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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first detected in December 2019, and shortly after pandemic has been declared by the World Health Organization (WHO) due to its unstoppable global spread. Considerable amount of effort has beenput around the World in order to develop a safe and effective vaccine against SARS-CoV-2. Inactivated and RNA vaccines have already passed phase three studies showing sufficient efficacy and safety, respectively. Nowadays, there is a noticeable dominance of SARS-CoV-2 variants with various mutations over the wild type SARS-CoV-2. However, there is no report showing the efficacy of these vaccines on these variants. This case study describes a thirty-eight-year-old male reported to be infected with SARS-CoV-2 alpha variant following two doses of inactive CoronaVac administration with a protective level of SARS-CoV-2 specific antibodies. The variant analysis of the virus reported to be positive for N501Y mutation.This is the first case in the literature demonstrating that inactive SARS-CoV-2 vaccine might have a lower efficacy on alpha variant.Copyright © 2022 Cenk Serhan Ozverel et al., published by Sciendo.
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Introduction. The rapid spread of a new coronavirus infection among populations in many countries worldwide has contributed to the genetic evolution of the virus, resulting in the emergence of multiple genetic variants of the SARSCoV-2 coronavirus. Mutations in the viral genome can affect the ability of the virus to bypass the immune system and complicate development of diagnostic and prophylactic drugs. Data on the neutralizing activity of the sera obtained against previously circulating genetic variants of the virus in relation to current SARS-CoV-2 strains may serve as a scientific basis for the selection of the antigens in vaccine development. The aim of this work was to study cross-reactivity of SARSCoV-2 coronavirus strains belonging to different genetic variants, which were isolated in the territory of the Russian Federation during 2020-2022 in the neutralization reaction using mouse hyperimmune sera. Materials and methods. Ten strains of SARS-CoV-2 coronavirus belonging to different genetic variants were used (three non-VOC strains, alpha, beta, gamma, delta, delta+AY, omicron 1 and omicron 2). The hCoV-19/Australia/VIC01/2020 strain (Wuhan) was included in the study as a prototypical variant. BALBc mice were immunized with inactivated concentrated antigen mixed with a 1:1 adjuvant, which was a virus-like immunostimulatory complex based on Quillaja saponaria (Quillaja saponaria). The antibody titer was determined in the neutralization reaction. Results. Essential decrease of neutralizing ability of antibodies specific to non-vOC genetic variants of SARS-CoV-2 coronavirus was revealed against beta VOC and to a lesser degree against alpha and gamma VOC variants. The differences in the neutralizing activity level of antibodies for alpha and beta VOC variants are not significant among themselves, and with gamma VOC variants - there are no significant differences. Neutralizing ability of antibodies specific to delta VOC against alpha and beta VOC variants decreased 4-fold. Neutralizing activity of sera obtained to omicron 1 and 2 variants in relation to the prototype coronavirus variant was reduced 18-fold, to the gamma variant - 12-fold, to delta variants - more than 30-fold;for other variants it was even lower. Conclusions. The results obtained testify to the presence of cross-reactivity between strains of coronavirus belonging to genetic lines Wuhan, alpha, beta, gamma;it is weaker for delta variants. Mutations in the genome of VOC omicron variants led to a significant decrease in antigenic cross-links with earlier genetic variants of the coronavirus. These findings explain the low efficacy of vaccines based on the Wuhan strain, synthetic immunogens, and recombinant proteins based on it against omicron VOC variants, which have caused a rise in morbidity since early 2022, as well as cases of re-infection of humans with new genetic variants of the coronavirus.Copyright © 2023 Saint Petersburg Pasteur Institute. All rights reserved.
