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1.
Viruses-Basel ; 14(4):14, 2022.
Article in English | Web of Science | ID: covidwho-1820406

ABSTRACT

This study aimed to exercise the Sanger sequencing strategy for screening of variants among confirmed COVID-19 cases and validate our strategy against NGS strains in Hiroshima retrieved from GISAID. A total of 660 samples from confirmed COVID-19 cases underwent screening for variants by Sanger-based partial sequencing to the targeted spike gene (nt22,735 similar to nt23,532) using an in-house-developed primer set. The identification of variants was done by unique checkpoints of base nucleotide changes in the targeted spike gene. Moreover, we amplified one full-length genome using Sanger method and an in-house-developed primer library. Using NGS strains of the same sampling period from GISAID, a phylogenetic tree was constructed to examine the distribution pattern of variants in Hiroshima and to validate our Sanger method. The modified primer set provided 100% validation and 99.2% amplification. PANGO Lineage R.1 was detected in late in the third wave, followed by Alpha (B.1.1.7) domination in the fourth wave, Delta (B.1.617.2) domination in the fifth wave, and Omicron (B.1.1.529) domination in the sixth wave, and there was no significant difference in viral copies between variants (p = 0.09). The variants showed different transmission patterns, but the distribution of variants is consistent to that shown by the phylogenetic tree. The Sanger method also provided successful amplification of the full-length genome of the SARS-CoV-2 virus. Our Sanger sequencing strategy was useful for the screening of SASR-CoV-2 variants without the need for full-genome amplification. The modified primer set was validated to use universally, which allows an understanding of the variants' distribution in real time and provides the evidence for policy-making and the formulation or modification of preventive strategies.

2.
Viruses-Basel ; 14(4):10, 2022.
Article in English | Web of Science | ID: covidwho-1820405

ABSTRACT

Coronavirus disease 19 (COVID-19) clinical manifestations include the involvement of the gastrointestinal tract, affecting around 10% of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected children. In the present work, the consequence of a short time of viral absorption (5, 15, 30 and 60 min) was tested on the Caco-2 intestinal epithelial cell line. Our findings show that Caco-2 cells are highly permissive to SARS-CoV-2 infection, even after 5 min of viral inoculation at a multiplicity of infection of 0.1. No cytopathic effect was evident during the subsequent 7 days of monitoring;nevertheless, the immunofluorescence staining for the viral nucleocapsid confirmed the presence of intracellular SARS-CoV-2. Our findings highlight the very short time during which SARS-CoV-2 is able to infect these cells in vitro.

3.
Viruses-Basel ; 14(4):12, 2022.
Article in English | Web of Science | ID: covidwho-1820404

ABSTRACT

Recent research using UV radiation with wavelengths in the 200-235 nm range, often referred to as far-UVC, suggests that the minimal health hazard associated with these wavelengths will allow direct use of far-UVC radiation within occupied indoor spaces to provide continuous disinfection. Earlier experimental studies estimated the susceptibility of airborne human coronavirus OC43 exposed to 222-nm radiation based on fitting an exponential dose-response curve to the data. The current study extends the results to a wider range of doses of 222 nm far-UVC radiation and uses a computational model coupling radiation transport and computational fluid dynamics to improve dosimetry estimates. The new results suggest that the inactivation of human coronavirus OC43 within our exposure system is better described using a bi-exponential dose-response relation, and the estimated susceptibility constant at low doses-the relevant parameter for realistic low dose rate exposures-was 12.4 +/- 0.4 cm(2)/mJ, which described the behavior of 99.7% +/- 0.05% of the virus population. This new estimate is more than double the earlier susceptibility constant estimates that were based on a single-exponential dose response. These new results offer further evidence as to the efficacy of far-UVC to inactivate airborne pathogens.

