scholarly journals Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan

2021 ◽  
Vol 17 (6) ◽  
pp. e1009619
Author(s):  
Yosuke Hirotsu ◽  
Masao Omata
Keyword(s):  
United States ◽  
Severe Acute Respiratory Syndrome ◽  
The United States ◽  
Spike Protein ◽  
Taqman Assay ◽  
Receptor Binding Domain ◽  
Genome Sequences ◽  
Protein Receptor ◽  
History Of ◽  
Global Initiative

We aimed to investigate novel emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages in Japan that harbor variants in the spike protein receptor-binding domain (RBD). The total nucleic acid contents of samples from 159 patients with coronavirus disease 2019 (COVID-19) were subjected to whole genome sequencing. The SARS-CoV-2 genome sequences from these patients were examined for variants in spike protein RBD. In January 2021, three family members (one aged in their 40s and two aged under 10 years old) were found to be infected with SARS-CoV-2 harboring W152L/E484K/G769V mutations. These three patients were living in Japan and had no history of traveling abroad. After identifying these cases, we developed a TaqMan assay to screen for the above hallmark mutations and identified an additional 14 patients with the same mutations. The associated virus strain was classified into the GR clade (Global Initiative on Sharing Avian Influenza Data [GISAID]), 20B clade (Nextstrain), and R.1 lineage (Phylogenetic Assignment of Named Global Outbreak [PANGO] Lineages). As of April 22, 2021, R.1 lineage SARS-CoV-2 has been identified in 2,388 SARS-CoV-2 entries in the GISAID database, many of which were from Japan (38.2%; 913/2,388) and the United States (47.1%; 1,125/2,388). Compared with that in the United States, the percentage of SARS-CoV-2 isolates belonging to the R.1 lineage in Japan increased more rapidly over the period from October 24, 2020 to April 18, 2021. R.1 lineage SARS-CoV-2 has potential escape mutations in the spike protein RBD (E484K) and N-terminal domain (W152L); therefore, it will be necessary to continue to monitor the R.1 lineage as it spreads around the world.

scholarly journals Covid-19 pandemic: What is the truth?

2021 ◽  
Vol 12 ◽  
pp. 591
Author(s):  
Russell L. Blaylock
Keyword(s):  
United States ◽  
Young People ◽  
Severe Acute Respiratory Syndrome ◽  
Early Treatment ◽  
The United States ◽  
Treatment Protocols ◽  
Scientific Support ◽  
Control And Prevention ◽  
History Of ◽  
Irreparable Damage

The ongoing “pandemic” involving the severe acute respiratory syndrome coronavirus 2 virus (SARS-CoV-2) has several characteristics that make it unique in the history of pandemics. This entails not only the draconian measures that some countries and individual states within the United States and initiated and made policy, most of which are without precedent or scientific support, but also the completely unscientific way the infection has been handled. For the 1st time in medical history, major experts in virology, epidemiology, infectious diseases, and vaccinology have not only been ignored, but are also demonized, marginalized and in some instances, become the victim of legal measures that can only be characterized as totalitarian. Discussions involving various scientific opinions have been eliminated, top scientists have been frightened into silence by threats to their careers, physicians have lost their licenses, and the concept of early treatment has been virtually eliminated. Hundreds of thousands of people have died needlessly as a result of, in my opinion and the opinion of others, poorly designed treatment protocols, mostly stemming from the Center for Disease Control and Prevention, which have been rigidly enforced among all hospitals. The economic, psychological, and institutional damage caused by these unscientific policies is virtually unmeasurable. Whole generations of young people will suffer irreparable damage, both physical and psychological, possibly forever. The truth must be told.

scholarly journals Undiagnosed SARS-CoV-2 Seropositivity During the First Six Months of the COVID-19 Pandemic in the United States

2021 ◽  
pp. eabh3826
Author(s):  
Heather Kalish ◽  
Carleen Klumpp-Thomas ◽  
Sally Hunsberger ◽  
Holly Ann Baus ◽  
Michael P Fay ◽  
...  
Keyword(s):  
United States ◽  
The United States ◽  
Spike Protein ◽  
Behavioral Risk ◽  
Urban Centers ◽  
Blood Samples ◽  
Protein Receptor ◽  
Behavioral Risk Factor Surveillance ◽  
Urban Rural ◽  
Quota Sampling

