The relationship between SARS-CoV-2 vaccination and COVID-19 in children

Objective: To analyze the vaccination status of SARS-CoV-2 in children, and explore the relationship between SARS-CoV-2 vaccination and COVID-19 in children. Methods: A retrospective study was conducted to analyze the clinical data of 335 cases of SARS-CoV-2 Omicron variant infection from February 15, 2022 to March 18, 2022 in Shenzhen Third People's Hospital. Results: Among 335 children with SARS-CoV-2 infection, 174(51.9%) cases were vaccinated with the SARS-CoV-2 vaccine;33(31.4%) cases were vaccinated in the 3-<6 years old group;141(61.3%) cases were vaccinated in the 6-<14 years old group. There was a statistically significant difference in the proportion of SARS-CoV-2 vaccination between the 6-<14 years old group and the 3-<6 years old group (X2=26.1, P < 0.05). In the study cohort, 3-<6 years old group and 6-<14 years old group, there was no significant difference in the incidence of COVID-19 in the vaccinated group compared with the unvaccinated group (P > 0.05). In the study cohort, the proportion of confirmed cases of 1 dose of SARS-CoV-2 vaccine and 2 doses or more of SARS-CoV-2 vaccine was 89.5% (68 cases) and 77.6% (76 cases), respectively;in the 6~<14 years old group, the proportion of confirmed cases of 1 dose of SARS-CoV-2 vaccine and 2 doses or more of SARS-CoV-2 vaccine was 90.0% (54 cases) and 76.5% (62 cases), respectively;the differences were statistically significant (X2=4.264, P < 0.05;X2=4.279, P < 0.05). The IgG levels of 18.28 (6.61, 55.2) AU/mL and 58.3 (25.85, 131.41) AU/mL in the study cohort who were vaccinated for 1 dose, 2 doses and more, respectively;the IgG levels of 20.13 (8.33, 44.33) AU/mL and 56.57 (25.85, 150.07) AU/mL in the 6~<14 years old group who were vaccinated for 1 dose, 2 doses and more, respectively;and the differences were statistically significant (Z=-4.37, P < 0.05;Z=-3.96, P < 0.05). Conclusions: Children who received 2 doses of SARS-CoV-2 vaccine have a lower incidence of COVID-19 and higher levels of SARS-CoV-2 antibodies compared with who received 1 dose. It is recommended that children are advised to be vaccinated against the COVID-19.

Influencing factors of negative conversion time of nucleic acid detection in 228 patients infected with Omicron variant of SARS-CoV-2 in Shanghai

Objective: To analyze and compare the effects of different clinical characteristics on the negative conversion time of nucleic acid detection after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant infection, and to provide a scientific basis for the isolation and treatment of coronavirus disease 2019 (COVID-19). Methods: The epidemiological and clinical data of 228 mild SARS-CoV-2 Omicron variant infected patients diagnosed in Shanghai were retrospectively collected from April 27, 2022 to June 8, 2022 in Wujiaochang designated Hospital, Yangpu District, Shanghai. The negative conversion time of nucleic acid detection was used as the outcome variable, and the patients were divided into A (18 days) and B (>18 days). Univariate and multivariate logistic regression analysis were used to analyze the influencing factors of the negative conversion time of nucleic acid detection. Results: The mean nucleic acid conversion time of 228 patients was (18.7+or-12.1) d, with the median time of 18 (2-46) d. Among them, 120 patients in group A had an average nucleic acid conversion time of (13.2+or-2.0) d, and 108 cases in group B had an average nucleic acid conversion time of (20.8+or-1.3) d. Univariate analysis showed that there were no statistically significant differences in the effects of hypertension, coronary heart disease, diabetes, hypokalemia, malignant tumors, neuropsychiatric diseases, chronic digestive diseases on the negative nucleic acid conversion time (P > 0.05);however, there were significant differences in the effects of combined cerebrovascular disease, leukopenia, chronic respiratory system diseases and vaccination on the negative nucleic acid conversion time (P < 0.05). Further multivariate logistic regression analysis revealed that the combination of chronic respiratory diseases and non-vaccination were significant risk factors for prolongation of negative nucleic acid conversion time (P < 0.05). Conclusions: The results of this study show that gender, age and whether hypertension, coronary heart disease, diabetes mellitus, hypokalemia, malignant tumor, neuropsychiatric disease and chronic digestive disease have no significant effect on the nucleic acid conversion time, whereas chronic respiratory disease and no vaccination are significantly correlated with the prolongation of nucleic acid conversion time in SARS-CoV-2 Omicron-infected patients.