4.
Viruses-Basel ; 14(4):20, 2022.
Article in English | Web of Science | ID: covidwho-1818212

ABSTRACT

Coronaviruses (CoVs) have caused several global outbreaks with relatively high mortality rates, including Middle East Respiratory Syndrome coronavirus (MERS)-CoV, which emerged in 2012, and Severe Acute Respiratory Syndrome (SARS)-CoV-1, which appeared in 2002. The recent emergence of SARS-CoV-2 highlights the need for immediate and greater understanding of the immune evasion mechanisms used by CoVs. Interferon (IFN)-alpha is the body's natural antiviral agent, but its Janus kinase/signal transducer and activators of transcription (JAK/STAT) signalling pathway is often antagonized by viruses, thereby preventing the upregulation of essential IFN stimulated genes (ISGs). Therapeutic IFN-alpha has disappointingly weak clinical responses in MERS-CoV and SARS-CoV-1 infected patients, indicating that these CoVs inhibit the IFN-alpha JAK/STAT pathway. Here we show that in lung alveolar A549 epithelial cells expression of MERS-CoV-nsp2 and SARS-CoV-1-nsp14, but not MERS-CoV-nsp5, increased basal levels of total and phosphorylated STAT1 & STAT2 protein, but reduced IFN-alpha-mediated phosphorylation of STAT1-3 and induction of MxA. While MERS-CoV-nsp2 and SARS-CoV-1-nsp14 similarly increased basal levels of STAT1 and STAT2 in bronchial BEAS-2B epithelial cells, unlike in A549 cells, they did not enhance basal pSTAT1 nor pSTAT2. However, both viral proteins reduced IFN-alpha-mediated induction of pSTAT1-3 and ISGs (MxA, ISG15 and PKR) in BEAS-2B cells. Furthermore, even though IFN-alpha-mediated induction of pSTAT1-3 was not affected by MERS-CoV-nsp5 expression in BEAS-2B cells, downstream ISG induction was reduced, revealing that MERS-CoV-nsp5 may use an alternative mechanism to reduce antiviral ISG induction in this cell line. Indeed, we subsequently discovered that all three viral proteins inhibited STAT1 nuclear translocation in BEAS-2B cells, unveiling another layer of inhibition by which these viral proteins suppress responses to Type 1 IFNs. While these observations highlight cell line-specific differences in the immune evasion effects of MERS-CoV and SARS-CoV-1 proteins, they also demonstrate the broad spectrum of immune evasion strategies these deadly coronaviruses use to stunt antiviral responses to Type IFN.

5.
Viruses ; 14(4):668, 2022.
Article in English | ProQuest Central | ID: covidwho-1810311

ABSTRACT

[...]in several instances, advanced genomic diagnostics tools such as high-throughput sequencing (HTS) offer biological insights into the genomic structure of a complex viral pathogen, which is critical to new pathogen diagnostic design and ongoing development and implementation of viral disease management strategies. Eight original articles in this Special Issue provide comprehensive information on the immense potential of HTS in unraveling damaging crop viral pathogens and further aspects of current and future principles of crop viral disease management. According to the study [10], when Bph3-carrying backcross healthy lines were infested with BPH, they depicted sterile characteristics such as panicle enclosure and failure of seed production at maturity stage, probably due to the BPH viral infections [10]. [...]turnip mosaic virus in canola is controlled effectively by planting crop cultivars with virus resistance genes, but there exists a challenge of resistance-breaking virus strains that can overcome the present crop resistance genes [11,12].

