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Objective: COVID-19 has emerged as a significant global health crisis causing devastating effects on world population accounting for over 6 million deaths worldwide. Although acute RTI is the prevalent cause of morbidity, kidney outcomes centered on a spectrum of AKI have evolved over the course of the pandemic. Especially the emerging variants have posed a daunting challenge to the scientific communities, prompting an urging requirement for global contributions in understanding the viral dynamics. In addition to canonical genes, several subgroup- specific accessory genes are located between the S and E genes of coronaviruses regarding which little is known. Previous studies have shown that accessory proteins (aps) in viruses function as viroporins that regulate viral infection, propagation and egress [1]. In this study we attempted to characterize the function of aps of coronavirus variants as ion channels. Furthermore, we also probed the interaction of ap4 with the host system. Method(s): Serial passaging (selection pressure), growth kinetics, confocal imaging, genome sequence analysis and proteomics were performed in Huh-7, MRC5 cells and/or human monocyte derived macrophages. Potassium uptake assay was performed in a Saccharo myces cerevisiae strain, which lacks the potassium transporters trk1 and trk2. Ion conductivity experiments were performed in Xenopus laevis oocytes using Two Electrode Voltage Clamp (TEVC) method. Result(s): Serial passaging demonstrated the acquisition of several frameshift mutations in ORF4 resulting in C-terminally truncated protein versions (ap4 and ap4a) and indicate a strong selection pressure against retaining a complete ORF4 in vitro. Growth kinetics in primary cells illustrated a reduction of viral titers when the full-length ap4 was expressed compared to the C-terminally truncated protein ap4a. Confocal imaging showed that ap4 and ap4a are not exclusively located in a single cellular compartment. Potassium uptake assay in yeast and TEVC analyses in Xenopus oocytes showed that ap4 and ap4a act as a weak K+ selective ion channel. In addition, accessory proteins of other virus variants also elicited microampere range of currents. Conclusion(s): Our study provides the first evidence that ap4 and other accessory proteins of coronavirus variants act as viroporins. Future studies are aimed at demonstrating the role of ap4 during the viral life cycle by modulating ion homeostasis of host cell in vivo (interacting proteins obtained from proteomic studies) and thereby serve as a tool for potential drug target.
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Introduction/Objective In both the past and for the foreseeable future, SARS-CoV-2 (the coronavirus that causes COVID-19 disease) will continue to evolve. This evolution has already and will lead to new variants that will then cause surges of infection. These outbreaks in the past with the variant responsible have previously been reported individually. However, a timeline perspective on the changing SARS-CoV-2 variant landscape is sparse in the literature, particularly for testing performed at a Veteran Affairs Medical Center (VAMC). The Veteran population has increased comorbidities compared to the general population leading to susceptibility to infection including SARS-CoV-2. Hence, it is of utmost importance to explore the trending variants of SARS-CoV-2 in the veteran population as this epidemiological information may help in preventing transmission, which remains key in the management of COVID-19. Methods/Case Report Samples from selected patients from March 2021 to June 2022 who tested positive for SARS- CoV-2 by reverse transcriptase polymerase chain reaction with a cycle threshold or number <30 (required for sequencing) were sent for SARS-CoV-2 sequencing analysis. Results (if a Case Study enter NA) There were a total of 19 VAMC patients who were sequenced during the entire study period (March 2021 to June 2022). From March to May 2021, there were 8 patients, from which 6 demonstrated Pango Lineage B.1.1.7, 1 demonstrated Pango Lineage B.1.526.1, and 1 demonstrated Pango Lineage B.1. Later in 2021 (August to October 2021), there were 4 patients all of which demonstrates the Delta variant;2 of these 4 demonstrated the Delta subvariant Pango Lineage AY.25 and the other 2 demonstrated Pango Lineage AY.44. By May to June 2022, there were 7 patients, all of whom demonstrated infection by the Omicron variant. Interestingly, 6 of these 7 patients demonstrated the newly emerging subvariant BA.2.12.1 and the remaining 1 demonstrated BA.2.9. Conclusion SARS-CoV-2 has continued to evolve throughout the course of the pandemic, which has led to variants and subvariants that have predominated for a time to cause an outbreak only to be replaced later by a different strain. This timeline epidemiological perspective demonstrates that the Veteran population has also been affected by the variants that have led to outbreaks in the past within the general population.