On the Volatility and Market Inefficiency of Bitcoin During the COVID-19 Pandemic

The COVID-19 pandemic has been causing unprecedented economic downturn worldwide. As it wreaks havoc on every aspect of global economic activities, stakeholders are wondering how its impact can be quantified to craft viable responses. In the exotic field of cryptocurrencies, prior to the pandemic, everyone was excited about Bitcoin and its multitude of potentials. However, a day after COVID-19 was officially announced by the World Health Organization as a pandemic, the rate of return to Bitcoin dropped by an unheard-of one-day decline of-46.5%, and people started to rethink the prospects of Bitcoin. A day after this steep decline, Bitcoin recovered and started a sustained bull run which lasted for almost a year and even posted an all-time high daily uptick of 59.6%. By the end of July 2021, the price reached its all-time high but lost more than half of it at the end of the sample period. This study aims to empirically analyze the risk-return profile and the market efficiency of Bitcoin utilizing a 1,306-day data set conveniently subdivided into pre-pandemic and pandemic periods. The general conclusion of the study is: During the pandemic, Bitcoin is extremely volatile and does not subscribe to the efficient market hypothesis. © 2023 by De La Salle University.

SARS-CoV-2 Variants Impact on Key Signaling Pathways Metamorphoses into Severity

The Severe Acute Respiratory Syndrome Coronavirus-2 causes a dreadful Coronavirus Disease namely COVID-19. Respiratory system is the primary target of the virus. It also impairs other major organs such as kidney, heart, liver, brain etc. Multiple novel variants of SARS-CoV-2 have appeared since the SARS-CoV-2 pandemic occurred which are linked to increased virulence, disease transmission and severity. The virus attacks the host signalling pathways to maintain a favourable environment for its spread. The present study focuses on the comprehensive analysis of major signaling pathways affected due to several variants of SARS-CoV-2 leading to abnormalities in cell growth and differentiation. The information was curated from the weblinks of several platforms like WHO, CDC, PANGO, Nextstrain clade and GISAID clade. The data on signaling pathways and comorbidities was generated by screening of different research and review articles. SARS-CoV-2 consolidates the cytoskeleton of the host for effective cell invasion and modulates the transcription processes to enable the translation of viral protein(s). These events lead to significant increase and prolonged hyper inflammation. Further, a decreased interferon (IFN) response along with increased interleukin production leading to cytokine storm is observed. Deregulation of interleukin pathways, TNF-alpha signalling through JAK/STAT-3 signalling, MAPK1, mTOR, PI3K are few other signalling pathways that are affected on SARS-CoV-2 infection. This review represents a comprehensive analysis of the vigorous life cycle of SARS CoV-2, its different variants affecting host signalling pathways which eventually cause dysfunctioning of several organs and development of comorbidities.

Clinical characteristics of post-vaccination COVID-19 infection in health care workers exposed to Delta and Omicron variants in a COVID-19 dedicated facility from Qatar

