While SARS-CoV-2 continues to adapt for human infection and transmission, genetic variation outside of the spike gene remains largely unexplored. This study investigates a highly variable region at ...residues 203–205 in the SARS-CoV-2 nucleocapsid protein. Recreating a mutation found in the alpha and omicron variants in an early pandemic (WA-1) background, we find that the R203K+G204R mutation is sufficient to enhance replication, fitness, and pathogenesis of SARS-CoV-2. The R203K+G204R mutant corresponds with increased viral RNA and protein both
in vitro
and
in vivo
. Importantly, the R203K+G204R mutation increases nucleocapsid phosphorylation and confers resistance to inhibition of the GSK-3 kinase, providing a molecular basis for increased virus replication. Notably, analogous alanine substitutions at positions 203+204 also increase SARS-CoV-2 replication and augment phosphorylation, suggesting that infection is enhanced through ablation of the ancestral ‘RG’ motif. Overall, these results demonstrate that variant mutations outside spike are key components in SARS-CoV-2’s continued adaptation to human infection.
Postmortem fingerprinting is the fastest and most reliable way to scientifically identify unknown decedents from mass fatality incidents. In disaster victim identification (DVI), fingerprints, DNA, ...and dental examinations are the three primary methods of identification. Additional secondary identifiers such as comparative medical radiography, scars, marks, and tattoos can also be used if viable antemortem information can be located. As DNA technology continues to evolve, RAPID DNA may now identify a profile within 90 min if the remains are not degraded or comingled. When there are true unknowns, however, there is usually no DNA, dental, or medical records to retrieve for a comparison without a tentative identity. It is imperative to understand how to properly collect postmortem prints following various postmortem changes, which databases are available to search against, and what additional resources are available prior to any such event occurring. With advances in technology, automated fingerprint searching is faster than ever before. Mobile devices can now search all the major databases within a matter of minutes from a cell phone or tablet utilizing a peripheral fingerprint scanner. Preliminary research into the application of WD-40® when utilizing optical-capacitive scanners has shown to greatly increase the efficacy of capturing usable fingerprints. This additional step allows for the digital capture of fingerprints in even complicated settings, both in daily cases and DVI incidents. This article outlines all the available ways to obtain postmortem fingerprints in complex cases, and how they can be applied to efficiently and effectively used in the DVI process.
We report that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta spike mutation P681R plays a key role in the Alpha-to-Delta variant replacement during the coronavirus disease 2019 ...(COVID-19) pandemic. Delta SARS-CoV-2 efficiently outcompetes the Alpha variant in human lung epithelial cells and primary human airway tissues. The Delta spike mutation P681R is located at a furin cleavage site that separates the spike 1 (S1) and S2 subunits. Reverting the P681R mutation to wild-type P681 significantly reduces the replication of the Delta variant to a level lower than the Alpha variant. Mechanistically, the Delta P681R mutation enhances the cleavage of the full-length spike to S1 and S2, which could improve cell-surface-mediated virus entry. In contrast, the Alpha spike also has a mutation at the same amino acid (P681H), but the cleavage of the Alpha spike is reduced compared with the Delta spike. Our results suggest P681R as a key mutation in enhancing Delta-variant replication via increased S1/S2 cleavage.
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•SARS-CoV-2 spike P681R mutation contributes to Alpha-to-Delta variant replacement•Delta P681R mutation enhances the cleavage of full-length spike to S1 and S2•Mutations affecting S1/S2 cleavage must be closely monitored in variant surveillance
It is important to identify mutations that account for the emergence of SARS-CoV-2 variants. Liu et al. show that the Delta spike mutation P681R enhances the cleavage of full-length spike to S1 and S2, which improves cell-surface-mediated virus entry and leads to the Alpha-to-Delta variant replacement.
The published literature debates the extent to which naturally occurring stratospheric ozone intrusions reach the surface and contribute to exceedances of the U.S. National Ambient Air Quality ...Standard (NAAQS) for ground‐level ozone (75 ppbv implemented in 2008). Analysis of ozonesondes, lidar, and surface measurements over the western U.S. from April to June 2010 show that a global high‐resolution (∼50 × 50 km2) chemistry‐climate model (GFDL AM3) captures the observed layered features and sharp ozone gradients of deep stratospheric intrusions, representing a major improvement over previous chemical transport models. Thirteen intrusions enhanced total daily maximum 8‐h average (MDA8) ozone to ∼70–86 ppbv at surface sites. With a stratospheric ozone tracer defined relative to a dynamically varying tropopause, we find that stratospheric intrusions can episodically increase surface MDA8 ozone by 20–40 ppbv (all model estimates are bias corrected), including on days when observed ozone exceeds the NAAQS threshold. These stratospheric intrusions elevated background ozone concentrations (estimated by turning off North American anthropogenic emissions in the model) to MDA8 values of 60–75 ppbv. At high‐elevation western U.S. sites, the 25th–75th percentile of the stratospheric contribution is 15–25 ppbv when observed MDA8 ozone is 60–70 ppbv, and increases to ∼17–40 ppbv for the 70–85 ppbv range. These estimates, up to 2–3 times greater than previously reported, indicate a major role for stratospheric intrusions in contributing to springtime high‐O3events over the high‐altitude western U.S., posing a challenge for staying below the ozone NAAQS threshold, particularly if a value in the 60–70 ppbv range were to be adopted.
