scholarly journals Current understanding of an Emerging Coronavirus using in silico approach: Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2)

2023 ◽  
Vol 83 ◽  
Author(s):  
S. Khalid ◽  
R. Siddique ◽  
S. Shaheen ◽  
M. N. Shahid ◽  
Z. Shamim ◽  
...  

Abstract Novel coronavirus (nCoV) namely “SARS-CoV-2” is being found responsible for current PANDEMIC commenced from Wuhan (China) since December 2019 and has been described with epidemiological linkage to China in about 221 countries and territories until now. In this study we have characterized the genetic lineage of SARS-CoV-2 and report the recombination within the genus and subgenus of coronaviruses. Phylogenetic relationship of thirty nine coronaviruses belonging to its four genera and five subgenera was analyzed by using the Neighbor-joining method using MEGA 6.0. Phylogenetic trees of full length genome, various proteins (spike, envelope, membrane and nucleocapsid) nucleotide sequences were constructed separately. Putative recombination was probed via RDP4. Our analysis describes that the “SARS-CoV-2” although shows great similarity to Bat-SARS-CoVs sequences through whole genome (giving sequence similarity 89%), exhibits conflicting grouping with the Bat-SARS-like coronavirus sequences (MG772933 and MG772934). Furthermore, seven recombination events were observed in SARS-CoV-2 (NC_045512) by RDP4. But not a single recombination event fulfills the high level of certainty. Recombination mostly housed in spike protein genes than rest of the genome indicating breakpoint cluster arises beyond the 95% and 99% breakpoint density intervals. Genetic similarity levels observed among “SARS-CoV-2” and Bat-SARS-CoVs advocated that the latter did not exhibit the specific variant that cause outbreak in humans, proposing a suggestion that “SARS-CoV-2” has originated possibly from bats. These genomic features and their probable association with virus characteristics along with virulence in humans require further consideration.

2019 ◽  
Vol 8 (1) ◽  
Author(s):  
Hui-Min Zhu ◽  
Shu-Han Luo ◽  
Man Gao ◽  
Feng Tao ◽  
Jing-Peng Gao ◽  
...  

Abstract Background Species of the Anopheles hyrcanus group are widely distributed in Palearctic and Oriental regions and some of them are important malaria vectors. The cryptic species of An. hyrcanus group was almost impossible to identify based only on their morphology. The phylogenetic relationship of An. hyrcanus group was also not clear. Methods Five members of An. hyrcanus group were identified by rDNA ITS2 sequencing as An. yatsushiroensis, An. belenrae, An. kleini, An. lesteri and An. sineroides. The mitochondrial genome fragments were sequenced and annotated using the mitochondrial genome of An. sinensis as reference. Based on the four segments and Joint Data sequences of these species, and other four anopheline species downloaded from GenBank, intraspecific as well as interspecific genetic distances were calculated and the phylogenetic trees were reconstructed by the methods of neighbor joining, maximum parsimony, minimum evolution and maximum likelihood. Findings Four parts of mitochondrial genomes, which were partial fragments COI + tRNA + COII (F5), ATP6 + COIII(F7 + F8), ND1(F19) and lrRNA (F21), were obtained. All fragments were connected as one sequence (referred as Joint Data), which had a total length of 3393 bp. All fragment sequences were highly conservative within species, with the maximum p distance (0.026) calculated by F19 of An. belenrae. The pairwise interspecific p distance calculated by each fragment showed minor or even no difference among An. sinensis, An. kleini and An. belenrae. However, interspecific p distances calculated by the Joint Data sequence ranged from 0.004 (An. belenrae vs An. kleini) to 0.089 (An. sineroides vs An. minimus), and the p distances of the six members of An. hyrcanus group were all less than 0.029. The phylogenetic tree showed two major clades: all subgenus Anopheles species (including six members of An. hyrcanus group, An. atroparvus and An. quadrimaculatus A) and subgenus Cellia (including An. dirus and An. minimus). The An. hyrcanus group was divided into two clusters as ((An. lesteri, An. sineroides) An. yatsushiroensis) and ((An. belenrae, An. sinensis) An. kleini)). Conclusions The An. hyrcanus group in this study could be divided into two clusters, in one of which An. belenrae, An. sinensis and An. kleini were most closely related. More molecular markers would make greater contribution to phylogenetic analysis.