Background: Evidence suggests that vaccines efficacy lies on the prevention of severe symptomatic disease. We aim to describe the clinical characteristics of COVID-19 infection among healthcare professionals (HCPs) after vaccination, during periods of transmission of SARS CoV-2 variants in a COVID-19 dedicated facility. Methods: A retrospective observational study of HCPs confirmed with COVID-19 during the period March 2021 to Jan 2022 was conducted. Delta period (March-August 2021), and Omicron period (Dec 2021-Jan 2022) were defined. Clinical, laboratory, radiology and vaccination history was collected from electronic medical records. Results: COVID-19 infection was reported in 16 and 138 HCPs during the Delta and Omicron period respectively. By category the nurses predominate, and a significant contribution of the healthcare related transmission against the community-related one. Higher frequency of loss of taste (37.5% vs 4.3%), and loss of smell (43.8% vs 3.6%) was observed during Delta period. Myalgia (12.5% vs 37.7%), and sore throat (6.3% vs 55.8%) predominated in Omicron period. Bilateral ground-glass appearance of the lung was observed in 28.6% and 7.1% in the Delta and Omicron period, respectively. Higher cycle threshold values of the polymerase chain reaction test during Omicron period, in comparison with Delta period, was observed (22.98 vs 25.98). Time from previous vaccine dose to positive laboratory test was longer during the Delta period (131 vs 98.26 days). Conclusion: SARS CoV-2 viral variants infections in HCPs were associated to selected clinical and epidemiological characteristics, with less severe disease for Omicron variant, and potential shorter duration of the immune response to vaccination. © 2020 The author (s)..

Clinical characteristics of nucleic acid negative neonates delivered by pregnant women infected with SARS-CoV-2 in Sanya, Hainan

Objective: To explore the clinical characteristics of nucleic acid negative newborns delivered by pregnant women infected with SARS-CoV-2 (Omicron variant BA. 5.1.3) in Sanya area, and to provide evidence for understanding its clinical characteristics. Methods: A retrospective analysis was performed on 14 neonates with negative nucleic acid delivered by pregnant women who tested positive for SARS-CoV-2 (Omicron variant BA.5.1.3) in Sanya Central Hospital (the Third People's Hospital of Hainan Province) from June 2022 to September 2022 (observation group, n=14). The corresponding nucleic acid-negative newborns delivered by pregnant women detected negative with SARS-CoV-2 (Omicronon variant strain BA.5.1.3) were set as the control group (n=56), and the general data and clinical characteristics of neonates in the two groups were compared. Results: There was no significant difference between the observation group and the control group in pregnancy diabetes, pregnancy induced hypertension, gestational pre-eclampsia, fetal intrauterine distress, premature rupture of membranes (P > 0.05);there was no significant difference between the observation group and the control group in terms of sex, gestational age, birth weight, age, mode of delivery, birth Apgar score, heart screening, pulmonary disease, glucose 6-phosphate dehydrogenase (G6PD) deficiency, thalassemia, breast milk jaundice, hemolytic jaundice (P > 0.05). The bilirubin level, blue light irradiation cases and the duration of blue light irradiation of the newborns in the observation group at 7 days after birth were higher than those in the control group (P < 0.05);the ratio of blood oxygen saturation 90% in the observation group was lower than that in the control group (21.43% vs 89.29%, P < 0.05), and the ratio of blood oxygen saturation occasionally<90% was higher than that in the control group (57.14% vs 10.71%, P < 0.05). The ratio of blood oxygen saturation<90% had no significant difference compared with that in the control group (7.14% vs 0, P > 0.05), and the ratio of blood oxygen saturation reduced to the required oxygen uptake was higher than that in the control group (14.29% vs 0, P < 0.05). Conclusions: The jaundice manifestation of the nucleic acid-negative newborns delivered by pregnant women infected with SARS-CoV-2 (Omicronon variant strain BA.5.1.3) in Sanya area is relatively obvious, with blood oxygen saturation easily lower than 90% and even requiring oxygen inhalation in severe cases.

Genetic Analysis and Epitope Prediction of SARS-CoV-2 Genome in Bahia, Brazil: An In Silico Analysis of First and Second Wave Genomics Diversity