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The wholesale changes brought about by the COVID‐19 pandemic to men and women's paid work arrangements and work–family balance provide a natural experiment for testing the common elements of two theories, needs exposure (Schafer et al. Canadian Review of Sociology/Revue Canadienne De Sociologie, 57(4);2020:523–549) and parental proximity (Sullivan et al. Family Theory & Review, 2018;10(1):263–279) against a third theory also suggested by Schafer et al. (2020), and labelled in this article, entrenchment/exacerbation of gender inequality. Both needs exposure and parental proximity suggest that by being home because of the pandemic, in proximity to their children, fathers are exposed to new and enduring family needs, which may move them toward more equal sharing in childcare and other domestic responsibilities. By contrast to studies that have tested such theories using retrospective, self‐report survey data over a 2‐year period, we analyse more than a decade of time‐use diary data from the American Time Use Survey (ATUS) that covers the first 2 years of the pandemic. We model the secular and quarterly trends to predict what would have occurred in the absence of the pandemic, contrasting this to what indeed happened. Our analyses consider aggregate and individual impacts, using methods of sequence analysis, clustering, and matching. Among our results, we find that the division of childcare responsibilities did not become more equitable during the pandemic. Suggestions for future research are provided as are suggestions for the implementation of social policies that could influence greater gender equity in unpaid work and childcare. [ FROM AUTHOR] Copyright of International Journal of Social Welfare is the property of Wiley-Blackwell 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.)
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Introduction: Currently, isolated from SARS-CoV-2 virus exceed 600 million cases in the world. Objective(s): Isolation and characterization of the SARS-CoV-2 virus causing COVID-19 at the beginning of the pandemic in Peru. Method(s): Twenty nasal and pharyngeal swab samples were isolated from SARS-CoV-2 using two cell lines, Vero ATCC CCL-81 and Vero E-6;virus identification was performed by RT-PCR and the onset of cytopathic effect (CPE) was evaluated by indirect immunofluorescence and subsequent identification by genomic sequencing. One of the most widely circulating isolates were selected and named the prototype strain (PE/B.1.1/28549/2020). Then 10 successive passages were performed on Vero ATCC CCL-81 cells to assess mutation dynamics. Result(s): Results detected 11 virus isolates by cytopathic effect, and subsequently confirmed by RT-PCR and indirect immunofluorescence. Of these, six were sequenced and identified as the lineages B.1, B.1.1, B.1.1.1, and B.1.205 according to the Pango lineage nomenclature. The prototype strain corresponded to lineage B.1.1. The analysis of the strains from the successive passages showed mutations mainly at in the spike (S) protein of the virus without variation in the identity of the lineage. Conclusion(s): Four lineages were isolated in the Vero ATCC CCL-81 cell line. Subcultures in the same cell line showed mutations in the spike protein indicating greater adaptability to the host cell and variation in pathogenicity in vitro, a behavior that allows it to have more survival success.Copyright © 2023 Anales de la Facultad de Medicina. All rights reserved.
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Using data from 14 waves (2003-2016) of the Korean Labor and Income Panel Study (KLIPS) (N = 1,627 individuals aged 45-64; 22778 observations), in this study, we conducted sequence analysis and a multi-categorical variable mediation analysis (1) to examine to what extent long-term work histories exhibit varying degrees of de-standardization and precariousness using sequence analysis (2) to explore the potential mediating effects of work, material, and social environments in the association between multiple work sequences and self-rated health. We found the coexistence of a relatively stable long-term employment pattern and a high prevalence of precariousness. The health and economic risks of precarious work fall disproportionately on older workers. Future researchers should continue to analyze whether the COVID-19 pandemic will lead to long-term changes in the workforce to improve our understanding of and response to working in later life and its health effects.