7.
J Clin Invest ; 2022.
Article in English | PubMed | ID: covidwho-1807770

ABSTRACT

The protective human antibody response to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus focuses on the spike (S) protein which decorates the virion surface and mediates cell binding and entry. Most SARS-CoV-2 protective antibodies target the receptor-binding domain or a single dominant epitope ('supersite') on the N terminal domain (NTD). Here, using the single B cell technology LIBRA-seq, we isolated a large panel of NTD-reactive and SARS-CoV-2 neutralizing antibodies from an individual who had recovered from COVID-19. We found that neutralizing antibodies to the NTD supersite commonly are encoded by the IGHV1-24 gene, forming a genetic cluster that represents a public B cell clonotype. However, we also discovered a rare human antibody, COV2-3434, that recognizes a site of vulnerability on the SARS-CoV-2 S protein in the trimer interface and possesses a distinct class of functional activity. COV2-3434 disrupted the integrity of S protein trimers, inhibited cell-to-cell spread of virus in culture, and conferred protection in human ACE2 transgenic mice against SARS-CoV-2 challenge. This study provides insight about antibody targeting of the S protein trimer interface region, suggesting this region may be a site of virus vulnerability.

8.
Archives of Disease in Childhood ; 105(7):i, 2020.
Article in English | ProQuest Central | ID: covidwho-1807342

ABSTRACT

[...]perhaps, to invert a Runsfeldianism, we also know more about what we don’t know… and the breadth of this month’s manuscripts testify to this: UK reference data ( see page 613 ), global health implications ( see page 616 and the WHO group, see page 620 ), the arguments around school closure ( see page 618 ), the disappearance of children from emergency departments ( see page 704 ) and (and this is unexpectedly dystopian) the implications for chronic disease management using inflammatory bowel disease as an example ( see page 706 ). Linear growth There’s a long held perception that skeletal growth rate has a more or less linear relationship with skeletal maturity, itself measurable by a number of radiological techniques based on extent of ossification. High-sensitivity C reactive protein was measured at three points in time (13, 17 and 21 years) and categorised in tertiles separately for each wave;chronic low-grade inflammation in adolescence was defined as having hs-CRP levels in the highest tertile in at least two waves.

9.
Journal of Virology ; 96(7):5, 2022.
Article in English | Web of Science | ID: covidwho-1807317

ABSTRACT

The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spreads rapidly and harbors many mutations in the spike protein, but the origin of this virus variant remains unclear. We address the role of unusual virus evolution mechanisms such as hypermutation, out-of-frame reading, and recombination. Rather, regular Darwinian evolution, that is, the repeated selection of beneficial spike mutations, seems to have led to the appearance of the grossly altered spike protein of the Omicron variant.

11.
Mikrochimica Acta ; 189(3):128, 2022.
Article in English | MEDLINE | ID: covidwho-1802751

ABSTRACT

This review focuses on critical scientific barriers that the field of point-of-care (POC) testing of SARS-CoV-2 is facing and possible solutions to overcome these barriers using functional nucleic acid (FNA)-based technology. Beyond the summary of recent advances in FNA-based sensors for COVID-19 diagnostics, our goal is to outline how FNA might serve to overcome the scientific barriers that currently available diagnostic approaches are suffering. The first introductory section on the operationalization of the COVID-19 pandemic in historical view and its clinical features contextualizes essential SARS-CoV-2-specific biomarkers. The second part highlights three major scientific barriers for POC COVID-19 diagnosis, that is, the lack of a general method for (1) designing receptors of SARS-CoV-2 variants;(2) improving sensitivity to overcome false negatives;and (3) signal readout in resource-limited settings. The subsequent part provides fundamental insights into FNA and technical tricks to successfully achieve effective COVID-19 diagnosis by using in vitro selection of FNA to overcome receptor design barriers, combining FNA with multiple DNA signal amplification strategies to improve sensitivity, and interfacing FNA with portable analyzers to overcome signal readout barriers. This review concludes with an overview of further opportunities and emerging applications for FNA-based sensors against COVID-19.

