•We are witnessing arms race between evolution of SARS-CoV-2 and research community for timely management of its detection and therapeutic regime.•Comprehensive genome dynamics study of omicron ...variant with the previously reported variants (VOC, VOI and VUM) suggests its mutational cascade.•Phylogenomics suggests a shared ancestry between omicron and lambda variant.•18,261 mutations were detected among 302 high-quality genomes of omicron variant majority of which were non-synonymous in the coding region.•Non-synonymous mutations were skewed towards spike (∼60%) (A67, T547K, D614G, H655Y, N679K, P681H, D796Y, N856K, Q954H), RNA dependent RNA polymerase (∼20%) (A1892T, I189V, P314L, K38R, T492I, V57V) and ∼5% in nucleocapsid (RG203KR).
Emergence of new variant of SARS-CoV-2, namely omicron, has posed a global concern because of its high rate of transmissibility and mutations in its genome. Researchers worldwide are trying to understand the evolution and emergence of such variants to understand the mutational cascade events.
We have considered all omicron genomes (n = 302 genomes) available till 2nd December 2021 in the public repository of GISAID along with representatives of variants of concern (VOC), i.e., alpha, beta, gamma, delta, and omicron; variant of interest (VOI) mu and lambda; and variant under monitoring (VUM). Whole genome-based phylogeny and mutational analysis were performed to understand the evolution of SARS CoV-2 leading to emergence of omicron variant.
Whole genome-based phylogeny depicted two phylogroups (PG-I and PG-II) forming variant specific clades except for gamma and VUM GH. Mutational analysis detected 18,261 mutations in the omicron variant, majority of which were non-synonymous mutations in spike (A67, T547K, D614G, H655Y, N679K, P681H, D796Y, N856K, Q954H), followed by RNA dependent RNA polymerase (rdrp) (A1892T, I189V, P314L, K38R, T492I, V57V), ORF6 (M19M) and nucleocapsid protein (RG203KR).
Delta and omicron have evolutionary diverged into distinct phylogroups and do not share a common ancestry. While, omicron shares common ancestry with VOI lambda and its evolution is mainly derived by the non-synonymous mutations.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversity has the potential to impact the virus transmissibility and the escape from natural infection- or vaccine-elicited ...neutralizing antibodies. Here, representative samples from circulating SARS-CoV-2 in Colombia between January and April 2021, were processed for genome sequencing and lineage determination following the nanopore amplicon ARTIC network protocol and PANGOLIN pipeline. This strategy allowed us to identify the emergence of the B.1.621 lineage, considered a variant of interest (VOI) with the accumulation of several substitutions affecting the Spike protein, including the amino acid changes I95I, Y144T, Y145S and the insertion 146 N in the N-terminal domain, R346K, E484K and N501Y in the Receptor binding Domain (RBD) and P681H in the S1/S2 cleavage site of the Spike protein. The rapid increase in frequency and fixation in a relatively short time in Magdalena, Atlantico, Bolivar, Bogotá D.C, and Santander that were near the theoretical herd immunity suggests an epidemiologic impact. Further studies will be required to assess the biological and epidemiologic roles of the substitution pattern found in the B.1.621 lineage.
•Monitoring the emergence of new variants of SARS-CoV-2 in real time is a worldwide priority.•Emerging variants of SARS-CoV-2 may have high impact biological implications for public health•The SARS-CoV-2 B.1.621 variant of interest was characterized by several substitutions: T95I, Y144T, Y145S, 146N, R346K, E484K and N501Y in spike protein.
We address whether T cell responses induced by different vaccine platforms (mRNA-1273, BNT162b2, Ad26.COV2.S, and NVX-CoV2373) cross-recognize early SARS-CoV-2 variants. T cell responses to early ...variants were preserved across vaccine platforms. By contrast, significant overall decreases were observed for memory B cells and neutralizing antibodies. In subjects ∼6 months post-vaccination, 90% (CD4+) and 87% (CD8+) of memory T cell responses were preserved against variants on average by AIM assay, and 84% (CD4+) and 85% (CD8+) preserved against Omicron. Omicron RBD memory B cell recognition was substantially reduced to 42% compared with other variants. T cell epitope repertoire analysis revealed a median of 11 and 10 spike epitopes recognized by CD4+ and CD8+ T cells, with average preservation > 80% for Omicron. Functional preservation of the majority of T cell responses may play an important role as a second-level defense against diverse variants.
