history, demographic factors, comorbidities, vaccine doses, brand, and adverse events. Results: Higher levels of anti-S IgG and IgA to Wuhan, Delta, and Omicron were associated with protection against vaccine breakthroughs (IgG against Omicron S antigen HR, 0.06, 95%CI, 0.26–0.01). Previous SARS-CoV-2 infection was positively associated with antibody levels and protection against breakthroughs, and a longer time since last infection was associated with lower protection. In addition, priming with BNT162b2 followed by mRNA-1273 booster was associated with higher antibody responses than homologous mRNA-1273 vaccination. Conclusions: Data show that IgG and IgA induced by vaccines against the original strain or by hybrid immunization are valid correlates of protection against Omicron BA.1 despite immune escape and support the benefits of heterologous vaccination regimens to enhance antibodies and the prioritization of booster vaccination in individuals without recent infections. [ABSTRACT FROM AUTHOR]

While the first infection of an emerging disease is often unknown, information on early cases can be used to date it. In the context of the COVID-19 pandemic, previous studies have estimated dates of emergence (e.g., first human SARS-CoV-2 infection, emergence of the Alpha SARS-CoV-2 variant) using mainly genomic data. Another dating attempt used a stochastic population dynamics approach and the date of the first reported case. Here, we extend this approach to use a larger set of early reported cases to estimate the delay from first infection to the Nth case. We first validate our framework by running our model on simulated data. We then apply our model using data on Alpha variant infections in the UK, dating the first Alpha infection at (median) August 21, 2020 (95% interpercentile range across retained simulations (IPR): July 23–September 5, 2020). Next, we apply our model to data on COVID-19 cases with symptom onset before mid-January 2020. We date the first SARS-CoV-2 infection in Wuhan at (median) November 28, 2019 (95% IPR: November 2–December 9, 2019). Our results fall within ranges previously estimated by studies relying on genomic data. Our population dynamics-based modelling framework is generic and flexible, and thus can be applied to estimate the starting time of outbreaks in contexts other than COVID-19. Author summary: While the first infection of an emerging disease is often unknown, information on early cases can be used to date it. In the context of the COVID-19 pandemic, previous studies have estimated dates of emergence of epidemic outbreaks (e.g., first human SARS-CoV-2 infection, emergence of the Alpha SARS-CoV-2 variant) using mainly genomic data. Another dating attempt used a population-level stochastic approach and the date of the first reported case. Here, we extend this generic and flexible approach to use a larger set of early reported cases to estimate the time elapsed between the first infection and the Nth case. Our model dates the first Alpha infection at around August 21, 2020, and the first SARS-CoV-2 infection in Wuhan at around November 28, 2019. Our findings fall within ranges previously estimated by studies relying on genomic data. [ABSTRACT FROM AUTHOR]

Simple Summary: The COVID-19 pandemic showcases the impact of mitigation and elimination strategies across the globe, including the development of effective vaccines, antiviral drugs and diagnostic tools. However, the virus changes rapidly over time. Consequently, control strategies have been limited by time-consuming experimental acquisition of three-dimensional atomic protein structures of the fast-developing mutant 'variants' of the virus, which remains an unviable strategy for fast and effective disease control. Here, we use AlphaFold2 to model the atomic structure of the ever-changing SARS-CoV-2 spike protein in silico. AlphaFold2 is an artificial intelligence (AI) deep learning computational tool capable of producing models at experimental resolution in only a few hours. Structural models for major Variants of Concern (Alpha, Delta, and Omicron) and latitude-delimited haplotypes, sets of genetically linked and highly prevalent mutations that impact the epidemic calendar of the virus, were compared to the structure of the reference Wuhan strain. We find that patterns of structural change triggered by seasonal haplotype diversification could help predict the changing face of the virus, understand seasonal behavior, and develop more resilient vaccines and drugs. The slow experimental acquisition of high-quality atomic structures of the rapidly changing proteins of the COVID-19 virus challenges vaccine and therapeutic drug development efforts. Fortunately, deep learning tools such as AlphaFold2 can quickly generate reliable models of atomic structure at experimental resolution. Current modeling studies have focused solely on definitions of mutant constellations of Variants of Concern (VOCs), leaving out the impact of haplotypes on protein structure. Here, we conduct a thorough comparative structural analysis of S-proteins belonging to major VOCs and corresponding latitude-delimited haplotypes that affect viral seasonal behavior. Our approach identified molecular regions of importance as well as patterns of structural recruitment. The S1 subunit hosted the majority of structural changes, especially those involving the N-terminal domain (NTD) and the receptor-binding domain (RBD). In particular, structural changes in the NTD were much greater than just translations in three-dimensional space, altering the sub-structures to greater extents. We also revealed a notable pattern of structural recruitment with the early VOCs Alpha and Delta behaving antagonistically by suppressing regions of structural change introduced by their corresponding haplotypes, and the current VOC Omicron behaving synergistically by amplifying or collecting structural change. Remarkably, haplotypes altering the galectin-like structure of the NTD were major contributors to seasonal behavior, supporting its putative environmental-sensing role. Our results provide an extensive view of the evolutionary landscape of the S-protein across the COVID-19 pandemic. This view will help predict important regions of structural change in future variants and haplotypes for more efficient vaccine and drug development. [ABSTRACT FROM AUTHOR]