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Background: At the global level, the dynamics of the COVID-19 pandemic have been driven by several epidemiological waves, determined by the emergence of new SARS-CoV-2 variants from the original viral lineage from Wuhan, China. While the SARS-CoV-2 dynamic has been described globally, there is a lack of data from Sub-Saharan African. Method(s): A laboratory-based survey was conducted in Cameroon, from March 1, 2020 to March 30, 2022, through an assessment of the evolutionary patterns of SARS-CoV-2 lineages across the four COVID-19 waves in the country. Data on full-length sequencing from all four sequencing laboratories were consecutively entered into the GISAID platform. These data were downloaded, and the molecular phylogeny of the SARS-CoV-2 sequences was performed using Nexstrain. The Mann-Whitney U test was used to calculate the correlation between the duration of each outbreak and the number of confirmed cases and between hospitalised cases and CFR, with a p value < 0.05 considered statistically significant. Result(s): A total of 3,881 samples were successfully processed, of which 38.9% (n=1,509) using PCR mutation assay, 41.5% (n=1,612) using targeted sequencing, and 19.6% (n=760) using whole-genome sequencing. The mean age of the study population was 36 years (min-max: 2-86), and 45% were within the age range 26-45. Regarding gender distribution, 50.9% were male, and 49.1% were female. Phylogenetic analysis of the 760 whole-genome sequences generated from March 2020 to March 2022 revealed that the greater proportion of SARS-CoV-2 circulating in Cameroon belonged to the viral sub-lineages of the original strain from Wuhan (74%), 15% Delta variant, 6% Omicron variant, 3% Alpha variant and 2% Beta variant.The pandemic was driven by SARS-CoV-2 lineages of origin in Wave 1 (16 weeks, 2.3% CFR), the Alpha and Beta variants in Wave 2 (21 weeks, 1.6% CFR), Delta variants in Wave 3 (11 weeks, 2.0% CFR), and Omicron variants in Wave 4 (8 weeks, 0.73% CFR), with a declining trend over time (p=0.01208). Conclusion(s): In a nutshell, the SARS-CoV-2 epidemic in Cameroon appears to have been driven by the SARS-CoV-2 lineage of origin in Wave 1, the cointroduction of the Alpha and Beta variants in Wave 2, the Delta variant in Wave 3, and the Omicron variant in Wave 4, with an overall declining trend in the wave duration, confirmed cases and hospitalisations over time.The SARS-CoV-2 lineage of origin and the Delta variant appeared to be the drivers of COVID-19 severity in Cameroon.
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Currently, the variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the mainstream of COVID-19 in the world, are the omicron type SARS-CoV-2 BA.4 variant and BA.5 variant derived from the omicron variant. In Japan, the Pfizer/BioNTech COVID-19 vaccine (BNT162b2) and the Moderna COVID-19 mRNA-1273 vaccine, which were created based on the viral gene of the Wuhan-type SARS-CoV-2 B.1.1.7 variant, have been inoculated. Previous clinical studies have reported that vaccination with these mRNA-based COVID-19 vaccines secretes a large amount of anti-SARSCoV- 2 IgA, which is mucosal immunity, into breast milk. However, recent clinical studies revealed that SARS-CoV-2 BA.4 and BA.5 variants have possessed the ability to successfully circumvent anti-SARS-CoV-2 immune mechanisms conferred by COVID-19 vaccination or prior SARS-CoV-2 infection. Therefore, we investigated the affinity of anti-SARS-CoV-2 IgA (PDB:CV2.1169 and PDB: CR3022) against SARS-CoV-2 B.1.1.7 variant (PDB: 7QEZ_A), SARS-CoV-2 BA.4 variant and BA.5 variant (PDB: 7XNS) by in silico analysis. As a result of the in silico analysis, the affinity of IgA CV2.1169 for each SARS-CoV-2 variant (B.1.1.7 variant, BA.4 variant, BA.5 variant) was -15.92 Kcal/mol, -9.26 Kcal/mol, -8.94 Kcal/ mol. The affinities of IgA CR3022 for each SARS-CoV-2 variant (B.1.1.7 variant, BA.4 variant, BA.5 variant) were -16.35 Kcal/ mol, -9.85 Kcal/mol, and -9.24 Kcal/mol. In addition, IgA derived from individuals vaccinated with the Pfizer/BioNTech COVID-19 vaccine (BNT162b2) or the Moderna COVID- 19 mRNA-1273 vaccine was found to have no high affinity to the omicron type SARS-CoV-2 BA.4 and BA.5 variants. In other words, the anti-SARS-CoV-2 IgA (PDB: CV2.1169 and PDB: CR3022), which has strong binding power to Wuhan type SARS-CoV-2 B.1.1.7 variant, was found not to have a strong affinity for omicron type SARS-CoV- 2 BA.4 variant and the BA.5 variant. In Japan, it has been reported that the COVID-19 vaccine for omicron type SARS-CoV-2 BA.4 variant and BA.5 variant may be approved in November 2022. We hope that the new COVID-19 vaccine will become widespread. Funding(s): This research was performed with research funding from the following: Japan Society for Promoting Science for TH (Grant No. 19K09840), and Japan Science and Technology Agency for TH (Grant No. STSC20001). Acknowledgments: We thank all medical staff for providing medical care to this patient at the National Hospital Organization Kyoto Medical Center.Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.
