Changes within the P681 residue of spike dictate cell fusion and syncytia formation of Delta and Omicron variants of SARS-CoV-2 with no effects on neutralization or infectivity.

The rapid spread and dominance of the Omicron SARS-CoV-2 lineages have posed severe health challenges worldwide. While extensive research on the role of the Receptor Binding Domain (RBD) in promoting viral infectivity and vaccine sensitivity has been well documented, the functional significance of the 681PRRAR/SV687 polybasic motif of the viral spike is less clear. In this work, we monitored the infectivity levels and neutralization potential of the wild-type human coronavirus 2019 (hCoV-19), Delta, and Omicron SARS-CoV-2 pseudoviruses against sera samples drawn four months post administration of a third dose of the BNT162b2 mRNA vaccine. Our findings show that in comparison to hCoV-19 and Delta SARS-CoV-2, Omicron lineages BA.1 and BA.2 exhibit enhanced infectivity and a sharp decline in their sensitivity to vaccine-induced neutralizing antibodies. Interestingly, P681 mutations within the viral spike do not play a role in the neutralization potential or infectivity of SARS Cov-2 pseudoviruses carrying mutations in this position. The P681 residue however, dictates the ability of the spike protein to promote fusion and syncytia formation between infected cells. While spike from hCoV-19 (P681) and Omicron (H681) promote only modest cell fusion and formation of syncytia between cells that express the spike-protein, Delta spike (R681) displays enhanced fusogenic activity and promotes syncytia formation. Additional analysis shows that a single P681R mutation within the hCoV-19 spike, or H681R within the Omicron spike, restores fusion potential to similar levels observed for the Delta R681 spike. Conversely, R681P point mutation within the spike of Delta pseudovirus abolishes efficient fusion and syncytia formation. Our investigation also demonstrates that spike proteins from hCoV-19 and Delta SARS-CoV-2 are efficiently incorporated into viral particles relative to the spike of Omicron lineages. We conclude that the third dose of the Pfizer-BNT162b2 provides appreciable protection against the newly emerged Omicron sub-lineages. However, the neutralization sensitivity of these new variants is diminished relative to that of the hCoV-19 or Delta SARS-CoV-2. We further show that the P681 residue within spike dictates cell fusion and syncytia formation with no effects on the infectivity of the specific viral variant and on its sensitivity to vaccine-mediated neutralization.

HR121 targeting HR2 domain in S2 subunit of spike protein can serve as a broad-spectrum SARS-CoV-2 inhibitor via intranasal administration.

The continuously emerging SARS-CoV-2 variants pose a great challenge to the efficacy of current drugs, this necessitates the development of broad-spectrum antiviral drugs. In the previous study, we designed a recombinant protein, heptad repeat (HR) 121, as a variant-proof vaccine. Here, we found it can act as a fusion inhibitor and demonstrated broadly neutralizing activities against SARS-CoV-2 and its main variants. Structure analysis suggested that HR121 targets the HR2 domain in SARS-CoV-2 spike (S) 2 subunit to block virus-cell fusion. Functional experiments demonstrated that HR121 can bind HR2 at serological-pH and endosomal-pH, highlighting its inhibition capacity when SARS-CoV-2 enters via either cellular membrane fusion or endosomal route. Importantly, HR121 can effectively inhibit SARS-CoV-2 and Omicron variant pseudoviruses entering the cells, as well as block authentic SARS-CoV-2 and Omicron BA.2 replications in human pulmonary alveolar epithelial cells. After intranasal administration to Syrian golden hamsters, it can protect hamsters from SARS-CoV-2 and Omicron BA.2 infection. Together, our results suggest that HR121 is a potent drug candidate with broadly neutralizing activities against SARS-CoV-2 and its variants.

MRI of fatal course of acute hemorrhagic leukoencephalitis in a child with SARS-CoV-2 omicron BA 2.0 infection.