Asymptomatic SARS-CoV-2 infection and delayed implementation of diagnostics have led to poorly defined viral prevalence rates in the United States and elsewhere. To address this, we analyzed seropositivity in 9,089 adults in the United States who had not been diagnosed previously with COVID-19. Individuals with characteristics that reflected the US population (n = 27,716) were selected by quota sampling from 462,949 volunteers. Enrolled participants (n = 11,382) provided medical, geographic, demographic, and socioeconomic information, and dried blood samples. Survey questions coincident with the Behavioral Risk Factor Surveillance System survey, a large probability-based national survey, were used to adjust for selection bias. The majority (88.7%) of blood samples were collected between May 10th and July 31st, 2020 and were processed using ELISA to measure seropositivity (IgG and IgM antibodies against SARS-CoV-2 spike protein and the spike protein receptor binding domain). The overall weighted undiagnosed seropositivity estimate was 4.6% (95% CI: 2.6-6.5%) with race, age, sex, ethnicity, and urban/rural subgroup estimates ranging from 1.1% to 14.2%; the highest seropositivity estimates were in African American participants, younger, female, and Hispanic participants, and residents of urban centers. These data indicate that there were 4.8 undiagnosed SARS-CoV-2 infections for every diagnosed case of COVID-19, and an estimated 16.8 million infections were undiagnosed by mid-July 2020 in the United States.

scholarly journals Evaluation of Anti-SARS-Cov-2 S-RBD Igg Antibodies after COVID-19 mRNA BNT162b2 Vaccine

Diagnostics ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1135
Author(s):  
Bruna Lo Sasso ◽  
Rosaria Vincenza Giglio ◽  
Matteo Vidali ◽  
Concetta Scazzone ◽  
Giulia Bivona ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Spike Protein ◽  
Receptor Binding Domain ◽  
Igg Antibodies ◽  
Chemiluminescence Immunoassay ◽  
Protein Receptor ◽  
Short Period ◽  
Previous Infection ◽  
Individual Protection ◽  
The Individual

(1) Background: The evaluation of anti-spike protein receptor-binding domain (S-RBD) antibodies represents a useful tool to estimate the individual protection against Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) infection; (2) Methods: We evaluated anti S-RBD IgG levels by indirect chemiluminescence immunoassay on Maglumi 800 (SNIBE, California) in 2248 vaccinated subjects without previous SARS-CoV-2 infection, 91 vaccinated individuals recovered from COVID-19, and 268 individuals recovered from COVID-19 who had not been vaccinated. Among those who were healthy and vaccinated, 352 subjects performed a re-dosing after about 72 days from the first measurement. (3) Results: Anti S-RBD IgG levels were lower in subjects with previous infection than vaccinated subjects, with or without previous infection (p < 0.001). No difference was observed between vaccinated subjects, with and without previous SARS-CoV-2 infection. Overall, anti-RBD IgG levels were higher in females than males (2110 vs. 1341 BAU/mL; p < 0.001) as well as in subjects with symptoms after vaccination than asymptomatic ones (2085 vs. 1332 BAU/mL; p = 0.001) and lower in older than younger subjects. Finally, a significant decrease in anti-RBD IgG levels was observed within a short period from a complete two-dose cycle vaccination. (4) Conclusions: Our results show an efficacy antibody response after vaccination with age-, time- and sex-related differences.

scholarly journals Two SARS-CoV-2 Genome Sequences of Isolates from Rural U.S. Patients Harboring the D614G Mutation, Obtained Using Nanopore Sequencing

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Piroon Jenjaroenpun ◽  
Visanu Wanchai ◽  
Kikumi D. Ono-Moore ◽  
Jennifer Laudadio ◽  
Laura P. James ◽  
...  
Keyword(s):  
United States ◽  
Severe Acute Respiratory Syndrome ◽  
Viral Genome ◽  
The United States ◽  
Network Protocol ◽  
Nanopore Sequencing ◽  
Genome Sequences ◽  
Oxford Nanopore ◽  
Complete Sequences ◽  
Oxford Nanopore Technologies

ABSTRACT Two coding-complete sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were obtained from samples from two patients in Arkansas, in the southeastern corner of the United States. The viral genome was obtained using the ARTIC Network protocol and Oxford Nanopore Technologies sequencing.

scholarly journals Geographic and Phylodynamic Distribution of SARS-CoV-2 from Environmental Origin

2021 ◽  
Author(s):  
Elijah Kolawole Oladipo ◽  
Boluwatife Ayobami Irewolede ◽  
Precious Moyosoluwa Oyewole ◽  
Emmanuel Oluwatobi Dairo ◽  
Ayodele Eugene Ayeni ◽  
...  
Keyword(s):  
United States ◽  
Severe Acute Respiratory Syndrome ◽  
Common Ancestor ◽  
Evolutionary Process ◽  
Geographic Location ◽  
The United States ◽  
Transmission Dynamics ◽  
Whole Genome ◽  
Genome Sequences ◽  
Phylodynamic Analysis

The coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread globally. Understanding the transmission dynamics of SARS-CoV-2 contamination in the environment is essential for infection control policies. This study aims to provide a phylodynamic analysis and distribution pattern of SARS-CoV-2 from the environment in terms of Source, clades, lineages, and their location. Ninety (90) retrieved whole-genome sequences of environmental sources from GISAID were investigated to determine the evolutionary process of SARS-CoV-2 and mutation in the isolated nucleotide sequences. The analysis was carried out using R, MAFFT, and MEGA X software. Out of the five countries studied, Austria has the highest distribution with sixty-five samples (72.2%), and the highest isolates of 68 (75.6%) were from raw sewage. The highest clade in circulation as obtained from the study is G with lineages B. The phylogeny of SARS-CoV-2 whole-genome sequences from Austria, the United States, China, Brazil, and Liechtenstein indicated that the SARS-CoV-2 viruses were all clustered together, irrespective of sequence geographic location. The study concluded by demonstrating a clear interconnection between the phylogeny of SARS-CoV-2 isolates from various geographic locations, all of which were locked in the same cluster regardless of their environment specimen. Thus, depicting the possibility of their origination from a common ancestor.

scholarly journals Structural Basis of a Human Neutralizing Antibody Specific to the SARS-CoV-2 Spike Protein Receptor-Binding Domain

2021 ◽  
Author(s):  
Mei Yang ◽  
Jiaqi Li ◽  
Zhaoxia Huang ◽  
Heng Li ◽  
Yueming Wang ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Global Health ◽  
Respiratory Disease ◽  
Receptor Binding ◽  
Neutralizing Antibody ◽  
Binding Domain ◽  
Spike Protein ◽  
Structural Basis ◽  
Receptor Binding Domain ◽  
Protein Receptor

COVID-19 is a respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The COVID-19 pandemic has posed a serious threat to global health and the economy, so it is necessary to find safe and effective antibody drugs and treatments.

scholarly journals Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations

2021 ◽  
Author(s):  
Lishuang Shen ◽  
Jennifer Dien Bard ◽  
Timothy J Triche ◽  
Alexander R Judkins ◽  
Jaclyn A Biegel ◽  
...  
Keyword(s):  
United States ◽  
Phylogenetic Analysis ◽  
Structural Analysis ◽  
United States Of America ◽  
The United States ◽  
Spike Protein ◽  
M Protein ◽  
Receptor Binding Domain ◽  
S Protein ◽  
The U.S

The SARS-CoV-2 B.1.1.7 lineage is highly infectious and as of April 2021 accounted for 92% of COVID-19 cases in Europe and 59% of COVID-19 cases in the U.S. It is defined by the N501Y mutation in the receptor binding domain (RBD) of the Spike (S) protein, and a few other mutations. These include two mutations in the N terminal domain (NTD) of the S protein, HV69-70del and Y144del (also known as Y145del due to the presence of tyrosine at both positions). We recently identified several emerging SARS-CoV-2 variants of concerns, characterized by Membrane (M) protein mutations, including I82T and V70L. We now identify a sub-lineage of B.1.1.7 that emerged through sequential acquisitions of M:V70L in November 2020 followed by a novel S:D178H mutation first observed in early February 2021. The percentage of B.1.1.7 isolates in the U.S. that belong to this sub-lineage increased from 0.15% in February 2021 to 1.8% in April 2021. To date this sub-lineage appears to be U.S.-specific with reported cases in 31 states, including Hawaii. As of April 2021 it constituted 36.8% of all B.1.1.7 isolates in Washington. Phylogenetic analysis and transmission inference with Nextstrain suggests this sub-lineage likely originated in either California or Washington. Structural analysis revealed that the S:D178H mutation is in the NTD of the S protein and close to two other signature mutations of B.1.1.7, HV69-70del and Y144del. It is surface exposed and may alter NTD tertiary configuration or accessibility, and thus has the potential to affect neutralization by NTD directed antibodies.

scholarly journals Real Concerns over COVID-19 Variants of Concern

2021 ◽  
Author(s):  
Hatem ◽  
Rashika El Rii
Keyword(s):  
United States ◽  
Severe Acute Respiratory Syndrome ◽  
Receptor Binding ◽  
Immune Evasion ◽  
The United States ◽  
Binding Domain ◽  
Receptor Binding Domain ◽  
Spike Glycoprotein ◽  
Terminal Domain ◽  
Corona Virus

Severe acute respiratory syndrome corona virus (SARS-CoV)-2 obtained from patients infected despite being fully vaccinated with either BNT162b2 (Pfizer/BioNTech), mRNA-1273 (Moderna), or JNJ-78436735 (Janssen) showed increased mutations rates in the N-terminal domain (NTD) and receptor-binding domain (RBD) of the spike glycoprotein when compared with virus from unvaccinated controls (1). These changes are associated with immune evasion and diagnostic failures, prominent characteristics of variants of concern (2). Variants of concern (VOC) appeared to be overrepresented in numerous breakthrough infections of fully vaccinated people in the United States and (1, 3-6), and Israel (7). These findings confirm concerns about the relation of SARS-CoV-2 variants with vaccine breakthrough, and urged us to attempt clarifying the likely link between vaccination with the currently used vaccines and VOC emergence.

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