•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.
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•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.
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) circulates in the world and acquires mutations during evolution. To identify the new emergent variants, the surveillance of the ...variants of concern (VOC) and variants of interest (VOI) is ongoing. This study aimed to determine how the transition of viral lineage occurred by stationary genome analysis in Yamanashi, Japan.
We performed the whole genome sequencing using SARS-CoV-2 positive samples collected from February 2020 to the end of June 2021. Viral lineage was defined by the Phylogenetic Assignment of Named Global Outbreak (PANGO) lineages.
We successfully obtained 325 viral genome sequences and the number of analyzed samples accounted for 15.4% of the total 2109 COVID-19 patients identified in our district. We identified 13 types of viral lineages including R.1, P.1, B.1.1.7 (Alpha) and B.1.617.2 (Delta). These virus lineages had distinct periods of expansion and decline. After the emerging of the R.1 lineage harboring E484K variant (designated VOI in Japan), the prevalent B.1.1.214 lineage were no longer identified. The R.1 lineages were temporarily prevalent afterwards, but the influx of B.1.1.7 lineage (designated VOC) led to a decline in R.1. Currently, B.1.1.7 has become dominant after mid-April 2021.
We clearly elucidated the transition and replacement of viral lineage by the community-based analysis. The virus completely replaced by more infectious lineages, therefore, it will be necessary to continue to monitor the VOC and VOI.
•WGS of SARS-CoV-2 in 325 patients in a community of Japan from Feb 2020 to Jun 2021.•The transition of viral lineage was observed during four waves of infection spread.•B.1.1.214 rapidly declined after the emergence of the R.1 lineage with E484K.•R.1 temporally expanded, but declined rapidly after the influx of B.1.1.7 (Alpha).•B.1.617.2 (Delta) has just been detected and the VOC needs to be studied continuously.
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.
The ultra-reliable and low-latency communication (URLLC) service of the fifth-generation (5G) mobile communication network struggles to support safe robot operation. Nowadays, the sixth-generation ...(6G) mobile communication network is proposed to provide hyper-reliable and low-latency communication to enable safer control for robots. However, current 5G/ 6G research mainly focused on improving communication performance, while the robotics community mostly assumed communication to be ideal. To jointly consider communication and robotic control with a focus on the specific robotic task, we propose goal-oriented semantic communication in robotic control (GSRC) to exploit the context of data and its importance in achieving the task at both transmitter and receiver. At the transmitter, we propose a deep reinforcement learning algorithm to generate optimal control and command (C&C) data and a proactive repetition scheme (DeepPro) to increase the successful transmission probability. At the receiver, we design the value of information (VoI) and age of information (AoI) based queue ordering mechanism (VA-QOM) to rank the queue based on the semantic information extracted from AoI and VoI. The simulation results validate that our proposed GSRC framework achieves a 91.5% improvement in the mean square error compared to the traditional unmanned aerial vehicle control framework.
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