We present a pediatric case of acute hemorrhagic leukoencephalitis associated with SARS-CoV-2 Omicron BA 2.0 infection. A previously healthy girl presented with ataxia and diplopia three weeks after the COVID-19 confirmation from a nasopharyngeal swab. Acute and symmetrical motor weakness and drowsiness ensued within the following 3 days. She then became spastic tetraplegic. MRI revealed multifocal lesions in the cerebral white matter, basal ganglia, and brainstem, with hemorrhagic changes confirmed with T1-hyperintensity and hypointensity on susceptibility-weighted images. Peripheral areas of decreased diffusion, increased blood flow, and rim contrast enhancement were noted in the majority of lesions. She was treated with a combination of intravenous immunoglobulin and methylprednisolone pulse therapy. Neurological deterioration ensued with coma, ataxic respiratory pattern and decerebrate posture. Repeated MRI performed on day 31 revealed progression of abnormalities, hemorrhages and brain herniation. Despite the administration of plasma exchange, she died two months after admission.

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

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

Association between time of onset and Omicron BA.2 RNA clearance time in children: a retrospective cohort study.

Background: The association between the time of onset [time from the date of detection of a positive real-time reverse-transcription polymerase chain reaction (RT-PCR) to the date of detection of a positive RT-PCR in the first child] and viral RNA clearance time (time from first positive RT-PCR to two consecutive negative RT-PCR) remains unclear. Our study aimed to evaluate their association. That can provide a reference for the number of nucleic acid tests. Methods: We conducted a retrospective analysis of children diagnosed with Omicron BA.2 infection at Fujian Medical University Affiliated First Quanzhou Hospital between March 14, 2022 (date the first child in the outbreak was found positive for RT-PCR) and April 9, 2022 (date the last child was found positive for RT-PCR). We used the electronic medical record to extract demographic data, symptoms, radiology and laboratory findings, treatments, and viral RNA clearance time. The 282 children were divided equally into 3 groups according to the time of onset. We calculated the factors affecting viral RNA clearance time by univariate and multivariate analysis. We used the generalized additive model to investigate the relationship between the time of onset and viral RNA clearance time. Results: 46.45% of children were female. Fever (62.06%) and cough (15.60%) were the dominant onset symptoms. We found no serious cases and all children were cured. The median time to viral RNA clearance was 14 days (IQR 12-17 days), with a range of 5 to 35 days. After adjustment for potential confounders, the viral RNA clearance time was reduced by 2.45 (95% CI: 0.85, 4.04) days in the 7-10 days group and by 4.62 (95% CI: 2.38, 6.14) days in > 10 days group compared to the ≤6 days group. There was a non-linear association between the time of onset and viral RNA clearance time. Conclusions: Time of onset was non-linearly associated with Omicron BA.2 RNA clearance time. During the first 10 days of the outbreak, viral RNA clearance time decreased with increasing onset date. After 10 days of the outbreak, viral RNA clearance time did not decrease with increasing onset date.

Protection probability against SARS-CoV-2 Omicron variant BA.1, BA.2 and BA.5 in asympto- matic infection caused by prototype strain