Display omitted
•T cells of vaccinees recognize SARS-CoV-2 variants, including Omicron•RBD memory B cells’ recognition of Omicron is reduced•A median of 11 CD4 and 10 CD8 spike epitopes are recognized in vaccinees•Average preservation > 80% for Omicron at the epitope level
Human memory T cells induced by SARS-CoV-2 vaccines maintain the ability to recognize viral variants, including the Omicron variant.
Rationale: SARS-CoV-2 has been identified as a highly infective and contagious viral infection. The SARS-CoV-2 pandemic has been spread worldwide and affected more than 210 countries. Globally, the ...fast spread of novel SARS-CoV-2 variants has been mostly attributed to international travel.
Patient concerns: We are reporting the genomic evidence of SARS-CoV-2 Eta VOI among two international travelers. Both travelers were males from Nigeria aged 24 and 34 years and both were asymptomatic.
Diagnosis: The nasopharyngeal swab samples were in both travelers positive by real-time RT-PCR followed by COVIDSeq-NGS.
Interventions: Paracetamol 3 times daily for 5 days.
Outcomes: Patient recovered completely within 10 days and discharged after 14 days of quarantine duration.
Lessons: This report highlights genomic variation of SARS-CoV-2 among the travelers. For managing the present health crisis, molecular identification of viral variants present in different geographical locations will be very helpful.
•Detection of HV69/70 del, N501Y and E484K by the allplex SARS-CoV-2 variant I assay.•98.9% of all specimens tested on the variants I assay were corroborated by WGS.•100% sensitivity and specificity ...for HV69/70 deletion and N501Y.•100% sensitivity and 98.11% specificity for E484K.•The E484Q mutation was detected in specimens containing the kappa variant.
High-throughput assays for the detection of SARS-CoV-2 variants of concern (VOC) and interest (VOI) are a diagnostic alternative when whole genome sequencing (WGS) is unavailable or limited.
This study evaluated the clinical and analytical performance of the Seegene Allplex™ SARS-CoV-2 Variants I assay, which detects the HV69/70 deletion, N501Y and E484K mutations of the S gene.
Genotyping was evaluated on -871 SARS-CoV-2 RNA positive specimens, 408 nasopharyngeal (NP) swabs and 463 saline gargle (SG) specimens, with WGS used as the reference standard. Analytical performance was assessed including stability, reproducibility, limit of detection (LOD), cross-reactivity and interference with various respiratory microorganisms.
The clinical study revealed sensitivity of 100% (95% CI 99.27%–100%) and specificity of 100% (95% CI 98.99%–100%) for HV69/70 deletion, sensitivity of 100% (95% CI 99.55%–100%) and specificity of 100% (95% CI 93.73% – 100%) for N501Y, and sensitivity of 100% (95% CI 98.94% – 100%) and specificity of 98.10% (95% CI 96.53% – 99.08%) for E484K mutation. The E484Q mutation was detected in 10 specimens of the Kappa variant (B.1.627.1). Analytical performance demonstrated stability and reproducibility over 7 days, and LOD was calculated at 698 cp/mL for NP swab specimens, and 968 cp/mL for SG specimens. No interference or cross-reactivity with other microorganisms was noted.
The Allplex™ SARS-CoV-2 Variants I assay is acceptable for clinical use for the detection of variant of concern and variant of interest.
In addition to the rapid, global spread of SARS-CoV-2, new and comparatively more contagious variants are of considerable concern. These emerging mutations have become a threat to the global public ...health, creating COVID-19 surges in different countries. However, information on these emerging variants is limited and scattered. In this review, we discuss new variants that have emerged worldwide and identify several variants of concern, such as B.1.1.7, B.1.351, P.1, B.1.617.2 and B.1.1.529, and their basic characteristics. Other significant variants such as C.37, B.1.621, B.1.525, B.1.526, AZ.5, C.1.2, and B.1.617.1 are also discussed. This review highlights the clinical characteristics of these variants, including transmissibility, pathogenicity, susceptible population, and re-infectivity. It provides the latest information on the recent variants of SARS-CoV-2. The summary of this information will help researchers formulate reasonable strategies to curb the ongoing COVID-19 pandemic.
