The SARS-CoV-2 RNA interactome

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The Best Gastric Site for Obtaining a Positive Rapid Urease Test

Background Rapid urease tests (RUTs) provide a simple, sensitive method of detecting Helicobacter pylori infection.
Objectives. Our aim, therefore, was to determine whether the yield of detecting H. pylori infection by RUT varied depending on the site of gastric biopsy.
Materials and Methods. Gastric biopsies were obtained from 50 patients for RUT by use of hp fast (GI Supply, Camp Hill, PA). Biopsies were taken from the prepyloric greater curve antrum, from the gastric angle, and from the greater curve in mid-corpus. One biopsy specimen was placed in the RUT gel, and the biopsy from the adjacent mucosa was placed in formalin for subsequent histological evaluation by using the Genta stain. RUTs were examined and scored at intervals of 5, 10, 15, 30, and 45 minutes and after 1, 2, 4, and 24 hours.
Results. Fifty patients were entered in the test (150 RUTs), 32 having H. pylori infection. There were no false-positive RUTs (specificity, 100%). The gastric angle site was positive in 100%. The prepyloric site was positive in 87%, and the corpus site was positive in 84.4% ( p < .052 for angle or prepyloric antrum versus corpus). The most common pattern was for all to be positive (74%). The median time to positivity was similar with angle and prepyloric sites (37.5 and 60 minutes, respectively, p = not significant) and shorter than the corpus biopsy (180 minutes); ( p < .05 for angle or prepyloric antrum versus corpus).
Conclusion. The maximum probability for detecting H. pylori infection using a RUT is to obtain a biopsy from the gastric angle. To prevent missing a positive result when intestinal metaplasia is present, we recommend that (at a minimum) biopsies be taken from both the angle and the corpus.     

The antigenic anatomy of SARS-CoV-2 receptor binding domain

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新型冠状病毒实验室检测方法研究进展

世界范围内流行的SARS-CoV-2已造成大批新型冠状病毒肺炎(COVID-19)患者,严重威胁着全人类生命健康.新型冠状病毒肺炎尚没有特效药,也没有疫苗,实验室确诊新型冠状病毒肺炎,隔离传染源,尽早治愈患者对整个疫情防控起着非常重要的作用.目前实验室检测方法有病毒分离培养、实时荧光定量PCR、环介导等温扩增技术、CRISPR/Cas技术、测序技术、基因芯片和抗原抗体检测.本文就上述几种方法做一综述,为确诊COVID-19提供参考.     

The effect of spike mutations on SARS-CoV-2 neutralization

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Metal-based complexes against SARS-CoV-2

BioMetals - The first appearance of SARS-CoV-2 is dated back to 2019. This new member of the coronavirus family has caused more than 5 million deaths worldwide up until the end of January 2022. At...     

The flexibility of ACE2 in the context of SARS-CoV-2 infection

The coronavirus disease 2019 (COVID-19) pandemic has swept over the world in the past months, causing significant loss of life and consequences to human health. Although numerous drug and vaccine development efforts are underway, there are many outstanding questions on the mechanism of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral association to angiotensin-converting enzyme 2 (ACE2), its main host receptor, and host cell entry. Structural and biophysical studies indicate some degree of flexibility in the viral extracellular spike glycoprotein and at the receptor-binding domain (RBD)-receptor interface, suggesting a role in infection. Here, we perform explicitly solvated, all-atom, molecular dynamics simulations of the glycosylated, full-length, membrane-bound ACE2 receptor in both an apo and spike RBD-bound state to probe the intrinsic dynamics of the ACE2 receptor in the context of the cell surface. A large degree of fluctuation in the full-length structure is observed, indicating hinge bending motions at the linker region connecting the head to the transmembrane helix while still not disrupting the ACE2 homodimer or ACE2-RBD interfaces. This flexibility translates into an ensemble of ACE2 homodimer conformations that could sterically accommodate binding of the spike trimer to more than one ACE2 homodimer and suggests a mechanical contribution of the host receptor toward the large spike conformational changes required for cell fusion. This work presents further structural and functional insights into the role of ACE2 in viral infection that can potentially be exploited for the rational design of effective SARS-CoV-2 therapeutics.     