Objective To estimate the protection probability against SARS-CoV-2 variant Omicron strains BA.1, BA.2 and BA.5 infection, symptomatic infection and severe disease outcomes in asymptomatic individuals infected with SARS-CoV-2 prototype strain previously. Methods Our previous study had shown that the dynamic change of neutralizing antibodies in asymptomatic individuals infected with the SARS-CoV-2 prototype strain. Based on our previous study, a peer–reviewed predictive model on the basis of logistic model was used to estimate the protection probability of asymptomatic individuals against Omicron strains BA.1, BA.2 and BA.5. We estimate the protection probability against infection, symptomatic infection and severe disease outcomes on 28, 51 and 261 days after confirmation. Results The protection probability against reinfection of Omicron variant strains BA.1, BA.2, and BA.5 on 28 days after confirmation were 30% (95% CI: 16%–52%) , 23% (95% CI: 15%–36%) and 8% (95% CI: 4%–16%) respectively, while decreased to 9% (95% CI: 3%–21%) , 6% (95% CI: 3%–12%) and 2% (95% CI: 1%–4%) on 261 days after confirmation. The protection probability against symptomatic infection of Omicron strains BA.1, BA.2, and BA.5 were 51% (95% CI: 28%–80%) , 42% (95% CI: 26%–67%) and 16% (95% CI: 7% – 40%) respectively on 28 days after confirmation, while decreased to 16% (95% CI: 7%–35%) , 12% (95% CI: 7% – 22%) and 3% (95% CI: 1% – 8%) on 261 days after confirmation. The protection probability against severe disease of Omicron strains BA.1, BA.2, and BA.5 were 91% (95% CI: 72%–98%) , 88% (95% CI: 70%–97%) and 66% (95% CI: 35%–90%) respectively on 28 days after confirmation, while decreased to 60% (95% CI: 35%–86%) , 51% (95% CI: 32%–75%) and 22% (95% CI: 10%–50%) on 261 days after confirmation. Conclusions Neutralizing antibodies induced in asymptomatic individuals infected with prototype strain could provide higher protection against Omicron strain BA.5 than Omicron strains BA.1 and BA.2. Among the three clinical outcomes, the protective probability against severe disease outcome was better, followed by symptomatic infection, and the protective probability against infection was poor. © 2023, Publication Centre of Anhui Medical University. All rights reserved.

Effect Analysis of Different Environmental Disinfection Methods on Reducing Contamination of Surfaces by the Omicron BA.2.2 Variant of SARS-CoV-2 and the Characteristics of Fomite Contamination in the Fever Clinic in the Out-Broken of Shanghai.

This study aimed to investigate the effect of different environmental disinfection methods on reducing contaminated surfaces (CSs) by the Omicron BA.2.2 variant of SARS-CoV-2 in the fever clinic between March 20 and May 30, 2022, and to analyze the influences and related factors of CSs. This study includes survey data from 389 positive patients (SPPs) and 204 CSs in the fever clinic, including the CS type, disinfection method, length of time spent in the clinic, cycle threshold (CT) value, name, age, weight, mask type, mask-wearing compliance, hand-mouth touch frequency and sex. Associations between study variables and specified outcomes were explored using univariate regression analyses. Mask-wearing compliance had a significant negative correlation with CSs (r = - 0.446, P = 0.037). Among the 389 SPPs, 22 SPPs (CRP, 5.66%) caused CSs in the separate isolation room. A total of 219 SPPs (56.30%) were male. The mean age of SPPs was 4.34 ± 3.92 years old, and the mean CT value was 12.44 ± 5.11. In total, 9952 samples with exposure history were taken, including 204 (2.05%) CSs. Among the CSs, the positive rate of flat surfaces was the highest in public areas (2.52%) and separate isolation rooms (4.75%). Disinfection methods of ultraviolet radiation + chemical irradiation significantly reduced the CSs in both the public area (0% vs. 4.56%) and the separate isolation room (0.76% vs. 2.64%) compared with the chemical method alone (P < 0.05). Compared with ordinary SPPs, CRPs were older (6.04 year vs. 4.23 year), and the male proportion was higher (72.73% vs. 55.31%). In particular, it was found that SPPs contaminated their surroundings and therefore imposed risks on other people. Environmental disinfection with ultraviolet radiation + chemical treatment should be emphasized. The findings may be useful to guide infection control practices for the Omicron BA.2.2 variant of SARS-CoV-2.

A machine learning model for predicting serum neutralizing activity against Omicron SARS-CoV-2 BA.2 and BA.4/5 sublineages in the general population.