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Objectives: We aimed to compare biomarkers of COVID-19 patients with the Alpha variant (B.1.1.7), the Delta variant (B.1.617), and no mutation detected in our study. Method(s): A total of 600 patients with positive COVID PCR test and Alpha, Delta variant and no mutation detected with Covid PCR mutation test were included in the study. Troponin I, creatinine, Alanine Aminotransferase (ALT), Aspartate Aminotransferase (AST), Lactate Dehydrogenase (LDH), fibrinogen, D-dimer, ferritin, number of lymphocytes, lymphocytes (%), platelet (PLT), mean platelet volume (MPV), platelet distribution width (PDW), trombosite ratio in the blood (PCT), C-reactive protein (CRP) values were analyzed retrospectively. The age, gender, and hospitalization of the patients were evaluated concurrently. Result(s): Age, troponin, creatinine, LDH, PLT, MPV, and D-dimer were laboratory parameters that vary significantly with COVID-19 virus mutation. Age, troponin, LDH, and MPV values were lower in patients with Delta variant according to patients with the Alpha variant. Lymphocytes (N) and lymphocytes (%) values were lower in hospitalized patients relative to outpatients while age, troponin, LDH, CRP, and D-dimer values were higher in hospitalized patients than outpatients irrespective of mutation. Creatinine values were higher only in hospitalized patients with no mutation detected while ferritin and fibrinogen values were higher in hospitalized patients with Delta variant and no mutation detected. Conclusion(s): Age, troponin, creatinine, LDH, PLT, MPV, D-dimer, fibrinogen, ferritin, CRP, lymphocytes (N), and lymphocytes (%) values can guide to evaluate the diagnosis and hospitalization of patients with future different mutations.Copyright © 2023 by Prusa Medical Publishing.
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Background: SARS-CoV-2 continues to change over time due to genetic mutations and viral recombination.1 Given the changing landscape of COVID-19 variants and availability of COVID-19 vaccinations, disease severity during acute infection has also been variable. However, most research related to COVID-19 to date has not focused on evaluating differences in outcomes by the dominant variant and the impact it might have on post-acute sequalae of COVID-19 (PASC). Method(s): We developed a data mart of electronic health record data pertaining to COVID-19 in a single North American metropolitan health system (RUSH University Medical Center). Patients were selected for analysis if they had at least one documented infection of COVID-19. Date ranges were established per dominant variant, and the date of diagnosis was matched to variant. Variants were determined by the most prominent variant of concern (VOC) circulating in the city of Chicago. Variants were categorized by the following by date ranges: Wildtype+D614G (3/7/20-3/20/21), Alpha (3/21/21-6/19/21), Delta (6/20/21-12/11/21), Omicron BA.1 (12/12/21-3/19/22), Omicron BA.2 (3/20/22- 6/18/22), and Omicron BA.4/BA.5 (6/19/22-present (9/30/22). Subsequent clinical outcomes were examined, including hospitalization, intensive care unit admission, or death. We characterized our sample by conducting descriptive statistics including frequency and percent of outcome by variant. Result(s): 44,499 patients were included in this analysis with 30.23% requiring hospitalization, 4.25% being admitted to intensive care unit (ICU), and 2.35% resulting in death. The greatest percentage of hospitalizations occurred with the Alpha variant at 41.88% (N=928), and the greatest percentage of ICU admissions (6.43%) and death (3.15%) occurred with the Delta variant. The latest Omicron variant (Wave 6) showed an increase in hospitalizations (35.18%), as compared to early Omicron waves (Wave 4 and 5) but maintained similar ICU rates. Death rates continued to decline during the Omicron waves (Table 1). Conclusion(s): Although Alpha and Delta variants seem to have more severe outcomes compared to other variants, it is important to note that COVID-19 prevention, treatment access, and management continues to change, potentially influencing how outcomes may differ over time. Future work should determine factors to adjust for when examining variant-level differences.
