SARS-CoV-2 variants genome analysis of Indonesian isolates and their responses to available vaccines

Background SARS-CoV-2 is a virus that initially appeared in Wuhan, China, at the end of 2019. Since then, the virus has spread until to almost all countries resulting in a global pandemic. Over time, this virus continues to mutate and produce several other variants. In Indonesia, there are multiple variants of SARS-CoV-2 identified, as well as various local variants that are not yet considered to be ‘variants of concern’. Therefore, this investigation is intended to understand the prevalence and epidemiology of the virus, along with detecting the mutations that occur in genes associated with whole-genome-sequences (WGS) isolated in Indonesia. Result Analyses were performed to investigate SARS-CoV-2 prevalence in Indonesia using data obtained from GISAID.org. A whole-genome sequencing was performed on the random samples taken from GISAID.org utilizing the BLAST tool from NCBI. The variants identified in Indonesia are Alpha, Beta and Delta variants, as well as local variants B.1.470 and B.1.466.2. As of the end of November, it was found that there are a total of 5.348 cases of the Delta, 78 cases of the Alpha, 22 cases of the Beta, 572 cases of the local variant B.1.470, and 1.833 cases of the local variant B.1.466.2. Other cases include 219 cases of local variant B.1.1.398, 160 cases of local variant B.1.459 and 1.028 cases of the wild type. In total there are 9.260 isolated genomes collected in GISAID that are located in Indonesia. Using BLAST, WGS of Alpha, Delta, Beta, B.1.470 and B.1.466.2 variants isolated in Indonesia was compared with the wild type from Wuhan NC.045512.2. It was found that multiple mutations have occurred in the samples. The mutations identified as are H69del, V70I, N501Y, D614G, A570D, P681H, T716I, S982A, and D1118H in the Alpha variant, T19R, L452R, T478K, D614G, and D950N in the Delta variant, D215G, D614G, A701V, L241-, L242-, K417N in the Beta variant, D614G, L242F, and S12F in the B.1.470 variant and D614G, N439K, and P681R in the B.1.466.2 variant. These mutations had caused alterations in the characteristics of the virus and how it may affect vaccine efficacy. Conclusions The results from whole-genome sequencing of variants isolated in Indonesia have found that multiple mutations have occurred in genes of the SARS-CoV-2 Virus and it caused alterations in the characteristics of the virus and may affect vaccine efficacy. It should be noted that classification from the GISAID website may change overtime. The result in this paper is based on the data taken at the end of November.

The 2016–2018 excavation of the cemetery at the Sunjiagang site, Lixian County, Hunan

Hunan Provincial Institute of Cultural Relics and Archaeology excavated at the site of Sunjiagang during 2016–2018 after 33 earthen pit tombs were uncovered in 1991. It yielded 192 pit tombs and one urn burial along with a number of pottery vessels and jade artifacts. The whole cemetery was laid out with a clear pattern of spatial arrangement, organized in an orderly style. A unique burial practice prevailed in the cemetery, for which the deceased was laid upon a layer of grave goods. According to the typology of unearthed pottery vessels and jade artifacts, the cemetery at the Sunjiagang site dates sometime from 2200 to 1800 BCE. It represents a new local variant of the Xiaojiawuji culture, and thus can be named the Sunjiagang type culture.

DCT Domain Detail Image Enhancement for More Resolved Images

This paper develops a detail image signal enhancement that makes images perceived as being clearer and more resolved and so more effective for higher resolution displays. We observe that the local variant signal enhancement makes images more vivid, and the more revealed granular signals harmonically embedded on the local variant signals make images more resolved. Based on this observation, we develop a method that not only emphasizes the local variant signals by scaling up the frequency energy in accordance with human visual perception, but also strengthens the granular signals by embedding the alpha-rooting enhanced frequency components. The proposed energy scaling method emphasizes the detail signals in texture images and rarely boosts noisy signals in plain images. In addition, to avoid the local ringing artifact, the proposed method adjusts the enhancement direction to be parallel to the underlying image signal direction. It was verified through subjective and objective quality evaluations that the developed method makes images perceived as clearer and highly resolved.

Algorithms of Adaptation in Inductive Inference

We investigate the idea that human concept inference utilizes local incremental search within a compositional mental theory space. To explore this, we study judgments in a challenging task, where participants actively gather evidence about a symbolic rule governing the behavior of a simulated environment. Participants construct mini-experiments before making generalizations and explicit guesses about the hidden rule. They then collect additional evidence themselves (Experiment 1) or observe evidence gathered by someone else (Experiment 2) before revising their own generalizations and guesses. In each case, we focus on the relationship between participants’ initial and revised guesses about the hidden rule concept. We find an order effect whereby revised guesses are anchored to idiosyncratic elements of the earlier guesses. To explain this pattern, we develop a family of process accounts that combine program induction ideas with local (MCMC-like) adaptation mechanisms. A particularly local variant of this adaptive account captures participants’ revisions better than a range of alternatives. We take this as suggestive that people deal with the inherent complexity of concept inference partly through use of local adaptive search in a latent compositional theory space.