12.
chemRxiv; 2022.
Preprint in English | ChemRxiv | ID: ppcovidwho-333402

ABSTRACT

From a designed library of indolyl pyrimidinamines we identified a highly potent and cell-active chemical probe (analog 17) that inhibits phosphatidylinositol-3-phosphate 5-kinase (PIKfyve). Comprehensive evaluation of inhibitor selectivity confirmed that this PIKfyve probe demonstrates excellent kinome-wide selectivity. A structurally related indolyl pyrimidinamine (analog 30) was characterized as a suitable negative control analog that lacks PIKfyve inhibitory activity and exhibits exquisite selectivity when profiled against the screenable human kinome. Our chemical probe disrupts multiple phases of the life cycle of β-coronaviruses. We observed potent inhibition of viral replication, reduced viral entry, and impacts on a mediator of viral transmission (lysosomes). Our scaffold is a distinct chemotype versus published PIKfyve inhibitors and lacks the canonical morpholine hinge-binder of classical lipid kinase inhibitors. Our chemical probe set can be used by the community to characterize the role of PIKfyve in virology and beyond.

13.
Journal of Clinical Virology ; 148:5, 2022.
Article in English | Web of Science | ID: covidwho-1799873

ABSTRACT

Rationale/Objectives: SARS-CoV-2 is the cause of worldwide COVID-19, which severity has been linked to the immune and inflammatory response. Here, we investigate Torquetenovirus (TTV) DNA load a marker reflecting the intensity of the overall immune response as well as SARS-CoV-2 RNAemia and IgM/IgG antibodies in COVID-19-positive patients.Methods: Two hundred and fifteen COVID-19-positive patients were enrolled, including 87 severe cases and 128 mild-moderate cases. SARS-CoV-2 RNAemia and IgM/IgG antibodies, as well as TTV DNA loads, were measured on longitudinal plasma samples.Results: The rate of severe cases was higher in patients with low TTV DNA load in plasma considering a threshold of 700 copies/mL. In severe patients, SARS-CoV-2 RNAemia positivity rates were higher than those in mild moderate cases at any timepoint. When combined, TTV DNA load and SARS-CoV-2 RNAemia allowed to predict the outcome of COVID-19 infection, with a higher risk (HR=12.4) of ICU admission in patients with low TTV DNA load and positive SARS-CoV-2 RNAemia.Conclusions: TTV DNA load and SARS-CoV-2 RNAemia may be effective, non-invasive markers reflecting disease severity and poor outcome that could be conveniently measured in a clinical laboratory setting, as soon as COVID-19 diagnosis is made.

14.
Journal of Clinical Virology ; 148:11, 2022.
Article in English | Web of Science | ID: covidwho-1799872

ABSTRACT

Introduction: : Active SARS-CoV-2 infection is confirmed mainly through the detection of viral nucleic acid via the reverse transcriptase polymerase chain reaction (RT-PCR) technique. Methods to assess humoral responses contribute to the monitoring of the disease and confirmation of exposure to the virus.Objective: : To evaluate the accuracy of tests for IgM and IgG antibodies for SARS-CoV-2 infection confirmed by RT-PCR and utility as complementary data for immunosurveillance. Methods: : Literature research was performed by searching the terms "COVID-19", "COVID-19 diagnostic testing" and "test" in the databases MEDLINE, EMBASE, Cochrane Library, Web of Science and Cumulative Index to Nursing and Allied Health Literature to search for potentially eligible observational studies without language restrictions published up to September 2020. Results: : The pooled sensitivity and specificity, regardless of collection moment, was 80.0% (CI 95% 72.0-86.0) and 97.0% (CI 95% 94.0-98.0) for "IgM and/or IgG", respectively. Serology considering immunoglobulins M and G together had a high accuracy performance on "fifteenth day and after": sensitivity and specificity was 91.0% (CI 95% 85.0-94.0) and 98.0% (CI 95% 95.0-99.0) respectively, DOR 461 and AUC 0.98.Conclusion: : This study shows that serology is a group of tests with high accuracy, mainly following the second week after infection.