Supervised machine learning (ML) methods have been used to predict antibody responses elicited by COVID-19 vaccines in a variety of clinical settings. Here, we explored the reliability of a ML approach to predict the presence of detectable neutralizing antibody responses (NtAb) against Omicron BA.2 and BA.4/5 sublineages in the general population. Anti-SARS-CoV-2 receptor-binding domain (RBD) total antibodies were measured by the Elecsys® Anti-SARS-CoV-2 S assay (Roche Diagnostics) in all participants. NtAbs against Omicron BA.2 and BA4/5 were measured using a SARS-CoV-2 S pseudotyped neutralization assay in 100 randomly selected sera. A ML model was built using the variables of age, vaccination (number of doses) and SARS-CoV-2 infection status. The model was trained in a cohort (TC) comprising 931 participants and validated in an external cohort (VC) including 787 individuals. Receiver operating characteristics analysis indicated that an anti-SARS-CoV-2 RBD total antibody threshold of 2300 BAU/mL best discriminated between participants either exhibiting or not detectable Omicron BA.2 and Omicron BA.4/5-Spike targeted NtAb responses (87% and 84% precision, respectively). The ML model correctly classified 88% (793/901) of participants in the TC: 717/749 (95.7%) of those displaying ≥2300 BAU/mL and 76/152 (50%) of those exhibiting antibody levels <2300 BAU/mL. The model performed better in vaccinated participants, either with or without prior SARS-CoV-2 infection. The overall accuracy of the ML model in the VC was comparable. Our ML model, based upon a few easily collected parameters for predicting neutralizing activity against Omicron BA.2 and BA.4/5 (sub)variants circumvents the need to perform not only neutralization assays, but also anti-S serological tests, thus potentially saving costs in the setting of large seroprevalence studies.

Protection probability against SARS-CoV-2 Omicron variant BA.1, BA.2 and BA.5 in asympto- matic infection caused by prototype strain.

Objective To estimate the protection probability against SARS-CoV-2 variant Omicron strains BA.1, BA.2 and BA.5 infection, symptomatic infection and severe disease outcomes in asymptomatic individuals infected with SARS-CoV-2 prototype strain previously. Methods Our previous study had shown that the dynamic change of neutralizing antibodies in asymptomatic individuals infected with the SARS-CoV-2 prototype strain. Based on our previous study, a peer-reviewed predictive model on the basis of logistic model was used to estimate the protection probability of asymptomatic individuals against Omicron strains BA.1, BA.2 and BA.5. We estimate the protection probability against infection, symptomatic infection and severe disease outcomes on 28, 51 and 261 days after confirmation. Results The protection probability against reinfection of Omicron variant strains BA.1, BA.2, and BA.5 on 28 days after confirmation were 30% (95% CI: 16%-52%) , 23% (95% CI: 15%-36%) and 8% (95% CI: 4%-16%) respectively, while decreased to 9% (95% CI: 3%-21%) , 6% (95% CI: 3%-12%) and 2% (95% CI: 1%-4%) on 261 days after confirmation. The protection probability against symptomatic infection of Omicron strains BA.1, BA.2, and BA.5 were 51% (95% CI: 28%-80%) , 42% (95% CI: 26%-67%) and 16% (95% CI: 7% - 40%) respectively on 28 days after confirmation, while decreased to 16% (95% CI: 7%-35%) , 12% (95% CI: 7% - 22%) and 3% (95% CI: 1% - 8%) on 261 days after confirmation. The protection probability against severe disease of Omicron strains BA.1, BA.2, and BA.5 were 91% (95% CI: 72%-98%) , 88% (95% CI: 70%-97%) and 66% (95% CI: 35%-90%) respectively on 28 days after confirmation, while decreased to 60% (95% CI: 35%-86%) , 51% (95% CI: 32%-75%) and 22% (95% CI: 10%-50%) on 261 days after confirmation. Conclusions Neutralizing antibodies induced in asymptomatic individuals infected with prototype strain could provide higher protection against Omicron strain BA.5 than Omicron strains BA.1 and BA.2. Among the three clinical outcomes, the protective probability against severe disease outcome was better, followed by symptomatic infection, and the protective probability against infection was poor.Copyright © 2023, Publication Centre of Anhui Medical University. All rights reserved.

An updated atlas of antibody evasion by SARS-CoV-2 Omicron sub-variants including BQ.1.1 and XBB.