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Intro: In Australia, the main methods to diagnose COVID-19 are through rapid antigen tests (RATs) and through nucleic acid amplification testing (NAAT, including polymerase chain reaction) on healthcare worker (HCW)-collected combined nose/throat swabs. With self-collection widely used by the public for RATs, the aim of this study was to evaluate the performance of self-collected samples using commercial NAAT for SARS-CoV-2. Method(s): Consenting participants aged 14 years and older were provided with a self-collection pack containing instructions and either a FLOQSwab (Copan) or a Rhinoswab (Rhinomed). Participants collected their own nasal sample unsupervised prior to having a HCW-collected combined nose and throat swab taken for standard of care NAAT. Paired self-collected and HCW samples were tested on the cobas SARS-CoV-2 assay (Roche) and the Aptima SARS-CoV-2 assay (Hologic). Finding(s): We demonstrated comparable sensitivity, specificity, and agreement between self-collected nasal and Rhinoswab samples, compared to HCW- collected samples tested using the cobas SARS-CoV-2 and Aptima SARS-CoV-2 assays. In our study the clinical performance of self-collected specimens was comparable to HCW-collected samples, with both self-collect nasal and Rhinoswab samples resulting in 90-95% sensitivity, and in most cases >95% specificity. Discussion(s): Without the availability of samples for NAAT the ability to perform genomic testing is limited, reducing surveillance and public health investigations. We showed that genomic sequencing from self-collected samples can correctly identify the virus lineage and that the main determination of successful genomic testing is a high viral load rather than collection method. Conclusion(s): These data support self-collection as an accessible method for community testing for COVID-19 and introduces a novel collection device, the Rhinoswab as an alternative to the standard nasal swab. The testing method of self-collection can be expanded from the widely used RATs to NAAT and genomic testing which may inform the management and public health response to the COVID-19 pandemic.Copyright © 2023
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Humoral immunity is sensitive to evasion by SARS-CoV-2 mutants, but CD8 T cells seem to be more resistant to mutational inactivation. By a systematic analysis of 30 spike variant peptides containing the most relevant VOC and VOI mutations that have accumulated overtime, we show that in vaccinated and convalescent subjects, mutated epitopes can have not only a neutral or inhibitory effect on CD8 T cell recognition but can also enhance or generate de novo CD8 T cell responses. The emergence of these mutated T cell function enhancing epitopes likely reflects an epiphenomenon of SARS-CoV-2 evolution driven by antibody evasion and increased virus transmissibility. In a subset of individuals with weak and narrowly focused CD8 T cell responses selection of these heteroclitic-like epitopes may bear clinical relevance by improving antiviral protection. The functional enhancing effect of these peptides is also worth of consideration for the future development of new generation, more potent COVID-19 vaccines.
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Objective To identify the pathogen and track the genetic source of a cluster of cases with fever in a kindergarten in Fengtai district during the normalization of COVID-19 prevention and control in Beijing.Methods A descriptive analysis method was used to investigate this cluster of cases with fever in April 2021.Pharyngeal swabs were collected and viral nucleic acid was extracted, real-time PCR was performed to identify SARS-CoV-2 and other common respiratory virus. G gene of human metapneumovirus（hMPV） was amplified by RT-PCR and was then sequenced. BioEdit was used for G gene sequence analysis and the Neighbor-Joining model in MEGA 5. 0 software was used to construct the phylogenic tree of G gene. Results A total of 16 cases were reported in one class with the incidence of 53. 3%（16/30） during 8 days of a cluster outbreak. All pharyngeal swabs collected from 12 cases were tested SARS-CoV-2 negative, six were found to be hMPV positive by multiplex-PCR, and one was positive for both human adenovirus and hMPV. Full-length sequences of G genes were obtained from 2 strains of hMPV. Sequence analysis showed that both strains were hMPV B2 and the nucleic acid homology of G gene was 96. 73%-98. 01% with strains from Japan（LC337940, LC337935, LC1922349） in 2016 and over 98. 40%with strains from Shandong（OL625642, OL625644） in 2019, Henan MN944096 in 2019.Compared with the amino acid sequence of hMPV-B2 reference strain（AY297748）, six amino acid insertions containing EKEKEK were identified between 161-166 amino acid location and N-glycosylation of G protein analysis showed that the two strains had four N-glycosylation sites. Conclusions The leading pathogen for this cluster outbreak is found to be hMPV-B2, which are highly homologous with strains from Japan, Shandong and Henan. Therefore, a non-stop surveillance of hMPV is necessary during the normalization control and prevention period for COVID-19.