15.
Virus Research ; 310:15, 2022.
Article in English | Web of Science | ID: covidwho-1799665

ABSTRACT

Tracking the evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through genomic surveillance programs is undoubtedly one of the key priorities in the current pandemic situation. Although the genome of SARS-CoV-2 acquires mutations at a slower rate compared with other RNA viruses, evolutionary pressures derived from the widespread circulation of SARS-CoV-2 in the human population have progressively favored the global emergence, though natural selection, of several variants of concern that carry multiple nonsynonymous mutations in the spike glycoprotein. These are often placed in key sites within major antibody epitopes and may therefore confer resistance to neutralizing antibodies, leading to partial immune escape, or otherwise compensate infectivity deficits associated with other non-synonymous substitutions. As previously shown by other authors, several emerging variants carry recurrent deletion regions (RDRs) that display a partial overlap with antibody epitopes located in the spike N-terminal domain (NTD). Comparatively, very little attention had been directed towards spike insertion mutations prior to the emergence of the B.1.1.529 (omicron) lineage. This manuscript describes a single recurrent insertion region (RIR1) in the N-terminal domain of SARSCoV-2 spike protein, characterized by at least 49 independent acquisitions of 1-8 additional codons between Val213 and Leu216 in different viral lineages. Even though RIR1 is unlikely to confer antibody escape, its association with two distinct formerly widespread lineages (A.2.5 and B.1.214.2), with the quickly spreading omicron and with other VOCs and VOIs warrants further investigation concerning its effects on spike structure and viral infectivity.

16.
Jundishapur Journal of Microbiology ; 15(1), 2022.
Article in English | EMBASE | ID: covidwho-1798771

ABSTRACT

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has clinical manifestations similar to other common respiratory viral infections. There are limited data on the frequency of viral respiratory coinfection among patients infected with SARS-CoV-2 in Iran. Objectives: This cross-sectional study investigated the prevalence of multiple respiratory viruses among SARS-CoV-2-positive and negative patients during the coronavirus disease 2019 (COVID-19) pandemic in Iran. Methods: We included oropharyngeal/nasopharyngeal swab specimens of patients suspected of COVID-19 from December 2020 to March 2021. A reliable multiplex TaqMan one-step real-time PCR method was employed to detect 17 viral respiratory pathogens si-multaneously. Descriptive analyses were performed to characterize the specimens concerning age, gender, clinical manifestations, and underlying disease. Results: Multiple respiratory viruses with a frequency of 18.78% were detected in 197 studied patients. Human metapneumovirus was the most prevalent pathogen detected in both SARS-CoV-2-positive (n = 7, 7.7%) and negative (n = 7, 6.6%) patients. Moreover, the frequency rate of viral infection was almost the same in both SARS-CoV-2-positive (18.68%) and negative (18.86%) patients. Altogether, there were no differences in baseline demographic characteristics such as age, sex, clinical symptoms, and comorbidities between the two groups (P > 0.05). Conclusions: The data presented here expand our understanding of the epidemiology of multiple types of viral respiratory pathogens in suspected COVID-19 patients. Therefore, simultaneous screening of other viral respiratory pathogens will be helpful for clinicians and researchers interested in the control of viral respiratory tract infections.