COVID-19 is an infectious disease caused by SARS-CoV-2. This virus presents high levels of mutation and transmissibility, which contributed to the emergence of the pandemic. Our study aimed to analyze, in silico, the genomic diversity of SARS-CoV-2 strains in Bahia State by comparing patterns in variability of strains circulating in Brazil with the first isolated strain NC_045512 (reference sequence). Genomes were collected using GISAID, and subsequently aligned and compared using structural and functional genomic annotation. A total of 744 genomes were selected, and 20,773 mutations were found, most of which were of the SNP type. Most of the samples presented low mutational impact, and of the samples, the P.1 (360) lineage possessed the highest prevalence. The most prevalent epitopes were associated with the ORF1ab protein, and in addition to P.1, twenty-one other lineages were also detected during the study period, notably B.1.1.33 (78). The phylogenetic tree revealed that SARS-CoV-2 variants isolated from Bahia were clustered closely together. It is expected that the data collected will help provide a better epidemiological understanding of the COVID-19 pandemic (especially in Bahia), as well as helping to develop more effective vaccines that allow less immunogenic escape. [ FROM AUTHOR] Copyright of COVID is the property of MDPI and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full . (Copyright applies to all s.)

The Road Ahead (Editors)

This final chapter of the book "Frontiers of COVID-19: Scientific and Clinical Perspectives of the Novel SARS-CoV-2" takes the contents of the book and lesson learned of the clinical and epidemiological aspects of COVID-19 to the next level and provides guidelines and the road map into the future, beyond COVID-19. The aim is to present the most recent understanding of the fast-changing dynamics of COVID-19 and to help our clinicians and physicians better prepare for the road ahead. © The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Switzerland AG 2022.

Bivalent COVID-19 vaccine antibody responses to Omicron variants suggest that responses to divergent variants would be improved with matched vaccine antigens.

We compared neutralizing antibody responses to BA.4/5, BQ.1.1, XBB, and XBB.1.5 Omicron SARS-CoV-2 variants after a bivalent or ancestral COVID-19 mRNA booster vaccine or post-vaccination infection. We found that the bivalent booster elicited moderately high antibody titers against BA.4/5 that were approximately two-fold higher against all Omicron variants than titers elicited by the monovalent booster. The bivalent booster elicited low but similar titers against both XBB and XBB.1.5 variants. These findings inform risk assessments for future COVID-19 vaccine recommendations and suggest that updated COVID-19 vaccines containing matched vaccine antigens to circulating divergent variants may be needed.

[COVID-19 vaccination in children and adolescents]. / COVID-19-Impfung bei Kindern und Jugendlichen: Hatten wir alles im Blick?

Background: The COVID-19 pandemic posed special challenges for the existing structures for vaccination prevention in Germany with respect to 1) understanding the role and aims of those involved and the interests of the children and 2) the definition of adequate criteria and assessment of the risk of severe diseases in children. Objectives: Do the priorities of different groups of interest differ in the recommendations for COVID-19 vaccination? Which data on the pathogenicity of different variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV­2) are necessary and how did they change during the pandemic? Methods: The tasks, objectives and perception of politics and the German national vaccination advisory committee regarding vaccination of children are discussed in the face of summarized recent data on clinical manifestations of pediatric SARS-CoV­2 infections among children and adolescents in Germany, which could be estimated by combining different German data sources. Results: The perspectives of politics and children differ but are legitimate when they are clearly stated. The decisive risk for a severe course or the pediatric inflammatory multisystem syndrome temporally associated with SARS-CoV­2 (PIMS-TS) per 10,000 SARS-CoV­2 infections for the decision on vaccination from the perspective of children, decreased during the course of the pandemic with dominance of the omicron variant. Severe courses of COVID-19 still predominantly affect children with underlying diseases. The age-stratified analysis of vaccinated and nonvaccinated children showed that the alterations in the pathogenicity of the virus in the course of the pandemic is particularly reflected in the reduction in the risk of PIMS-TS. The general reduction of severe courses of COVID-19 again can be explained by the characteristics of variants of concern (VOC) as well as increasing vaccination rates and immunity following a SARS-CoV­2 infection. Conclusion: The primary goal of COVID-19 vaccination in children and adolescents is the prevention of severe courses of the disease. In pediatric risk groups the best possible immunity or immune protection by vaccination should be strived for. It is currently unclear whether catch-up vaccination in already infected or vaccinated children or whether forthcoming healthy children will need vaccination, aiming for hybrid immunity.