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In this study, the most recent American Time Use Surveys containing reported activity-based emotions and sensations information before (10,378 respondents in 2013) and during (6,902 respondents in 2021) the COVID-19 pandemic are used to assess if time use related individuals' subjective wellbeing (SWB) decreased in the pandemic. Given that the coronavirus has been shown to strongly influence activity decisions and social interactions, sequence analysis is applied to find daily time allocation patterns and changes in daily time allocation. Then, those derived daily patterns and other activity-travel factors, as well as social and demographic, temporal, spatial, and other contextual characteristics are added as explanatory variables in regression models of SWB measures. This provides a holistic framework of exploring the direct and indirect effects (via activity-travel schedules) of the recent pandemic on SWB while controlling for contexts such as the life assessments, daily schedule of activities, and living environment. The results show that respondents in the COVID year reported a new time allocation pattern that has a substantial amount of time at home, and they experienced more negative emotions. Three relatively happier daily patterns in 2021 contained substantial amounts of outdoor and indoor activities. In addition, no significant correlation was observed between metropolitan areas and individuals' SWB in 2021. However, comparisons among states show Texas and Florida residents experienced more positive wellbeing presumably due to fewer COVID-related restrictions.
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The COVID-19 pandemic has dramatically underlined the desperate need for novel therapeutic options for treatment of respiratory viral infections to provide fast and efficacious drugs against new upcoming pathogens. RNA interference (RNAi)-based approaches depict a promising alternative to conventional medication, as they can be rapidly adjusted to the respective viral genome or its host cellular interaction partners. Here, we pursued both strategies. We designed and screened nine siRNAs targeting the viral entry receptor ACE2. SiA1, (siRNA against exon1 of ACE2 mRNA) was most efficient, with up to 90 % knockdown of the ACE2 mRNA and protein for at least six days, as assessed by a specially designed fluorescent reporter assay. siA1 application was found to protect Vero E6 and Huh-7 cells from infection with SARS-CoV-2 with an up to ~92 % reduction of the viral burden. In parallel, we exploited the respective sequence in generation miR30a-embedded lentivirally or AAV encoded shRNAs, which performed equally powerful, with shA1 being the most potent. Since the RNA-encoded genome makes SARS-CoV-2 vulnerable to RNA interference (RNAi), we designed and analyzed eight siRNAs directly targeting the Orf1a/b region of the SARS-CoV-2 RNA genome, encoding for non-structural proteins (nsp). We identified siV1, which targets the nsp1-encoding sequence as particularly efficient. SiV1 inhibited SARS-CoV-2 replication in Vero E6 or Huh-7 cells by more than 99 % or 97 %, respectively. It neither led to toxic effects nor induced type I or III interferon production. Of note, sequence analyses revealed the target sequence of siV1 to be highly conserved in SARS-CoV-2 variants. Thus, our results identify the direct targeting of the viral RNA genome (ORF1a/b) by siRNAs as highly efficient and introduce siV1 as a particularly promising drug candidate for therapeutic intervention. Preliminary in vivo pilot experiments carried out in a K18-hACE-2 mice model showed first promising results. Thereby siRNAs complexed with nanoparticles (LP10Y) were applicated systemically by intravenous injection. Mice were intranasally infected with SARS-CoV-2, euthanized 48 hours later, and the viral burden was determined by RT-qPCR in lung homogenates. A positive trend in viral reduction was found in comparison to corresponding control group.