Emerging Omicron sub-variants are causing global concerns, and their immune evasion should be monitored continuously. We previously evaluated the escape of Omicron BA.1, BA.1.1, BA.2, and BA.3 from an atlas of 50 monoclonal antibodies (mAbs), covering seven epitope classes of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) receptor-binding domain (RBD). Here, we update the atlas of totally 77 mAbs against emerging sub-variants including BQ.1.1 and XBB and find that BA.4/5, BQ.1.1, and XBB display further evasion. Besides, investigation into the correlation of binding and neutralization of mAbs reveals the important role of antigenic conformation in mAb functioning. Moreover, the complex structures of BA.2 RBD/BD-604/S304 and BA.4/5 RBD/BD-604/S304/S309 further elucidate the molecular mechanism of antibody evasion by these sub-variants. By focusing on the identified broadly potent mAbs, we find a general hotspot epitope on the RBD, which could guide the design of vaccines and calls for new broad-spectrum countermeasures against COVID-19.

Emergence and Persistent Dominance of SARS-CoV-2 Omicron BA.2.3.7 Variant, Taiwan.

Since April 2022, waves of SARS-CoV-2 Omicron variant cases have surfaced in Taiwan and spread throughout the island. Using high-throughput sequencing of the SARS-CoV-2 genome, we analyzed 2,405 PCR-positive swab samples from 2,339 persons and identified the Omicron BA.2.3.7 variant as a major lineage within recent community outbreaks in Taiwan.

Higher risk of SARS-CoV-2 Omicron BA.4/5 infection than of BA.2 infection after previous BA.1 infection, the Netherlands, 2 May to 24 July 2022.

BackgroundIn summer 2022, SARS-CoV-2 Omicron BA.5 became dominant in Europe. In vitro studies have shown a large reduction of antibody neutralisation for this variant.AimWe aimed to investigate differences in protection from previous infection and/or vaccination against infection with Omicron BA.4/5 vs BA.2.MethodsWe employed a case-only approach including positive PCR tests from community testing between 2 May and 24 July 2022 that were tested for S gene target failure (SGTF), which distinguishes BA.4/5 from BA.2 infection. Previous infections were categorised by variant using whole genome sequencing or SGTF. We estimated by logistic regression the association of SGTF with vaccination and/or previous infection, and of SGTF of the current infection with the variant of the previous infection, adjusting for testing week, age group and sex.ResultsThe percentage of registered previous SARS-CoV-2 infections was higher among 19,836 persons infected with Omicron BA.4/5 than among 7,052 persons infected with BA.2 (31.3% vs 20.0%). Adjusting for testing week, age group and sex, the adjusted odds ratio (aOR) was 1.4 (95% CI: 1.3-1.5). The distribution of vaccination status did not differ for BA.4/5 vs BA.2 infections (aOR = 1.1 for primary and booster vaccination). Among persons with a previous infection, those currently infected with BA4/5 had a shorter interval between infections, and the previous infection was more often caused by BA.1, compared with those currently infected with BA.2 (aOR = 1.9; 95% CI: 1.5-2.6).ConclusionOur results suggest immunity induced by BA.1 is less effective against BA.4/5 infection than against BA.2 infection.

Fatal Fulminant Cerebral Edema in Six Children with SARS-CoV-2 Omicron BA.2 Infection in Taiwan.

Acute fulminant cerebral edema in children following SARS-CoV-2 infection has been rarely reported. Such patients frequently demonstrate rapid progression rapid progression and are usually fatal. In this retrospective study, we describe the detailed clinical, laboratory, and neuroimaging features of six fatal cases in Taiwan. All patients had shock initially, five showed rapid progression to multi-organ failure and disseminated intravascular coagulation, and three developed acute respiratory distress syndromes. The inflammatory biomarkers in the first 3 days, including interleukin 6, ferritin, lactate dehydrogenase and D-dimer, showed significant elevation in all cases. Hyper-inflammatory response may play a role in the pathophysiology.