The immunodominant and neutralization linear epitopes for SARS-CoV-2

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新型冠状病毒进化与变异

本文分析了新型冠状病毒(SARS-CoV-2,新冠病毒)的进化来源及刺突蛋白(spike protein,S)基因的突变情况.从GenBank数据库中下载相关病毒全基因组序列及S基因序列,运用DNAMAN9.0、MEGAX等生物信息学软件,进行多序列比对,构建系统进化树,并统计S基因位点突变情况.分析结果提示,新冠病毒...     

新型冠状病毒的相关研究进展

2019年12月出现于湖北武汉的一种新型冠状病毒(SARS-CoV-2)感染所致肺炎疫情,给人类生命安全造成威胁。迄今为止,对2019年出现的SARS-CoV-2的研究仍处于起步阶段,本文就其相关研究进展进行综述,重点阐述了目前关于SARS-CoV-2的病原学与致病机制方面的研究成果,同时对其流行病学以及该病毒引发的肺炎临床特点加以总结,有助于读者及时了解SARS-CoV-2最新的研究动态,并为今后开展治疗药物及疫苗研发提供方向。     

Remdesivir is a delayed translocation inhibitor of SARS-CoV-2 replication

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The challenge of emerging SARS-CoV-2 mutants to vaccine development

正Since the outbreak of the pandemic, waves of epidemics caused by severe acute respiratory syndrome coronavirus 2 (SARS-Co V-2) variants that harbor novel mutations have never paused. Globally, it undergoes rapid mutations that involve single-nucleotide polymorphism(SNP) dominantly, whereas ORF1ab and spike genes contain the most of more than 20,000 mutation sites reported within a year (Fang et al.,2021). Mutations inside spike protein are highly concerned for their potential impact on viral transmissibility and immune evasion, as spike protein is responsible for the interaction with the viral receptor angiotensin-converting enzyme 2 (ACE2) to mediate viral entry to the target cells. D614G identified in early 2020 is a globally dominant mutation (Korber et al., 2020). In late 2020, several variants were reported, which had caused continental and eventually worldwide epidemics. These notable variants include B.1.1.7 lineage (501Y.V1,Variant of Concern [VOC] 202012/01), 501Y.V2 variant (known as B.1.351 lineage), and P.1 lineage (also named 501Y.V3). In comparison with the D614G and D614 lineages identified in early 2020, they contain a large number of mutations within spike protein (Fig. 1).     

Overview of SARS-CoV-2 genome-encoded proteins

Science China Life Sciences - Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) has spread rapidly throughout the world. SARS-CoV-2 is an enveloped, plus-stranded RNA virus with a...     

Development of a charged model of the SARS-CoV-2 viral surface

A recent study provided experimental evidence of inactivation of viral activity after radio-frequency (RF) exposures in the 6–12 GHz band that was hypothesized to be caused by vibrations of an acoustic dipole mode in the virus that excited the viral membrane to failure. Here, we develop an atomic-scale molecular dynamics (MD) model of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral surface to estimate the electric fields necessary to rupture the viral membrane via dipole shaking of the virus. We computed the absorption spectrum of the system via unbiased MD simulations and found no particular strong absorption in the GHz band. We investigated the mechanical resiliency of the viral membrane by introducing uniaxial strains in the system and observed no pore formation in the membrane for strains up to 50%. Because the computed absorption spectrum was found to be essentially flat, and the strain required to break the viral membrane was $>$0.5, the field strength associated with rupture of the virus was greater than the dielectric breakdown value of air. Thus, RF disinfection of enveloped viruses would occur only once sufficient heat was transferred to the virus via a thermal mechanism and not by direct action (shaking) of the RF field oscillations on the viral membrane.     

The SARS-CoV-2 subgenome landscape and its novel regulatory features

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