17.
J Am Soc Nephrol ; 2022 Mar 02.
Article in English | MEDLINE | ID: covidwho-1799028

ABSTRACT

BACKGROUND: Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) uses full-length angiotensin converting enzyme 2 (ACE2) as a main receptor to enter target cells. The goal of this study was to demonstrate the preclinical efficacy of a novel soluble ACE2 protein with increased duration of action and binding capacity in a lethal mouse model of COVID-19. METHODS: A human soluble ACE2 variant fused with an albumin binding domain (ABD) was linked via a dimerization motif hinge-like 4-cysteine dodecapeptide (DDC) to improve binding capacity to SARS-CoV-2. This novel soluble ACE2 protein (ACE2-1-618-DDC-ABD) was then administered intranasally and intraperitoneally to mice before intranasal inoculation of SARS-CoV-2 and then for two additional days post viral inoculation. RESULTS: Untreated animals became severely ill, and all had to be humanely euthanized by day 6 or 7 and had pulmonary alveolar hemorrhage with mononuclear infiltrates. In contrast, all but one mouse infected with a lethal dose of SARS-CoV-2 that received ACE2-1-618-DDC-ABD survived. In the animals inoculated with SARS-CoV-2 that were untreated, viral titers were high in the lungs and brain, but viral titers were absent in the kidneys. Some untreated animals, however, had variable degrees of kidney proximal tubular injury as shown by attenuation of the proximal tubular brush border and increased NGAL and TUNEL staining. Viral titers in the lung and brain were reduced or nondetectable in mice that received ACE2-1-618-DDC-ABD, and the animals developed only moderate disease as assessed by a near-normal clinical score, minimal weight loss, and improved lung and kidney injury. CONCLUSIONS: This study demonstrates the preclinical efficacy of a novel soluble ACE2 protein, termed ACE2-1-618-DDC-ABD, in a lethal mouse model of SARS-CoV-2 infection that develops severe lung injury and variable degrees of moderate kidney proximal tubular injury.

18.
Virus Evol. ; 8(1):14, 2022.
Article in English | Web of Science | ID: covidwho-1795112

ABSTRACT

COG-UK Mutation Explorer (COG-UK-ME, https://sars2.cyr.gla.ac.uk/cog-uk/-last accessed date 16 March 2022) is a web resource that displays knowledge and analyses on SARS-CoV-2 virus genome mutations and variants circulating in the UK, with a focus on the observed amino acid replacements that have an antigenic role in the context of the human humoral and cellular immune response. This analysis is based on more than 2 million genome sequences (as of March 2022) for UK SARS-CoV-2 data held in the CLIMB-COVID centralised data environment. COG-UK-ME curates these data and displays analyses that are cross-referenced to experimental data collated from the primary literature. The aim is to track mutations of immunological importance that are accumulating in current variants of concern and variants of interest that could alter the neutralising activity of monoclonal antibodies (mAbs), convalescent sera, and vaccines. Changes in epitopes recognised by T cells, including those where reduced T cell binding has been demonstrated, are reported. Mutations that have been shown to confer SARS-CoV-2 resistance to antiviral drugs are also included. Using visualisation tools, COG-UK-ME also allows users to identify the emergence of variants carrying mutations that could decrease the neutralising activity of both mAbs present in therapeutic cocktails, e.g. Ronapreve. COG-UK-ME tracks changes in the frequency of combinations of mutations and brings together the curated literature on the impact of those mutations on various functional aspects of the virus and therapeutics. Given the unpredictable nature of SARS-CoV-2 as exemplified by yet another variant of concern, Omicron, continued surveillance of SARS-CoV-2 remains imperative to monitor virus evolution linked to the efficacy of therapeutics.

19.
Antivir. Ther. ; 27(1):9, 2022.
Article in English | Web of Science | ID: covidwho-1794104

ABSTRACT

John Martin's untimely death in March 2021 was a huge loss for us personally, Gilead Sciences, the company he built over 30 years and the scientific community concerned with antiviral therapies. We wish to honor John's legacy by retelling the discovery and history of Tamiflu and his contributions to it. Without his vision, persistence, and keen eye for opportunities, Tamiflu would not exist and Gilead's path would not have been the same. His strategic thinking around the first oral flu drug is still quite relevant today, when we are still in the SARS-CoV-2 pandemic. John explained it simply in an interview with the Science History Institute in May 2020: " horizontal ellipsis most of my colleagues, we travel with Tamiflu when we go internationally, because it works for treatment and prevention, and hopefully, there will be a solution like that, eventually, for the Covid virus in addition to vaccines. Most people will get a flu vaccine every year, but there is still disease, we need a pill for treatment and prevention."

20.
Nature ; 2022 Apr 15.
Article in English | MEDLINE | ID: covidwho-1795824
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