Angiotensin-converting enzyme 2 (ACE2) polymorphisms and susceptibility of severe SARS-CoV-2 in a subset of Pakistani population.

Science is digging for the varied presentation of COVID-19 patients exposed to the same risk factors, and medical conditions may be influenced by the presence of polymorphic genetic variants. This study investigated the link between ACE2 gene polymorphisms and the severity of SARS-CoV-2. This cross-sectional study recruited COVID-19 PCR-positive patients by consecutive sampling from Ziauddin Hospital from April to September 2020. DNA was extracted from whole blood, followed by gene amplification and Sanger's sequencing. Most of the patients, 77: 53.8%, were serious. Males were higher (80; 55.9%) with age more than 50 years (106: 74.1%). We found 22 ACE2 SNPs. rs2285666 SNP was most prevalent with 49.2% CC, 45.2% TT, 4.8% CT heterozygosity, and 0.8% AA genotypes. Variants with multiple genotypes were also insignificantly associated with the severity of COVID-19 in the analysis of the dominant model. Only rs2285666 had a significant statistical link with gender (p-value 0.034, OR; 1.438, CI; 1.028-2.011) while rs768883316 with age groups (p-value 0.026, OR; 1.953, CI; 1.085-3.514). Haplotypes ATC of three polymorphisms (rs560997634, rs201159862, and rs751170930) commonly found in 120 (69.77%) and TTTGTAGTTAGTA haplotype consisting of 13 polymorphisms (rs756737634, rs146991645, rs1601703288, rs1927830489, rs1927831624, rs764947941, rs752242172, rs73195521, rs781378335, rs756597390, rs780478736, rs148006212, rs768583671) in 112 (90.32%) had statistically significant association with the severity having p = value 0.029 and 0.001 respectively. Males of old age and diabetics are found to have more severe COVID-19 infection in the current study. We also found that common ACE2 polymorphism rs2285666 influences the susceptibility of acquiring the severe SARS-CoV-2 infection.

CoVEffect: interactive system for mining the effects of SARS-CoV-2 mutations and variants based on deep learning.

BACKGROUND: Literature about SARS-CoV-2 widely discusses the effects of variations that have spread in the past 3 years. Such information is dispersed in the texts of several research articles, hindering the possibility of practically integrating it with related datasets (e.g., millions of SARS-CoV-2 sequences available to the community). We aim to fill this gap, by mining literature abstracts to extract-for each variant/mutation-its related effects (in epidemiological, immunological, clinical, or viral kinetics terms) with labeled higher/lower levels in relation to the nonmutated virus. RESULTS: The proposed framework comprises (i) the provisioning of abstracts from a COVID-19-related big data corpus (CORD-19) and (ii) the identification of mutation/variant effects in abstracts using a GPT2-based prediction model. The above techniques enable the prediction of mutations/variants with their effects and levels in 2 distinct scenarios: (i) the batch annotation of the most relevant CORD-19 abstracts and (ii) the on-demand annotation of any user-selected CORD-19 abstract through the CoVEffect web application (http://gmql.eu/coveffect), which assists expert users with semiautomated data labeling. On the interface, users can inspect the predictions and correct them; user inputs can then extend the training dataset used by the prediction model. Our prototype model was trained through a carefully designed process, using a minimal and highly diversified pool of samples. CONCLUSIONS: The CoVEffect interface serves for the assisted annotation of abstracts, allowing the download of curated datasets for further use in data integration or analysis pipelines. The overall framework can be adapted to resolve similar unstructured-to-structured text translation tasks, which are typical of biomedical domains.

Reverse vaccinology-based prediction of a multi-epitope SARS-CoV-2 vaccine and its tailoring to new coronavirus variants.