First described in December 2019 in Wuhan (China), COVID-19 disease rapidly spread worldwide, constituting the biggest pandemic in the last 100 years. Even if SARS-CoV-2, the agent responsible for COVID-19, is mainly associated with pulmonary injury, evidence is growing that this virus can affect many organs, including the heart and vascular endothelial cells, and cause haemostasis, CNS, and kidney and gastrointestinal tract abnormalities that can impact in the disease course and prognosis. In fact, COVID-19 may affect almost all the organs. Hence, SARS-CoV-2 is essentially a systemic infection that can present a large number of clinical manifestations, and it is variable in distribution and severity, which means it is potentially life-threatening. The goal of this comprehensive review paper in the series is to give an overview of non-pulmonary involvement in COVID-19, with a special focus on underlying pathophysiological mechanisms and clinical presentation. [ABSTRACT FROM AUTHOR]

Introduction: The world has been badly affected by the spread of a novel virus known as Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) that was first reported in Wuhan, China back in December 2019. As the virus is transmitted through aerosol, respiratory droplets and close contact, hand hygiene and wearing mask are the most important preventive measures for COVID-19. Studies showed hand hygiene intervention improved compliances. This paper discussed the development of a hand hygiene intervention module, validation, usability and effectiveness reports. Methods: This study involved 5 stages; need analysis, module development, validation, usability and effectiveness studies. Need analysis and module development were carried out through brainstorming and literature search. The content was evaluated by three experts, whereas the usability was screened by four preschool teachers. The effectiveness of knowledge transfer was evaluated via pre and post intervention surveys. Results: The hand hygiene educational module received valuable comments from the content expert and the end-users (teachers). Knowledge score related to COVID-19 transmission, prevention and hand hygiene moments among pre-school children were significantly increased after the intervention. Conclusion: This module can be used to improve teaching method related to COVID-19 and hand hygiene. The 'learn and play' approach may increase excitement, thus make learning process enjoyable and memorable. [ABSTRACT FROM AUTHOR]

As there are limited data on B-cell epitopes for the nucleocapsid protein in SARS-CoV-2, we sought to identify the immunodominant regions within the N protein, recognized by patients with varying severity of natural infection with the Wuhan strain (WT), delta, omicron, and in those who received the Sinopharm vaccines, which is an inactivated, whole virus vaccine. Using overlapping peptides representing the N protein, with an in-house ELISA, we mapped the immunodominant regions within the N protein, in seronegative (n = 30), WT infected (n = 30), delta infected (n = 30), omicron infected + vaccinated (n = 20) and Sinopharm (BBIBP-CorV) vaccinees (n = 30). We then investigated the sensitivity and specificity of these immunodominant regions and analyzed their conservation with other SARS-CoV-2 variants of concern, seasonal human coronaviruses, and bat Sarbecoviruses. We identified four immunodominant regions aa 29–52, aa 155–178, aa 274–297, and aa 365–388, which were highly conserved within SARS-CoV-2 and the bat coronaviruses. The magnitude of responses to these regions varied based on the infecting SARS-CoV-2 variants, >80% of individuals gave responses above the positive cut-off threshold to many of the four regions, with some differences with individuals who were infected with different VoCs. These regions were found to be 100% specific, as none of the seronegative individuals gave any responses. As these regions were highly specific with high sensitivity, they have a potential to be used to develop diagnostic assays and to be used in development of vaccines. We identified four immunodominant regions within SARS-CoV-2 N protein, aa 29–52, aa 155–178, aa 274–297, and aa 365–388, were highly conserved within SARS-CoV-2 and the bat coronaviruses. As these regions were highly specific with high sensitivity, they have a potential to be used to develop diagnostic assays and to be used in development of vaccines. Graphical Abstract [ABSTRACT FROM AUTHOR]

The SARS-CoV-2 Omicron sub-variants BA.2.86 and JN.1 contain multiple mutations in the spike protein that were not present in previous variants of concern and Omicron sub-variants. Preliminary research suggests that these variants reduce the neutralizing capability of antibodies induced by vaccines, which is particularly significant for JN.1. This raises concern as many widely deployed COVID-19 vaccines are based on the spike protein of the ancestral Wuhan strain of SARS-CoV-2. While T cell responses have been shown to be robust against previous SARS-CoV-2 variants, less is known about the impact of mutations in BA.2.86 and JN.1 on T cell responses. We evaluate the effect of mutations specific to BA.2.86 and JN.1 on experimentally determined T cell epitopes derived from the spike protein of the ancestral Wuhan strain and the spike protein of the XBB.1.5 strain that has been recommended as a booster vaccine. Our data suggest that BA.2.86 and JN.1 affect numerous T cell epitopes in spike compared to previous variants; however, the widespread loss of T cell recognition against these variants is unlikely. [ABSTRACT FROM AUTHOR]