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The genetic evolution of SARS-CoV-2 began in February 2020, with G614 spike protein strains superseding D614 strains globally. Since then with each subsequent mutations, the SARS-CoV-2 variants of concern, namely Alpha, Beta, Gamma, Delta and Omicron, superseded the previous one to become the dominant strain during the pandemic. By the end of November 2022, the Omicron variant and its descendent lineages account for 99.9% of sequences reported globally. All five VOCs have mutations located in the RBD of the spike protein, resulting in increased affinity of the spike protein to the ACE2 receptors resulting in enhanced viral attachment and its subsequent entry into the host cells. In vitro studies showed the mutations in spike protein help increase the viral fitness, enhancing both transmissibility and replication. In general, Alpha, Beta, Gamma, and Delta variants, were reported with higher transmissibility of 43-90%, around 50%, 170-240%, or 130-170% than their co-circulating VOCs, respectively. The Omicron however was found to be 2.38 times and 3.20 times more transmissible than Delta among the fully-vaccinated and booster-vaccinated households. Even the SARS-Cov-2 Omicron subvariants appear to be inherently more transmissible than the ones before. With the broader distribution, enhanced evasion, and improved transmissibility, SARS-CoV-2 variants infection cause severe diseases due to immune escape from host immunity and faster replication. Reports have shown that each subsequent VOC, except Omicron, cause increased disease severity compared with those infected with other circulating variants. The Omicron variant infection however, appears to be largely associated with a lower risk of hospitalisation, ICU admission, mechanical ventilation, and even a shorter length of hospital stay. It has been shown that the relatively much slower replication of the Omicron variants in the lung, resulted in a less severe disease.Copyright © 2022, Malaysian Society of Pathologists. All rights reserved.
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Coronavirus disease 2019 (COVID-19) outbreak started in Wuhan, China when people started with the symptoms of respiratory disorder. The onset of this disease have symptoms like fever, dry cough, fatigue, and difficulty in breathing. The nature of SARS-CoV-2 seems highly contagious as it also can be spread with asymptomatically infected individuals. It has been more than a year which this outbreak have been announced as a pandemic by World Health Organization (WHO) due to major public health crisis and uncontrollable around the globe. Some countries have taken initiatives in inventing vaccines and step up in the clinical trial process since a vaccine is an all-powerful tool which it always been a saviour in fighting infectious disease. In searching for the vaccine, researchers had studied the previously published article of SARS-CoV or MERS as in the beginning, in light, there will be a suitable vaccine to fight this pandemic situation. Recent research on the vaccine has been tested to seek the right vaccine for COVID-19. This study is to focus on the current vaccine development against COVID-19 and to explore the potential vaccines' characteristics that have been studied by the previous proven research findings. This review was done based on the research articles and reviews published until the end of April 2021 through established scientific search engines and related scientific platforms based on the inclusion criteria with its related keywords like coronavirus, SARS-CoV-2, COVID-19 Vaccine, clinical trials, and COVID-19 vaccine development. This review summarized a few vaccine candidates that have entered clinical trials and some supported evidence from Phase I until Phase III clinical trial studies that have been published and reported. In this review, 12 vaccine candidates have the potential to against SARS-CoV-2. Thus, their vaccine platform, characteristic as well as its efficacy studies have been discussed.Copyright © RJPT All right reserved.
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The year 2020 was the most challenging period due to the havoc caused by the outbreak of novel coronavirus SARS-CoV-2. Scientists and researchers all around the world have endeav-ored every possible approach to find solutions in context to therapeutics and vaccines to control the spread of this life-threatening virus. The acceleration instigated by the outbreak of SARS-CoV-2 and its mutated strains has leveraged the use of numerous platform technologies for the development of vaccines against this unfathomable disease. Vaccines could play an important role in miti-gating the effects of COVID-19 and reducing the ongoing health crisis. Various innovative plat-forms like proteins, nucleic acids, viruses, and viral vectors have been exploited to fabricate vaccines depicting almost 90% of efficacy like BNT162b2, AZD1222, Ad5-nCoV, etc. Some of these vaccines are multipotent and have shown potent activity against newly emerged malicious strains of SARS-CoV-2 like B.1.351 and B.1.1.7. In this review article, we have gathered key findings from various sources of recently popularized vaccine candidates, which will provide an overview of potential vaccine candidates against this virus and will help the researchers to investi-gate possible ways to annihilate this menace and design new moieties.Copyright © 2022 Bentham Science Publishers.
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Background: Rhinovirus is the most common trigger for exacerbations of asthma. Alveolar macrophages (AM) are a major site of RV infection and can also be infected by SARS-CoV-2. The pandemic caused by the SARS-CoV-2 raised concerns that patients with severe asthma (SA) would be at particularly high risk of developing severe disease. To date, evidence for poor outcomes in asthma remains limited suggesting a differential immune response to these two viruses. Method(s): Alveolar macrophages (AM) were isolated from bronchoalveolar lavage samples from patients with SA and infected with RV (n=13), SARS-CoV-2 alpha (B.1.1.7) (n=9) and delta (B.1.627.2)(n=8) variants. Antiviral mediators representing NF-KB-induced interferon-driven mRNAs (IL6 and IL8, RIGI and MDA5, respectively) were measured by qPCR, normalised to GAPDH and compared between infected AM and controls. Result(s): RV infected AM showed significant increases in mRNA expression of RIGI (4.39 fold change +/-4.68, p<0.001 vs control), MDA5 (2.96 fold change +/- 2.93, p=0.002 vs control) and IL6 (1.88 fold change +/- 0.98, p=0.006) compared to AM treated with control media alone, whilst IL8 did not significantly change. However, AM infected with SARS-CoV-2 alpha or delta variants showed no difference in levels of antiviral mediators compared to controls. Longitudinal analysis of AMs infected with SARS-CoV-2 alpha or delta variants showed no antiviral response. Conclusion(s): AM from subjects with severe asthma produce a pattern of anti-viral responses following RV infection that is absent when exposed to SARS-CoV-2 variants currently in circulation.