Key Points
Stratospheric intrusions can episodically increase surface ozone by 20‐40 ppbv
These intrusion events can push ground‐level ozone over the health‐based limit
Global high‐res model, satellite and in situ observations yield process insights
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein substitution D614G became dominant during the coronavirus disease 2019 (COVID-19) pandemic
. However, the effect of this ...variant on viral spread and vaccine efficacy remains to be defined. Here we engineered the spike D614G substitution in the USA-WA1/2020 SARS-CoV-2 strain, and found that it enhances viral replication in human lung epithelial cells and primary human airway tissues by increasing the infectivity and stability of virions. Hamsters infected with SARS-CoV-2 expressing spike(D614G) (G614 virus) produced higher infectious titres in nasal washes and the trachea, but not in the lungs, supporting clinical evidence showing that the mutation enhances viral loads in the upper respiratory tract of COVID-19 patients and may increase transmission. Sera from hamsters infected with D614 virus exhibit modestly higher neutralization titres against G614 virus than against D614 virus, suggesting that the mutation is unlikely to reduce the ability of vaccines in clinical trials to protect against COVID-19, and that therapeutic antibodies should be tested against the circulating G614 virus. Together with clinical findings, our work underscores the importance of this variant in viral spread and its implications for vaccine efficacy and antibody therapy.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-a new coronavirus that has led to a worldwide pandemic
-has a furin cleavage site (PRRAR) in its spike protein that is absent in other ...group-2B coronaviruses
. To explore whether the furin cleavage site contributes to infection and pathogenesis in this virus, we generated a mutant SARS-CoV-2 that lacks the furin cleavage site (ΔPRRA). Here we report that replicates of ΔPRRA SARS-CoV-2 had faster kinetics, improved fitness in Vero E6 cells and reduced spike protein processing, as compared to parental SARS-CoV-2. However, the ΔPRRA mutant had reduced replication in a human respiratory cell line and was attenuated in both hamster and K18-hACE2 transgenic mouse models of SARS-CoV-2 pathogenesis. Despite reduced disease, the ΔPRRA mutant conferred protection against rechallenge with the parental SARS-CoV-2. Importantly, the neutralization values of sera from patients with coronavirus disease 2019 (COVID-19) and monoclonal antibodies against the receptor-binding domain of SARS-CoV-2 were lower against the ΔPRRA mutant than against parental SARS-CoV-2, probably owing to an increased ratio of particles to plaque-forming units in infections with the former. Together, our results demonstrate a critical role for the furin cleavage site in infection with SARS-CoV-2 and highlight the importance of this site for evaluating the neutralization activities of antibodies.
The life cycle of HPV is tied to the differentiation status of its host cell, with productive replication, late gene expression and virion production restricted to the uppermost layers of the ...stratified epithelium. HPV DNA is histone-associated, exhibiting a chromatin structure similar to that of the host chromosome. Although HPV chromatin is subject to histone post-translational modifications, how the viral life cycle is epigenetically regulated is not well understood. SETD2 is a histone methyltransferase that places the trimethyl mark on H3K36 (H3K36me3), a mark of active transcription. Here, we define a role for SETD2 and H3K36me3 in the viral life cycle. We have found that HPV positive cells exhibit increased levels of SETD2, with SETD2 depletion leading to defects in productive viral replication and splicing of late viral RNAs. Reducing H3K36me3 by overexpression of KDM4A, an H3K36me3 demethylase, or an H3.3K36M transgene also blocks productive viral replication, indicating a significant role for this histone modification in facilitating viral processes. H3K36me3 is enriched on the 3' end of the early region of the high-risk HPV31 genome in a SETD2-dependent manner, suggesting that SETD2 may regulate the viral life cycle through the recruitment of H3K36me3 readers to viral DNA. Intriguingly, we have found that activation of the ATM DNA damage kinase, which is required for productive viral replication, is necessary for the maintenance of H3K36me3 on viral chromatin and for processing of late viral RNAs. Additionally, we have found that the HPV31 E7 protein maintains the increased SETD2 levels in infected cells through an extension of protein half-life. Collectively, our findings highlight the importance of epigenetic modifications in driving the viral life cycle and identify a novel role for E7 as well as the DNA damage response in the regulation of viral processes through epigenetic modifications.
A new tool to probe SARS-CoV-2 variants Johnson, Bryan A; Menachery, Vineet D
Science (American Association for the Advancement of Science),
2021-Dec-24, Volume:
374, Issue:
6575
Journal Article
Peer reviewed
Virus-like particles offer a new way to investigate genetic variation in SARS-CoV-2.
Background
Telemedicine was adopted to minimize exposure risks for patients and staff during the coronavirus disease 2019 pandemic. This study measured patient satisfaction and telemedicine usability ...in breast cancer care.
Methods
Adult breast cancer patients who had a telemedicine visit at a single academic institution (with surgical, radiation, or medical oncology) from 15 June 2020 to 4 September 2020 were surveyed anonymously. Patient and cancer characteristics were collected, and patient satisfaction and telemedicine usability were assessed using a modified Telehealth Usability Questionnaire with a 7-point Likert scale. Associations of satisfaction and usability with patient characteristics were analyzed using Wilcoxon rank-sum and Kruskal–Wallis tests.
Results
Of 203 patients who agreed to be contacted, 78 responded, yielding a response rate of 38%. The median age of the respondents was 63 years (range 25–83 years). The majority lived in an urban area (61%), were white (92%), and saw a medical oncologist (62%). The median patient satisfaction score was 5.5 (interquartile range IQR 4.25–6.25). The median telemedicine usability score was 5.6 (IQR 4.4–6.2). A strong positive correlation was seen between satisfaction and usability, with a Spearman correlation coefficient (
ρ
) of 0.80 (
p
< 0.001). Satisfaction and usability scores did not vary significantly according to patient age, race, location of residence, insurance status, previous visit commute time, oncology specialty seen, prior telemedicine visits, or whether patients were actively receiving cancer treatment.
Conclusions
Breast cancer patients were satisfied with telemedicine and found it usable. Patient satisfaction and telemedicine usability should not limit the use of telemedicine in future post-pandemic breast cancer care.
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