COI vs Ct: comparing automated antigen tests cut-off index (COI) to PCR cycle threshold (Ct)

Introduction: The objective of this study was to compare the numeric cut-off index (COI) of automated antigen tests with the cycle-threshold (Ct) value. Materials and methods: COI values of all samples processed with the Elecsys® SARS-CoV-2 Antigen (Roche, Switzerland) from January to February 2022 were retrieved and the positive were compared to RdRP Cts of Allplex Variants I (Seegene, Korea). COI between 0.6 and 1 were considered indeterminate and overproved by RT-PCR. Results: From 13,937 samples 7944(57%) were positive and 189(1.35%) indeterminate. There was a strong correlation between Cts and COI values at the positive samples, but that was not the case for indeterminates. Conclusions: COI values of the positive samples (COI >1) are comparable to Ct values and may therefore be used as proxy viral loads, however this is not the case for indeterminate samples. © 2022 Elsevier Inc.

Vaccination effects on post-infection outcomes in the Omicron BA.2 outbreak in Shanghai.

Omicron and its sublineages are currently predominant and have triggered epidemiological waves of SARS-CoV-2 around the world due to their high transmissibility and strong immune escape ability. Vaccines are key measures to control the COVID-19 burden. Omicron BA.2 caused a large-scale outbreak in Shanghai since March 2022 and resulted in over 0.6 million laboratory-confirmed infections. The vaccine coverage of primary immunization among residents aged 3 years and older in Shanghai exceeded 90%, and inactivated COVID-19 vaccines were mainly delivered. In the context of high vaccine coverage, we conducted a cohort study to assess vaccine effects on reducing the probability of developing symptoms or severity of disease in infections or nonsevere cases. A total of 48,243 eligible participants were included in this study, the majority of whom had asymptomatic infections (31.0%) and mild-to-moderate illness (67.9%). Domestically developed COVID-19 vaccines provide limited protection to prevent asymptomatic infection from developing into mild-to-moderate illness and durable protection to prevent nonsevere illness from progressing to severe illness caused by Omicron BA.2. Partial vaccination fails to provide effective protection in any situation. The level of vaccine effects on disease progression in the elderly over 80 years old was relatively lower compared with other age groups. Our study results added robust evidence for the vaccine performance against Omicron infection and could improve vaccine confidence.

A comparative study on epidemiological characteristics, transmissibility, and pathogenicity of three COVID-19 outbreaks caused by different variants.

OBJECTIVES: The Omicron BA.2 variant is probably the main epidemic strain worldwide at present. Comparing the epidemiological characteristics, transmissibility, and influencing factors of SARS-CoV-2, the results obtained in this paper will help to provide theoretical support for disease control. METHODS: This study was a historical information analysis, using the R programming language and SPSS 24.0 for statistical analysis. The Geoda and Arc GIS were used for spatial autocorrelation analysis. RESULTS: Local spatial autocorrelations of the incidence rate were observed in Delta and Omicron BA.1 outbreaks, whereas Omicron BA.2 outbreaks showed a random distribution in incidence rate. The time-dependent reproduction number of Delta, Omicron BA.1, and Omicron BA.2 were 3.21, 4.29, and 2.96, respectively, and correspondingly, the mean serial interval were 4.29 days (95% confidence interval [CI]: 0.37-8.21), 3.84 days (95% CI: 0-8.37), and 2.77 days (95% CI: 0-5.83). The asymptomatic infection rate of cases in Delta, Omicron BA.1, and Omicron BA.2 outbreaks were 21.71%, 6.25%, and 4.35%, respectively. CONCLUSION: The Omicron BA.2 variant had the greatest serial interval, transmissibility, and transmission speed, followed by BA.1, and then Delta. Compared with Delta and Omicron BA.1 variants, the Omicron BA.2 variant may be less pathogenic and more difficult to control than Omicron BA.1 and Delta.