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The Omicron variant of SARS-CoV-2 is a new variant of concern after Alpha, Beta, Gamma and Delta variants. The amino acid mutations in the viral antigens, especially in the receptor binding region (RBD) of spike protein, were significantly more than those of other variants, which lead to the significant increase of infectivity, transmissibility and immune escape of Omicron variant. In addition, those spike mutations impaired the protective effect of vaccination. When compared to the infection of other variants, the latency of Omicron variant infection was significantly shortened, and the pathogenicity decreased markedly, which is in consistence with the fact that the vast majority of infected individuals showed no symptoms or only mild disease. Exacerbations in patients infected by Omicron variant were often associated with the progress of underlying disease. Early detection and medical isolation of infected persons, careful personal protection measures to cut off transmission routes, and active vaccination to protect susceptible people are key measures to prevent the spread of Omicron variant epidemic. A small number of patients infected with Omicron variant may develop so-called long COVID-19, post-COVID-19 syndrome, or post-COVID-19 condition, which means that long-term follow-up is needed in those patients. Effective anti-Omicron variant therapy can shorten the course of infection, promote the recovery from infection, and also contribute to the control of infection. Therefore, the development of antiviral drugs with ideal cost-benefit ratio and convenient administration is one of the research hotspot in the future.Copyright © 2022 Authors. All rights reserved.
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Background: There is increasing evidence for aerosol-based transmission of SARS-CoV-2, with particulate matter (PM) a possible vector. Air surveillance is necessary to safeguard public spaces. Aim(s): To characterise SARS-CoV-2 distribution in aerosols collected in hospital and public spaces and determine best sampling methods for surveillance. Method(s): Over 8 months in 2021, 8 samplers collected liquid bioaerosols and size-fractioned particulate matter(PM) in hospitals (ICU, Respiratory ward and communal waiting areas), a London railway and underground station, a university, and a primary school. RNA was extracted from samples and RT-qPCR targeting the N-gene of SARSCoV-2 was performed. Samples were cultured on Vero cells. Result(s): 209 air samples were obtained with 20 positive for SARS-CoV-2. 15 positive samples were from hospitals, 10 from outpatient waiting areas (ED waiting area, Chemotherapy Day Unit), 2 of which had the B.1.1.7 mutation (alphavariant) on sequencing, and 5 positive samples from rooms housing SARS-CoV-2 positive patients on ICU and respiratory wards. 5 positive samples were obtained via a portable sampler on two separate journeys in a London underground carriage. SARS-CoV-2 was detected mostly in PM samplers (n=17) compared to liquid bioaerosol samplers (positive sample pick-up 13% vs 4%respectively), in fine particles <=2.5mum(PM2.5) in diameter (n=14). No samples were cultured on Vero cells. Conclusion(s): Size-fractioned particulate matter samplers may be more efficient than liquid bioaerosol samplers in detecting and monitoring SARS-CoV-2 in the air. SARS-CoV-2 is most detected on fine particles, giving support to PM2.5 acting as a vector for aerosol-based transmission.
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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing coronavirus disease 2019 (COVID-19), and SARS-CoV-2 variants pose an increased risk to global health. Therefore, monitoring of SARS-CoV-2 variants of concern (VOCs) is of high importance for the implementation of disease control methods, for timely public health decisions, and the development of vaccines against SARS-CoV-2 variants. In this study, which was performed before the delta and omicron variants of concern became dominant, a total of 111 SARS-CoV-2 positive samples from our hospital staff in Cologne, Germany, collected from March 2020 to May 2021 were analysed for VOCs. For determination of VOCs, mutation genotyping analysis (MGA) using mutation-specific simple (MSS) probes based on quantitative reverse transcription-polymerase chain reaction (RT-qPCR) of ten spike protein variants (SPVs) was performed. The MGA focuses on the detection of the spike protein mutation (SPM) of SPVs belonging to VOCs. By successful determination of SPV, the work concludes that 24.66 % of the samples belong to VOC B.1.1.7 and 1.37 % of the samples belong to VOC B.1.351. Based on these results, MGA proves to be a suitable alternative to sequencing technologies as it is a rapid, cost-effective, widely available, and feasible method that allows high sample throughput for the determination of circulating and monitored SARS-CoV-2 VOCs. With focus on the novel variants such as SARS-CoV-2 omicron BA.4 and BA.5 similar approaches could be used for a rapid initial screening, while, however, due to the increasing number of single nucleotide polymorphisms that determine the variants of concern in depth screening becomes more cost efficient by next generation sequencing.Copyright © 2022 AEPress, s.r.o.. All rights reserved.