Machine learning (ML) is a key focus in predicting protein mutations and aiding directed evolution. Research on potential virus variants is crucial for vaccine development. In this study, the machine learning software PyPEF was employed to conduct mutation analysis within the receptor-binding domain (RBD) of the Spike glycoprotein of SARS-CoV-2. Over 48,960,000 variants were predicted. Eight prospective variants that could surface in the future underwent modeling and molecular dynamics simulations. The study forecasts that the latest variant, ISOY2P5O1, may potentially emerge around 17 November 2023, with an approximate window of uncertainty of ±22 days. The ISOY8P5O2 variant displayed an increased binding capacity in the dry assay, with a total predicted binding energy of −110.306 kcal/mol. This represents an 8.25% enhancement in total binding energy compared to the original SARS-CoV-2 strain discovered in Wuhan (−101.892 kcal/mol). Reverse research confirmed the structural significance of mutation sites using ML models, particularly in the context of protein folding. The study validated regression methods (SVR, RF, and PLS) with different data structures. This study investigates the effectiveness of the "ML-Guided Design Correctly Predicts Combinatorial Effects Strategy" compared to the "ML-Guided Design Correctly Predicts Natural Evolution Prediction Strategy". To enhance machine learning, we created a timestamping algorithm and two auxiliary programs using advanced techniques to rapidly process extensive data, surpassing batch sequencing capabilities. This study not only advances machine learning in guiding protein evolution but also holds potential for forecasting future viruses and vaccine development. [ABSTRACT FROM AUTHOR]

Coronavirus disease 2019 (COVID-19) is an infectious viral disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that emerged at the end of 2019. SARS-CoV-2 can be transmitted through droplets, aerosols, and fomites. Disinfectants such as alcohol, quaternary ammonium salts, and chlorine-releasing agents, including hypochlorous acid, are used to prevent the spread of SARS-CoV-2 infection. In the present study, we investigated the efficacy of ionless hypochlorous acid water (HOCl) in suspension and by spraying to inactivate SARSCoV-2. The virucidal efficacy of HOCl solution in tests against SARS-CoV-2 was evaluated as 50% tissue culture infectious dose. Although the presence of organic compounds influenced the virucidal efficacy, HOCl treatment for 20 s was significantly effective to inactivate Wuhan and Delta strains in the suspension test. HOCl atomization for several hours significantly reduced the SARS-CoV-2 attached to plastic plates. These results indicate that HOCl solution with elimination containing NaCl and other ions may have high virucidal efficacy against SARS-CoV-2. This study provides important information about the virucidal efficacy and use of HOCl solution. [ABSTRACT FROM AUTHOR]

The onset of the COVID-19 pandemic in late 2019 triggered an unprecedented global health crisis. Originating in Wuhan, China, the spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to a worldwide upheaval, affecting every aspect of human life. As countries grappled with rising case counts, hospitalizations, and fatalities, the role of geospatial information and visualization in managing and understanding the pandemic became increasingly vital. This special issue of the Cartography and Geographic Information Science (CaGIS) Journal sought to explore the innovative and impactful ways in which geovisualization techniques have been employed to confront and elucidate the complexities of COVID-19. We describe significance and contribution of each paper that is part of the special issue, and avenues for new, exciting research around infectious diseases, keeping in mind that the research needs to be reproducible. [ABSTRACT FROM AUTHOR]

The etiological agent of coronavirus disease (COVID-19) that emerged at the end of year 2019 was first reported in Wuhan, China and was found to be SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2). The massive COVID-19 waves were due to various variants. As per the reports of other study it was also found that Omicron variant spread faster than various other variant such as delta variant. Omicron has been reported from various countries and now from many states of India too. Therefore, keeping this in mind, this study was undertaken to study all the lineages of SARS-CoV-2 Omicron variant of disease COVID-19 that are circulating in the population of Uttarakhand with objective to study next generation sequencing of all the RT-PCR positive of SARS-CoV-2 and to find out all the lineages of the Omicron variant of SARS-CoV-2. This was a retrospective study conducted from 1st January 2022 to 30th September 2022. Next generation sequencing was performed on all the samples that were tested for COVID-19 by using Ion AmpliSeq kit on Ion Chef instrument. A total of 2149 samples were tested in which majority of samples belong to age group of 21-40 years. Males were affected more than females. BA.2 was found to be the predominant lineage of total of 46 lineages that were identified. Their mutations were also studied. We conclude that different variants of clade 21L, 22B, 22D and Omicron subvariant BA.2, BA.2.38 and BA.2.75 were the ones that were circulating amongst the population of Uttarakhand. The characteristic mutation that was found were T19I and V213G in NTD, S373P, S375F, T376A, and D405N in RBD. [ABSTRACT FROM AUTHOR]