The genome feature of SARS-CoV-2 leads the virus to mutate and creates new variants of concern. Tackling viral mutations is also an important challenge for the development of a new vaccine. Accordingly, in the present study, we undertook to identify B- and T-cell epitopes with immunogenic potential for eliciting responses to SARS-CoV-2, using computational approaches and its tailoring to coronavirus variants. A total of 47 novel epitopes were identified as immunogenic triggering immune responses and no toxic after investigation with in silico tools. Furthermore, we found these peptide vaccine candidates showed a significant binding affinity for MHC I and MHC II alleles in molecular docking investigations. We consider them to be promising targets for developing peptide-based vaccines against SARS-CoV-2. Subsequently, we designed two efficient multi-epitopes vaccines against the SARS-CoV-2, the first one based on potent MHC class I and class II T-cell epitopes of S (FPNITNLCPF-NYNYLYRLFR-MFVFLVLLPLVSSQC), M (MWLSYFIASF-GLMWLSYFIASFRLF), E (LTALRLCAY-LLFLAFVVFLLVTLA), and N (SPRWYFYYL-AQFAPSASAFFGMSR). The second candidate is the result of the tailoring of the first designed vaccine according to three classes of SARS-CoV-2 variants. Molecular docking showed that the protein-protein binding interactions between the vaccines construct and TLR2-TLR4 immune receptors are stable complexes. These findings confirmed that the final multi-epitope vaccine could be easily adapted to new viral variants. Our study offers a shortlist of promising epitopes that can accelerate the development of an effective and safe vaccine against the virus and its adaptation to new variants.Communicated by Ramaswamy H. Sarma.

In Silico Evaluation of SARS-CoV-2 K417N, L452R, and E484K Detection Assays Against Omicron Variants.

The study's objective was to assess whether the performance of the DIAGNOVITAL SARS-CoV-2 Mutation Detection Assays is affected by Omicron mutations. In silico evaluation of 67,717 Variant of Concern, Variant of Interest sequences and 6,612 sequences of the Omicron variants involving BA1., BA2., BA3 sub-lineages downloaded from the GISAID database by 17 December 2021, were performed. The sequences were aligned according to the reference genome MN908947.3 using MAFFT multiple sequence alignment software version 7. Our findings showed that among 6,612 Omicron, 41 Spike gene mutations with a frequency of ≥70% were identified. Some of the Omicron mutations (R408S, N440K, G446S, Q493S, Q498R) could affect the diagnostic performance of K417N, L452R, and E484K assays against the Omicron sub-lineages. However, L452R and K417N mutation tests allow differentiation of the Delta and Omicron variants mutation profile. The COVID-19 pandemic lasted longer than expected, and the rapid modification of diagnostic kits seems necessary to combat the pandemic.

Identification of differences in the magnitude and specificity of SARS-CoV-2 nucleocapsid antibody responses in naturally infected and vaccinated individuals.

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 analysed 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 to 297 and aa 365 to 388, 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.

[Molecular epidemiological analysis of SARS-CoV-2 genovariants in Moscow and Moscow region].

INTRODUCTION: SARS-CoV-2, a severe acute respiratory illness virus that emerged in China in late 2019, continues to spread rapidly around the world, accumulating mutations and thus causing serious concern. Five virus variants of concern are currently known: Alpha (lineage B.1.1.7), Beta (lineage B.1.351), Gamma (lineage P.1), Delta (lineage B.1.617.2), and Omicron (lineage B.1.1.529). In this study, we conducted a molecular epidemiological analysis of the most prevalent genovariants in Moscow and the region. The aim of the study is to estimate the distribution of various variants of SARS-CoV-2 in Moscow city and the Moscow Region. MATERIALS AND METHODS: 227 SARS-CoV-2 sequences were used for analysis. Isolation of the SARS-CoV-2 virus was performed on Vero E6 cell culture. Sequencing was performed by the Sanger method. Bioinformatic analysis was carried out using software packages: MAFFT, IQ-TREE v1.6.12, jModelTest 2.1.7, Nextstrain, Auspice v2.34. RESULTS: As a result of phylogenetic analysis, we have identified the main variants of the virus circulating in Russia that have been of concern throughout the existence of the pandemic, namely: variant B.1.1.7, which accounted for 30% (9/30), AY.122, which accounted for 16.7% (5/30), BA.1.1 with 20% (6/30) and B.1.1 with 33.3% (10/30). When examining Moscow samples for the presence of mutations in SARS-CoV-2 structural proteins of different genovariants, a significant percentage of the most common substitutions was recorded: S protein D614G (86.7%), P681H/R (63.3%), E protein T9I (20.0%); M protein I82T (30.0%), D3G (20.0%), Q19E (20.0%) and finally N protein R203K/M (90.0%), G204R/P (73.3 %). CONCLUSION: The study of the frequency and impact of mutations, as well as the analysis of the predominant variants of the virus are important for the development and improvement of vaccines for the prevention of COVID-19. Therefore, ongoing molecular epidemiological studies are needed, as these data provide important information about changes in the genome of circulating SARS-CoV-2 variants.