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Background The spread of SARS-CoV-2 has become a global public health crisis. Nepal is facing the second wave of COVID-19 pandemic but, there is still a limited data on the genomic sequence of SARS-CoV-2 variants circulating in Nepal. Objective The objective of this study is to sequence the whole genome of SARS-CoV-2 in Nepal to detect possible mutation profiles and phylogenetic lineages of circulating SARS-CoV-2 variants. Method In this study, swab samples tested positive for SARS-CoV-2 were investigated. After RNA extraction, the investigation was performed through real-time PCR followed by whole genome sequencing. The consensus genome sequences were, then, analyzed with appropriate bioinformatics tools. Result Sequence analysis of two SARS-CoV-2 genomes from patient without travel history (Patient A1 and A2) were found to be of lineage B.1.1. Similarly, among other four samples from subjects returning from the United Kingdom, genomes of two samples were of lineage B.1.36, and the other two were of lineage B.1.1.7 (Alpha Variant). The mutations in the consensus genomes contained the defining mutations of the respective lineages of SARS-CoV-2. Conclusion We confirmed two genomic sequences of variant of concern VOC-202012/01 in Nepal. Our study provides the concise genomic evidence for spread of different lineages of SARS-CoV-2 - B.1.1, B.1.36 and B.1.1.7 of SARS-CoV-2 in Nepal.Copyright © 2021, Kathmandu University. All rights reserved.
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Introduction: A clinically significant variant of SARS-CoV-2 was identified in the UK in December 2020 and was designated VOC‐202012/01 (lineage B.1.1.7) on 14 December 2020. Our study aimed to evaluate the lineage B.1.1.7 prevalence over time and demographic, hematological, coagulation, inflammation characteristics in hospitalized patients with B.1.1.7 during February-March 2021. Materials and Methods: Between 5 February and 20 March 2021, 182 inpatients with B.1.1.7 were included in this study. Bio-Speedy, SARS-CoV-2 Double Gene RT-qPCR (Bioeksen, Ístanbul, Türkiye) kit was used to diagnose COVID-19. Cycle threshold< 27 samples were taken into mutation study with Bio-Speedy SARS-CoV-2 Variant Plus kit. Results: Of the 5187 SARS-CoV-2 positive cases, 2288 (69.65%) were evaluated as variant B.1.1.7 positive. Throughout the study, the case number's daily increase rate was 8.78% in SARS CoV-2, 13.16% in B.1.1.7;the case number's doubling time was calculated as 7.9 days in SARS CoV-2 and 5.27 days in B.1.1.7. In ICU patients, hemoglobin (p< 0.001), platelet (p= 0.034) and lymphocyte (p< 0.001) levels were lower but neutrophil (p= 0.025), monocyte/lymphocyte ratio (MLR) (p= 0.002), neutrophil/lymphocyte (NLR) (p< 0.001) ratio and D-dimer (p= 0.008) levels were dedected higher than non-ICU patients. Conclusion: Our study demonstrated that the infectiousness of B.1.1.7 was higher than previous variants and became the dominant SARS-CoV-2 in six weeks in our region. Therefore, urgent and decisive measures should be taken to minimize morbidity and mortality associated with COVID-19. In addition, our findings indicate that first hematologic markers of the patients can be an important biomarker for the prognosis of COVID-19 disease.