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The increase in human monkeypox virus (hMPXV) cases amidst the COVID-19 pandemic has raised fear among the general public. The monkeypox virus and the now-extinct smallpox virus belong to the orthopox family of viruses. Although first discovered in 1958, Monkeypox was only well recognized outside the sub-Saharan African countries until the world experienced a monkeypox pandemic in May 2022. The virus is common in some areas of Africa and is often spread through close contact with an infected person or animal. However, recent international trade, travel, and tourism developments have caused viral outbreaks outside Africa. The most recent pandemic in 2022 has been strange because epidemiologists have not found a link between cases and the virus's ability to spread through sexual contact. The structural and pathogenic activities of the virus that attack host cells need to be better understood. Because of this, it is important to know how viruses and the immune system work together to develop effective ways to treat and prevent diseases. To summarize existing research on Monkeypox, we conducted a narrative review using the MEDLINE, EMBASE, PUBMED, and Scopus databases to look at simultaneous zoonotic pandemics caused by the SARS-CoV-2 or COVID-19 coronavirus and presented the most to date information on the symptoms, epidemiology, diagnosis, prevention, and treatment of Monkeypox. However, more research on epidemiological details, ecology, and virus biology in endemic areas is required to understand the virus better and prevent further human infection. This short review discusses the research results that have already been published about how the monkeypox virus affects humans. © 2023, Liaquat University of Medical and Health Sciences. All rights reserved.
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Whole-genome sequencing of upper respiratory tract specimens from patients with confirmed COVID-19 in Henan Province was performed to compare the performance of the Illumina and Oxford Nanopore sequencing platforms, thus providing a reference for whole-genome monitoring of the novel coronavirus (SARS-CoV-2). Ten samples from COVID-19 cases in Henan Province from June 2021 to January 2022 were collected and sequenced with Illumina and Nanopore high-through-put sequencing technology to obtain full genome sequences of the novel coronavirus, which were compared with the Wuhan reference sequence (Wuhan-Hu-1). Bioinformatics software (CLC) was used for sequence alignment analysis. Three of the ten samples were Omicron (BA.1) variants with 55,61 nucleotide variation sites. One sample was an Alpha (B.1.1.7) variant with 41 nucleotide variation sites. Six samples were Delta (8.1.617.2) variants with 35,42,47 nucleotide variation sites. The sequence identity of mutation sites in six samples was 100%, and the mutation sites in the S genome segment of seven samples were consistent. For samples with a Ct value < 33, both next-generation and third-generation sequencing achieved high genome coverage and sequencing depth. A significant difference in coverage was observed between second-generation sequencing and third-generation sequencing (t=-2.037, P < 0.06). However, the coverage at different time points of the third-generation sequencing did not significantly differ (F=2.498, P > 0.05). The needs for SARS-CoV-2 mutant detection could be met through use of either high-throughput sequencing platform. The identification of mutations in the novel coronavirus through Illumina high-throughput sequencing was more accurate, whereas Nanopore high-throughput sequencing technology could be used for rapid detection and typing of different novel coronaviruses.