Comparative spatial transcriptomic profiling of severe acute respiratory syndrome coronavirus 2 Delta and Omicron variants infections in the lungs of cynomolgus macaques.

Recently emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variants are generally less pathogenic than previous strains. However, elucidating the molecular basis for pulmonary immune response alterations is challenging owing to the virus's heterogeneous distribution within complex tissue structure. Here, we revealed the spatial transcriptomic profiles of pulmonary microstructures at the SARS-CoV-2 infection site in the nine cynomolgus macaques upon inoculation with the Delta and Omicron variants. Delta- and Omicron-infected lungs had upregulation of genes involved in inflammation, cytokine response, complement, cell damage, proliferation, and differentiation pathways. Depending on the tissue microstructures (alveoli, bronchioles, and blood vessels), there were differences in the types of significantly upregulated genes in each pathway. Notably, a limited number of genes involved in cytokine and cell damage response were differentially expressed between bronchioles of the Delta- and Omicron-infection groups. These results indicated that despite a significant antigenic shift in SARS-CoV-2, the host immune response mechanisms induced by the variants were relatively consistent, with limited transcriptional alterations observed only in large airways. This study may aid in understanding the pathogenesis of SARS-CoV-2 and developing a clinical strategy for addressing immune dysregulation by identifying potential transcriptional biomarkers within pulmonary microstructures during infection with emerging variants.

Genomic surveillance of severe acute respiratory syndrome coronavirus 2 in Burundi, from May 2021 to January 2022.

BACKGROUND: The emergence and rapid spread of new severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) variants have challenged the control of the COVID-19 pandemic globally. Burundi was not spared by that pandemic, but the genetic diversity, evolution, and epidemiology of those variants in the country remained poorly understood. The present study sought to investigate the role of different SARS-COV-2 variants in the successive COVID-19 waves experienced in Burundi and the impact of their evolution on the course of that pandemic. We conducted a cross-sectional descriptive study using positive SARS-COV-2 samples for genomic sequencing. Subsequently, we performed statistical and bioinformatics analyses of the genome sequences in light of available metadata. RESULTS: In total, we documented 27 PANGO lineages of which BA.1, B.1.617.2, AY.46, AY.122, and BA.1.1, all VOCs, accounted for 83.15% of all the genomes isolated in Burundi from May 2021 to January 2022. Delta (B.1.617.2) and its descendants predominated the peak observed in July-October 2021. It replaced the previously predominant B.1.351 lineage. It was itself subsequently replaced by Omicron (B.1.1.529, BA.1, and BA.1.1). Furthermore, we identified amino acid mutations including E484K, D614G, and L452R known to increase infectivity and immune escape in the spike proteins of Delta and Omicron variants isolated in Burundi. The SARS-COV-2 genomes from imported and community-detected cases were genetically closely related. CONCLUSION: The global emergence of SARS-COV-2 VOCs and their subsequent introductions in Burundi was accompanied by new peaks (waves) of COVID-19. The relaxation of travel restrictions and the mutations occurring in the virus genome played an important role in the introduction and the spread of new SARS-COV-2 variants in the country. It is of utmost importance to strengthen the genomic surveillance of SARS-COV-2, enhance the protection by increasing the SARS-COV-2 vaccine coverage, and adjust the public health and social measures ahead of the emergence or introduction of new SARS-COV-2 VOCs in the country.