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BACKGROUND: Like other viral infections, severe acute respiratory syndrome coronavirus-2 infection could affect different human body systems, including host immune responses. Three years after its pandemic, we learn more about this novel coronavirus. As we expected, different co-infections with various organisms, such as viruses, bacteria, and even fungi, have been reported. However, concurrent infection with two severe acute respiratory syndrome coronavirus-2 strains and cytomegalovirus is extremely unusual. We have only a rudimentary understanding of such co-infections and their long-term consequences for patients with cancer. CASE PRESENTATION: An 18-year-old young Iranian adult with acute lymphoblastic leukemia presented with abdominal pain, diarrhea, nausea, and vomiting following a recent history of severe acute respiratory syndrome coronavirus-2 infection. The patient never experienced respiratory symptoms, and the chest imaging study was normal on admission. His primary laboratory investigation revealed prerenal azotemia and severe abnormal liver function tests (blood urea nitrogen 32 mg/dL, creatinine 1.75 mg/dL, prothrombin time 66 s, partial thromboplastin time 44.5 s, international normalized ratio 5.14, total bilirubin 2.9 mg/dL, and direct bilirubin 2.59 mg/dL). Cytomegalovirus disease was diagnosed by polymerase chain reaction in his blood and stool samples. The patient's gastrointestinal signs and symptoms improved shortly after receiving intravenous ganciclovir treatment. His gastrointestinal symptoms continued intermittently for weeks despite maintenance valganciclovir prescription, necessitating frequent hospitalizations. The patient was complicated by the recurrence of gastrointestinal symptoms during the sixth hospitalization, even though he had no respiratory symptoms, and the nasopharyngeal test revealed severe acute respiratory syndrome coronavirus-2 Wuhan strain for the first time. Remdesivir and valganciclovir were administrated due to persistent enteritis and evidence of intestinal tissue invasion by severe acute respiratory syndrome coronavirus 2 and cytomegalovirus on multiple intestinal biopsies, which led to partial clinical responses. Cytomegalovirus and severe acute respiratory syndrome coronavirus-2 fecal shedding continued for more than 6 months despite repeated antiviral therapy, and the Wuhan and Alpha strains were also detected in his nasopharyngeal samples through repeated sampling (confirmed by four nasopharyngeal sampling and multiple stool specimens and several intestinal biopsies). Finally, during the Delta-variant (B.1.617.2) outbreak in Iran, the patient was admitted again with febrile neutropenia and decreased level of consciousness, necessitating respiratory support and mechanical ventilation. During the Delta-variant peak, the patient's nasopharyngeal sample once more tested positive for severe acute respiratory syndrome coronavirus 2. The patient died a few days later from cardiopulmonary arrest. CONCLUSION: The coronavirus disease 2019 pandemic has encountered patients with cancer with critical diagnostic and treatment challenges. Patients who are immunocompromised may co-infect with multiple severe acute respiratory syndrome coronavirus-2 strains and cytomegalovirus, and even with timely diagnosis and treatment, the prognosis may be poor.
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COVID-19 , Coinfección , Infecciones por Citomegalovirus , Leucemia-Linfoma Linfoblástico de Células Precursoras , Masculino , Humanos , Adulto Joven , Adolescente , SARS-CoV-2 , Citomegalovirus , Valganciclovir , Irán , Infecciones por Citomegalovirus/complicaciones , Infecciones por Citomegalovirus/tratamiento farmacológico , Leucemia-Linfoma Linfoblástico de Células Precursoras/complicaciones , Leucemia-Linfoma Linfoblástico de Células Precursoras/tratamiento farmacológicoRESUMEN
Objectives: The aim is to investigate the usefulness of lactate dehydrogenase (LDH)/Albumin, LDH/Lymphocyte and LDH/Platelet ratios on the prognosis of coronavirus disease (COVID-19) Alpha (B.1.1.7) variant pneumonia. Method(s): A total of 113 patients who were diagnosed with COVID-19 pneumonia and 60 healthy control group were included in this study. The cases were divided into 2 as classic COVID-19 group, and COVID-19 B.1.1.7 variant group. Complete blood count (CBC) and biochemical parameters of the patients were analyzed retrospectively. Patients with COVID-19 B.1.1.7 variant group were also grouped according to the length of stay in the hospital and the days of hospitalization. Result(s): LDH/Albumin, LDH/Platelet, and LDH/Lymphocyte ratios were found to be higher in COVID-19 B.1.1.7 variant group when compared to the control group (p<0.001). The ferritin, neutrophils/lymphocyte (NLR) ratio, procalcitonin (PCT) and LDH/Albumin had the highest area under the curve (AUC) values in the COVID-19 B.1.1.7 variant group (0.950, 0.802, 0.759, and 0.742, respectively). Albumin, Lymphocytes and hemoglobin values were significantly higher in the COVID-19 B.1.1.7 variant group than in the classic COVID-19 group (p<0.05). Conclusion(s): LDH/Albumin and LDH/Lymphocyte ratios may be useful for clinicians in predicting the risk of progression to pneumonia in COVID-19 B.1.1.7 variant patients. Copyright © 2022 the author(s), published by De Gruyter.