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The ongoing SARS-CoV-2 pandemic demonstrates the utility of real-time sequence analysis in monitoring and surveillance of pathogens. However, cost-effective sequencing requires that samples be PCR amplified and multiplexed via barcoding onto a single flow cell, resulting in challenges with maximising and balancing coverage for each sample. To address this, we developed a real-time analysis pipeline to maximise flow cell performance and optimise sequencing time and costs for any amplicon based sequencing. We extended our nanopore analysis platform MinoTour to incorporate ARTIC network bioinformatics analysis pipelines. MinoTour predicts which samples will reach sufficient coverage for downstream analysis and runs the ARTIC networks Medaka pipeline once sufficient coverage has been reached. We show that stopping a viral sequencing run earlier, at the point that sufficient data has become available, has no negative effect on subsequent down-stream analysis. A separate tool, SwordFish, is used to automate adaptive sampling on Nanopore sequencers during the sequencing run. This enables normalisation of coverage both within (amplicons) and between samples (barcodes) on barcoded sequencing runs. We show that this process enriches under-represented samples and amplicons in a library as well as reducing the time taken to obtain complete genomes without affecting the consensus sequence.
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MOTIVATION: Viruses have coevolved with their hosts for over millions of years and learned to escape the host's immune system. Although not all genetic changes in viruses are deleterious, some significant mutations lead to the escape of neutralizing antibodies and weaken the immune system, which increases infectivity and transmissibility, thereby impeding the development of antiviral drugs or vaccines. Accurate and reliable identification of viral escape mutational sequences could be a good indicator for therapeutic design. We developed a computational model that recognizes significant mutational sequences based on escape feature identification using natural language processing along with prior knowledge of experimentally validated escape mutants. RESULTS: Our machine learning-based computational approach can recognize the significant spike protein sequences of severe acute respiratory syndrome coronavirus 2 using sequence data alone. This modelling approach can be applied to other viruses, such as influenza, monkeypox and HIV using knowledge of escape mutants and relevant protein sequence datasets. AVAILABILITY: Complete source code and pre-trained models for escape prediction of severe acute respiratory syndrome coronavirus 2 protein sequences are available on Github at https://github.com/PremSinghBist/Sars-CoV-2-Escape-Model.git. The dataset is deposited to Zenodo at: doi: 10.5281/zenodo.7142638. The Python scripts are easy to run and customize as needed. CONTACT: premsing212@jbnu.ac.kr.
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COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , COVID-19/genetics , Antibodies, Neutralizing , Mutation , Amino Acid SequenceABSTRACT
Coronaviruses are a leading cause of emerging life-threatening diseases, as evidenced by the ongoing coronavirus disease pandemic (COVID-19). According to complete genome sequence analysis reports, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which causes COVID-19, has a sequence identity highly similar to the earlier severe acute respiratory syndrome coronavirus (SARS-CoV). The SARS-CoV-2 has the same mode of transmission, replication, and pathogenicity as SARS-CoV. The SARS-CoV-2 spike protein's receptor-binding domain (RBD) binds to host angiotensin-converting enzyme-2 (ACE2). The ACE2 is overexpressed in various cells, most prominently epithelial cells of the lung (surface of type 1 and 2 pneumocytes), intestine, liver, kidney, and nervous system. As a result, these organs are more vulnerable to SARS-CoV-2 infection. Furthermore, renin-angiotensin system (RAS) blockers, which are used to treat cardiovascular diseases, intensify ACE2 expression, leading to an increase in the risk of COVID-19. ACE2 hydrolyzes angioten-sin-II (carboxypeptidase) to heptapeptide angiotensin (1-7) and releases a C-terminal amino acid. By blocking the interaction of spike protein with ACE2, the SARS-CoV-2 entry into the host cell and inter-nalization can be avoided. The pathogenicity of SARS-CoV-2 could be reduced by preventing the RBD from attaching to ACE2-expressing cells. Therefore, inhibition or down-regulation of ACE2 in host cells represents a therapeutic strategy to fight against COVID-19. However, ACE2 plays an essential role in the physiological pathway, protecting against hypertension, heart failure, myocardial infarction, acute respiratory lung disease, and diabetes. Given the importance of ACE's homeostatic role, targeting of ACE2 should be realized with caution. Above all, focusing on the SARS-CoV-2 spike protein and the ACE2 gene in the host cell is an excellent way to avoid viral mutation and resistance. The current review summarises the sequence analysis, structure of coronavirus, ACE2, spike protein-ACE2 complex, essential structural characteristics of the spike protein RBD, and ACE2 targeted approaches for anti-coronaviral drug design and development.Copyright © 2022 Bentham Science Publishers.