DCT-Domain Detail Image Enhancement for More Resolved Images

This paper develops a detail image signal enhancement that makes images perceived as clearer and more resolved and so is more effective for higher resolution displays. We observe that the local variant signal enhancement makes images more vivid, and the more revealed granular signals harmonically embedded on the local variant signals make images more resolved. Based on this observation, we develop a method that not only emphasizes the local variant signals by scaling up the frequency energy in accordance with human visual perception, but also strengths up the granular signals by embedding the alpha-rooting enhanced frequency components. The proposed energy scaling method emphasizes the detail signals in texture images and rarely boosts noisy signals in plain images. In addition, to avoid the local ringing artifact, the proposed method adjusts the enhancement direction to be parallel to the underlying image signal direction. It was verified through the subjective and objective quality evaluations that the developed method makes images perceived as clearer and highly resolved.

Near-Complete Genome Sequences of Nine SARS-CoV-2 Strains Harboring the D614G Mutation in Malaysia

Here, we report the nearly complete genome sequences of nine SARS-CoV-2 variants with the D614G mutation. These viruses were detected from various infected individuals with different levels of severity from Pahang, Malaysia. In addition, this study described the presence of lineage B.1.351 as a type of variant of concern (VOC), lineage B.1.466.2, and lineage B.1.524 as a local variant.

Variation in the Speech of Two Palestinian Immigrant Groups

Objectives. This sociolinguistic study aims to take a close look at the differences and similarities in the linguistic behavior of two Palestinian groups and analyze these in light of social and political factors. Methods. The study adopts the Labovian Paradigm, and face-to-face techniques are used to collect data. Results. The first group immigrated to Jordan from Palestine as a result of being forced from their homes in 1948. They came seeking refuge in Jordan, and, because they came from Palestine, they were treated as such. When the Arab-Israeli war began nearly two decades later, a new wave of Palestinians migrated to Jordan in 1967. Yet, at this time, their Palestinian village belonged to Jordan, politically, because Jordan had annexed the West Bank in 1950. Thus, the political status of both sets of Palestinians at the beginning of their exodus played a major role in the subsequent development of their linguistic behavior in Jordan. It influenced the kind of variation that occurred in their speech. The first people to arrive were treated as Palestinian refugees, which minimized them from a social perspective. Thus, the study shows that the middle-aged and younger generations of this ethnic group abandoned their dialect, and 98.0% of them adopted the local variant. The individuals of the second set of migrants were treated as Jordanian citizens as they had simply migrated from one part of the country, namely, the West Bank, to another part of it, namely, the East Bank (Jordan). The study found a strong correlation between an individual’s identity and the political status granted by a country. Though the members of both groups are Palestinians, the study shows that all individuals behaved linguistically differently depending how they were perceived socially and politically in Jordan. Conclusion. Palestinians emigrated in two large waves from their homeland to Jordan as the result of war. The first took place in 1948, and the second took place in 1967. The study shows that the linguistic behavior of both groups differs. The social and the political situations that each group found itself in determined, to a great extent, the linguistic behavior they adopted.

People and Place: The West Coast of New Zealand’s South Island in History and Literature.

In his poem “Zoetropes,” Bill Manhire, writing from London in 1981, notes the exhilaration with which an expat Kiwi keenly notices the letter ‘Z’ in any text, instinctively scanning down the page, hoping to find the word New Zealand, that jolt-to-the-heart moment in which one is reminded of home. There is a local variant even within Aotearoa-New Zealand experienced by West Coasters who no longer live there, ever on the lookout for mention of Westland or for meeting other people with a connection to it. In media, however, the Coast only very occasionally makes an appearance outside of the weather report. 2020 was quite an exception, with the much-anticipated mini-series dramatisation of Eleanor Catton’s The Luminaries, as well as A Madness of Sunshine, a thriller novel by bestseller romance writer, Nalini Singh, and an academic history by Greymouth expat Len Richardson, People and Place: The West Coast of New Zealand’s South Island in History and Literature. And so, like Manhire in London, I scan the screen and pages on the lookout for recognisable signals from home, of characters and place that capture West Coast experience.

A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel

The routine detection, surveillance, and reporting of novel SARS-CoV-2 variants is crucial, as these threaten to hinder global vaccination efforts. Herein we report a novel local variant with a non-synonymous mutation in the spike (S) protein P681H. This local Israeli variant was not associated with a higher infection rate or higher prevalence. Furthermore, the local variant was successfully neutralized by sera from fully vaccinated individuals at a comparable level to the B.1.1.7 variant and an Israel wild-type strain. While it is not a variant of concern, routine monitoring by sequencing is still required.

LocalVar: a local variant collection manager to asynchronously detect synonyms, HGVS expression changes, and variant interpretation changes from ClinVar

While there are several public repositories of biological sequence variation data and associated annotations, there is little open-source tooling designed specifically for the upkeep of local collections of variant data. Many clinics curate and maintain such local collections and are burdened by frequent changes in the representation of those variants and evolving interpretations of clinical significance. A dictionary of genetic variants from the Huntsman Cancer Institute was analyzed over a period of two years and used to inform the development of LocalVar. This tool is institution-agnostic and uses publicly available ClinVar files to provide the following functionality: auto-complete search bar to pre-empt duplicate entries; single or bulk new variant record entry; auto-detection and merge suggestions for duplicate variant records; auto-detection and merge suggestions for variant records with HGVS expressions that are marked as synonyms in ClinVar; asynchronous suggestion of HGVS expression or variant interpretation updates; history tracking of additions, merges, updates, or other manual edits made to variant records; and the easy export of the collection (.csv), edit history (.json), or HGVS synonym bins (.json).