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Background. One of Singapore's national strategies for the COVID-19 pandemic was containment. Efforts included a fourteen-day quarantine of close contacts, were subjected to an entry and exit SARS-CoV-2 PCR test, the latter being done between 11-14 days post exposure. Additionally, symptomatic contacts were tested for SARS-CoV-2. We aim to determine the trend in COVID-19 incubation periods during three distinct pandemic waves corresponding to different SARS-CoV-2 variants. Incubation Period Incubation period of the prevalent SARS-CoV-2 variant in circulation Methods. This is an ecological study and information collected from the SingHealth COVID-19 Registry, a database of all inpatients admitted to any of the SingHealth hospitals. For patients under quarantine, the start date of the quarantine period was assumed to be the last date of exposure to the index case. Incubation period was determined by the duration between date of exposure and date of the first positive SARS-CoV-2 PCR test. The prevalent strain in circulation was identified from the Singapore database in the GISAID collection. Only variants of concern, as categorized by WHO, Alpha (23rd Jan 2020 - 1st Mar 2021), Delta (5th May 2021 - 31st Oct 2021) and Omicron (1st Jan 2022 - Present) were considered. For the Omicron variant, quarantine was discontinued, hence the last date of arrival from international travel was assumed to be the date of exposure. Results. From January 2020 to March 2022, there were 19,905 patients in the COVID-19 registry, of whom 11,235 were under quarantine and 8,612 had preceding international travel. Of the 11,235 patients under quarantine, 8,189 patients were infected when SARS-CoV-2 Alpha variant and 3,046 patients were infected when SARS-CoV-2 Delta variant were in circulation. Of the 8,612 patients with preceding travel, 6,503 patients were infected when SARS-CoV-2 Omicron variant was in circulation. The median incubation period for the Alpha variant was 11 days (IQR: 7-14 days) versus 3 days (IQR: 2-4 days) for the Delta variant versus 3 days (IQR: 0-5 days) for the Omicron variant. Pairwise comparisons between the variants were (p-value = < .001) Conclusion. The significant differences between incubation periods of the SARS-CoV-2 variants in circulation poses a challenge to containment efforts and has emphasize the importance of dynamic national strategies.
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Objectives: Paediatric Multisystem Inflammatory Syndrome (PIMS-TS) is a rare life-threatening complication that typically occurs several weeks after SARS-CoV-2 infection in children and young people (CYP). We used national and regional-level data from the COVID-19 pandemic waves in England to develop a model to predict PIMS-TS cases. Methods: SARS-CoV-2 infections in CYP aged 0-15 years in England were estimated using the PHE-Cambridge real-time model. PIMS-TS cases were identified through the British Paediatric Surveillance Unit during (March-June 2020) and through Secondary Uses Services (SUS) from November 2020. A predictive model was developed to estimate PIMS-TS risk and lag times after SARS-CoV-2 infections. Results: During the Alpha wave, the model accurately predicted PIMS-TS cases (506 vs. 502 observed cases), with a median estimated risk of 0.038% (IQR, 0.037-0.041%) of paediatric SARS-CoV-2 infections. For the Delta wave, the median risk of PIMS-TS was significantly lower at 0.026% (IQR, 0.025-0.029%), with 212 observed PIMS-TS cases compared to 450 predicted by the model. Conclusions: The model accurately predicted national and regional PIMS-TS cases in CYP during the Alpha wave. PIMS-TS cases were 53% lower than predicted during the Delta wave. Further studies are needed to understand the mechanisms of the observed lower risk with the Delta variant.
RESUMEN
Critically ill patients infected with SARS-CoV-2 display adaptive immunity, but it is unknown if they develop cross-reactivity to variants of concern (VOCs). We profiled cross-immunity against SARS-CoV-2 VOCs in naturally infected, non-vaccinated, critically ill COVID-19 patients. Wave-1 patients (wild-type infection) were similar in demographics to Wave-3 patients (wild-type/alpha infection), but Wave-3 patients had higher illness severity. Wave-1 patients developed increasing neutralizing antibodies to all variants, as did patients during Wave-3. Wave-3 patients, when compared to Wave-1, developed more robust antibody responses, particularly for wild-type, alpha, beta and delta variants. Within Wave-3, neutralizing antibodies were significantly less to beta and gamma VOCs, as compared to wild-type, alpha and delta. Patients previously diagnosed with cancer or chronic obstructive pulmonary disease had significantly fewer neutralizing antibodies. Naturally infected ICU patients developed adaptive responses to all VOCs, with greater responses in those patients more likely to be infected with the alpha variant, versus wild-type.