The Red River shear zone (RRSZ) is a major left‐lateral strike‐slip shear zone, containing a ductilely deformed metamorphic core bounded by brittle strike‐slip and normal faults, which stretches for ...>1000 km from Tibet through Yunnan and North Vietnam to the South China Sea. The RRSZ exposes four high‐grade metamorphic core complexes along its length. Various lithologies from the southernmost core complex, the Day Nui Con Voi (DNCV), North Vietnam, provide new constraints on the tectonic and metamorphic evolution of this region prior to and following the initial India–Asia collision. Analysis of a weakly deformed anatectic paragneiss using P–T pseudosections constructed in the MnO–Na2O–CaO–K2O–FeO–MgO–Al2O3–SiO2–H2O–TiO2–O (MnNCKFMASHTO) system provides prograde, peak and retrograde metamorphic conditions, and in situ U–Th–Pb geochronology of metamorphic monazite yields texturally controlled age constraints. Tertiary metamorphism and deformation, overprinting earlier Triassic metamorphism associated with the Indosinian orogeny and possible Cretaceous metamorphism, are characterized by peak metamorphic conditions of ~805 °C and ~8.5 kbar between c. 38 and 34 Ma. Exhumation occurred along a steep retrograde P–T path with final melt crystallizing at the solidus at ≥~5.5 kbar at ~790 °C. Further exhumation at ~640–700 °C and ~4–5 kbar at c. 31 Ma occurred at subsolidus conditions. U–Pb geochronological analysis of monazite from a strongly deformed pre‐kinematic granite dyke from the flank of the DNCV provides further evidence for exhumation at this time. Magmatic grains suggest initial emplacement at 66.0 ± 1.0 Ma prior to the India–Asia collision, whereas grains with metamorphic characteristics indicate later growth at 30.6 ± 0.4 Ma. Monazite grains from a cross‐cutting post‐kinematic dyke within the core of the DNCV antiform provide a minimum age constraint of 25.2 ± 1.4 Ma for the termination of fabric development. A separate and significant episode of monazite growth at c. 83–69 Ma is suggested to be the result of fluid‐assisted recrystallization following the emplacement of magmatic units.
This paper studies scheduling multiple sensors for jointly optimizing remote state estimation and wireless sensor network lifetime. Each sensor in the network sends its packet to the remote center ...for further estimation over wireless communication channels. Sensors in the network will inevitably run out of battery power due to transmission consumption and then reach the end of sensor network lifetime. This article focuses on the problem how to schedule multiple sensors minimizing the total remote estimation errors and simultaneously prolonging the sensor network lifetime. The problem is formulated as a special class of Markov decision process (MDP), stochastic shortest path (SSP) problem. Under this framework, we first derive a set of conditions to guarantee the optimality of structural policies in SSP. Subsequently, threshold structure of the optimal scheduling scheme is obtained by verifying the conditions. Moreover, two Value-of-Information-based multi-sensor scheduling algorithms and a linear-architecture-based learning algorithm are designed to tackle the curse of dimensionality and unknown channel statistics in large-scale sensor networks. Numerical simulations are given to validate effectiveness of our results.
The Internet of Vehicles (IoV) can support applications in connected autonomous vehicles (CAVs), the implementation of which can effectively improve traffic efficiency. However, safety-related CAV ...applications have very strict requirements on the reliability and latency of each packet, which is difficult to achieve due to limited resources and the high dynamics of CAVs. In this article, we investigate communication resource scheduling for remote autonomous driving (AD) to improve the performance of the remote control system when network resources are constrained. Specifically, we introduce a novel performance metric, i.e., value of information (VoI), to capture how sending a packet will affect the performance of CAV driving safety and efficiency, i.e., the value of the packet on the considered CAV system. The formulation of VoI is derived using the Lyapunov optimization method, and the lower-bound for the performance of the AD system with a VoI-based scheduling strategy is analyzed. Then, a communication resource scheduling approach is proposed based on the VoI of each packet. Simulation results demonstrate that the proposed VoI-based resource scheduling approach is capable of accurately assessing the impact of information transfer on system performance, while ensuring the CAV's safety and enhancing traffic efficiency.
PDF