Genomic sequencing profile of SARS-CoV-2 in different parts of western Odisha, India

Genetic lineages of severe acute respiratory syndrome corona virus-2 (SARS-CoV-2) have continued to emerge and circulate around the world since the onset of the COVID-19 pandemic. There are numerous variants of SARS-CoV-2, the virus that causes corona virus disease 2019 (COVID-19). Like other viruses, SARS-CoV-2 evolves over time. Most mutations in the SARS-CoV-2 genome have no impact on viral function, but certain variants have gained worldwide attention because of their rapid emergence within populations, evidence of transmission, and clinical implications. During the pandemic, most parts of India were affected, including Odisha, leading to high rates of morbidity and mortality. For the present study, 368,303 samples were received by the COVID-19 lab i.e., medical college level (Virus Research Diagnostic Laboratory) VRDL from six districts of western Odisha, including approximately 25,000 COVID-19-positive samples. The diagnostic method of the quantitative RT-PCR cannot be used to distinguish among the variants created by mutation of the genes initially, therefore selected positive clinical samples were sent in cold chain for whole genome sequencing (WGS), using the Illumina Seq. at ILS, BBSR for variant detection. The reported observation from the next generation sequencing (NGS) based sequenced samples of western Odisha updated in the INSACOG-WGS portal confirms the presence of Delta (B.1.617.2) and Delta sublineages, Omicron (BA.2), and Omicron (B.1.1.529). Maximum infection was caused by Delta sublineages (83.5%) irrespective of age, sex, and geographic area followed by Delta and Omicron. Molecular diagnosis and WGS based study reveal the widespread transmission of the fatal virus, significantly affecting every corner of the globe. Copyright © 2023 Wolters Kluwer Medknow Publications. All rights reserved.

Molecular Medical Diagnosis of COVID-19 and Omicron Variant

Genetic lineages of severe acute respiratory syndrome corona virus-2 (SARS-CoV-2) have continued to emerge and circulate around the world since the onset of the COVID-19 pandemic. There are numerous variants of SARS-CoV-2, the virus that causes corona virus disease 2019 (COVID-19). Like other viruses, SARS-CoV-2 evolves over time. Most mutations in the SARS-CoV-2 genome have no impact on viral function, but certain variants have gained worldwide attention because of their rapid emergence within populations, evidence of transmission, and clinical implications. During the pandemic, most parts of India were affected, including Odisha, leading to high rates of morbidity and mortality. For the present study, 368,303 samples were received by the COVID-19 lab i.e., medical (Virus Research Diagnostic Laboratory) VRDL from six districts of western Odisha, including approximately 25,000 COVID-19-positive samples. The diagnostic method of the quantitative RT-PCR cannot be used to distinguish among the variants created by mutation of the genes initially. Therefore, selected positive clinical samples were sent in cold chain for whole genome sequencing (WGS), and disease severity was sequenced using the Illumina Seq at ILS, BBSR for variant detection. The reported observation from the next generation sequencing (NGS) based sequenced samples of western Odisha updated in the INSACOG-WGS portal confirms the presence of Delta (B.1.617.2) and Delta sub lineages, Omicron (BA.2), and Omicron (B.1.1.529). Maximum infection was caused by Delta sub lineages 83.5%) irrespective of age, sex, and geographic area followed by Delta and Omicron. Molecular diagnosis and WGS based study reveal the widespread transmission of the fatal virus, significantly affecting every corner of the globe. Copyright © 2022 Wolters Kluwer Medknow Publications. All rights reserved.

As the SARS-CoV-2 virus evolves, should Omicron subvariant BA.2 be subjected to quarantine, or should we learn to live with it?

It has been nearly 35 months since the COVID-19 outbreak. The pathogen SARS-CoV-2 has evolved into several variants. Among them, Omicron is the fifth variant of concern which have rapidly spread globally during the past 8 months. Omicron variant shows different characteristics from previous variants, which is highly infectious, highly transmissible, minimally pathogenic, vaccine and antibody tolerant; however, it is less likely to cause severe illness, resulting in fewer deaths. Omicron has evolved into five main lineages, including BA.1, BA.2, BA.3, BA.4, and BA.5. Before BA.5, Omicron BA.2 sublineage was the dominant strain all over the world for several months. The experience of prevention and treatment against BA.2 is worth studying and learning for overcoming other Omicron subvariants. Although the Omicron subvariant BA.2 is significantly less severe than that caused by ancestral strains, it is still far more dangerous than influenza, and its long-term sequelae are unknown. Effective treatments are currently limited; therefore, effective defense may be the key to controlling the epidemic today, rather than just "living with" the virus.