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Genome sequence analysis of Atlantic salmon bafinivirus (ASBV) revealed a small open reading frame (ORF) predicted to encode a Type I membrane protein with an N-terminal cleaved signal sequence (110 aa), likely an envelope (E) protein. Bioinformatic analyses showed that the predicted protein is strikingly similar to the coronavirus E protein in structure. This is the first report to identify a putative E protein ORF in the genome of members of the Oncotshavirus genus (subfamily Piscavirinae, family Tobaniviridae, order Nidovirales) and, if expressed would be the third family (after Coronaviridae and Arteriviridae) within the order to have the E protein as a major structural protein.Copyright © 2021 by the authors. Licensee MDPI, Basel, Switzerland.
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Coronavirus disease 2019 named COVID-19 caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been reported in Wuhan city of Hubei Province of China become a global pandemic. Genomic sequencing of SARS-CoV-2 unveils which showed multiple mutations relative to SARS-CoV. SARS-CoV-2 showed a very high receptor-binding domain (RBD) affinity towards the ACE-2 receptor in host cells, similar to SARS. Lack of immediate supervision and diagnostic measures hurdles prevention and treatment strategies against COVID-19. However, from SARS and MERS epidemics, WHO launched SOLIDARITY, a strategic and technical advisory group for infection hazards (STAG-IH) for the regular supervision and alert, which identified the estimated risk of COVID-19 and recommended the health emergence program to respond COVID-19. This article will briefly review the rationale history, structural genome with mutation, pathogenesis, preventive measure, and targeted treatment strategy to handle this pandemic COVID-19.Copyright © 2021 Bentham Science Publishers.
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The ongoing COVID-19 pandemic reminded once again that microbiological diagnostic methods are irreplaceable in both diagnosing and detecting asymptomatic persons. At present, real-time reverse transcriptase polymerase chain reaction (RT-PCR) is the gold standard method for diagnosing COVID-19, but the test's accuracy varies in sample quality. Especially in the last stages of the disease, negative results of nasopharyngeal or oropharyngeal swab samples or rapid antigen tests do not necessarily mean that these patients do not carry the virus. Considering that a significant number of COVID-19 patients need intensive care and mechanical ventilation in the late period, which sample should be taken from where and when should be evaluated. Lower respiratory tract samples have a more significant chance of finding viral RNA than upper respiratory tract samples. Technical recommendations and the virological diagnostic methodologies and used in the intensive care unit of patients infected with SARS-CoV-2 are summarized in this article. We aimed to emphasize the need to get a sample from the right place at the right time for a reliable virological diagnosis.Copyright © 2022 by The Cardiovascular Thoracic Anaesthesia and Intensive Care.
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Genetic sequencing is a scientific process of reading genetic material using advanced technology. Through genetic sequencing, we can better comprehend super-spreader events and outbreaks, and strengthen national public health responses. A better understanding of the transmission of viruses, the severity of patient illness, and mortality rates can be gained by combining this information with that from the IDSP and patient reports. Connecting the dots between the data and the host's genetics, immunology, clinical outcomes, and risk factors is also possible. Many roadblocks must be overcome before raw sequence data can be put to direct clinical application. Since DNA sequencing has so many potential applications in the field of nursing, it ought to be a required topic for students in the profession. Group wellness Preparing patients for procedures, identifying those most at risk, doing sentinel surveillance, and conducting in-depth studies are all areas in which nurses can be of assistance. The goals of this paper are twofold: (1) to present the notion of genetic sequencing and (2) to highlight the role of Community health nurses. To reduce the impact of pandemics and endemics and improve nursing care, Western countries are seeing an uptick in the participation of nurse scientists in genetic sequencing;the case of newborn screening provides a particularly apt example.Copyright © 2023, Institute of Medico-legal Publication. 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.