2005 ◽  
Vol 55 (5) ◽  
pp. 1973-1977 ◽  
Author(s):  
M. Abdul Alim Al-Bari ◽  
M. Shah Alam Bhuiyan ◽  
María Elena Flores ◽  
Pavel Petrosyan ◽  
Martín García-Varela ◽  
...  

The taxonomic position of an actinomycete strain isolated from soil from Natore, Bangladesh, was examined by using a polyphasic approach. The strain, designated AAB-4T, was assigned to the genus Streptomyces on the basis of chemical and morphological criteria. It formed Rectiflexibiles aerial hyphae that carried long chains of rounded spores. The 16S rRNA gene of strain AAB-4T was sequenced directly and then compared with those of previously studied streptomycetes following the generation of two phylogenetic trees by using maximum-likelihood and neighbour-joining algorithms. This confirmed the assignment of the novel strain to the genus Streptomyces. This strain showed a high level of 16S rRNA gene sequence similarity to Streptomyces thermoviolaceus, Streptomyces thermodiastaticus and Streptomyces longisporus, among others, but could be distinguished from them by phenotypic and physiological traits. This micro-organism produces bis-(2-ethylhexyl)phthalate, an antibacterial and antifungal agent. It is proposed that strain AAB-4T be classified as a novel species within the genus Streptomyces, as Streptomyces bangladeshensis sp. nov. (type strain, AAB-4T=LMG 22738T=NRRL B-24326T).


Sociobiology ◽  
2021 ◽  
Vol 68 (2) ◽  
pp. 5911
Author(s):  
Nurul Akmar Hussin ◽  
Abdul Hafiz Ab Majid

The subterranean higher termite Globitermes sulphureus (Blattodea: Termitidae), is a peridomestic forager and regarded as a significant pest in Southeast Asia. In this study, the populations of G. sulphureus from the USM main campus area were investigated based on partial sequences of the mitochondrial COII gene. The genetic diversity was determined using DnaSP v5 software while the phylogenetic relationship was defined using Neighbor-joining (NJ) and maximum likelihood (ML) methods using Molecular Evolutionary Genetics Analysis (MEGA 7) software. A total of 2 haplotypes were detected among the 5 sample sequences that differed by two variable sites. In addition, both phylogenetic trees gave similar topology and supporting the results from haplotype diversity. Based on the haplotype diversity and molecular phylogeny, it is proposed that geographic isolation and lack of human activities have contributed to the neutral genetic diversity of G. sulphureus.   


2020 ◽  
Vol 12 (2) ◽  
pp. 585-595
Author(s):  
Syamsul Bachry ◽  
Dedy D. Solihin ◽  
Rudhy Gustiano ◽  
Kadarwan Soewardi ◽  
Nurlisa A. Butet

Abalone Haliotis squamata Reeve 1846 is an abalone that has distribution on the southern coast of Java and Bali in Indonesia. The purpose of this study was to analyze the phylogenetic relationship of H. squamata from the southern coast of Java and Bali based on the cytochrome b (Cyt b) mitochondrial DNA sequence. A total of 38 samples were collected from Java (Binuangeun, Pangandaran, Banyuwangi, and Bali (Buleleng). Samples were extracted, applied using method PCR, and sequencing the method Sanger sequencing di 1st BASE Malaysia. Using primary sequences to applied namely forward primers forward AB-Cytb DivF (5'-TAAGCCAATTCGTAAGGTTC-3') dan primer reverse AB-Cytb DivR (5'-AAAATACCACTCTGGCTGAA-3'). Genetic distance was analyzed using the Kimura 2-parameter method and phylogenetic tree construction was carried out by Neighbor-Joining using the MEGA 7. The result showed that a specific nucleotide difference of 81 bp to 820 bp. The genetic distance between H. squamata intraspecies from the southern coast of Java and Bali is 0.96%-1.06%. This genetic distance is high enough to separate the two populations and form their clusters based on phylogenetic trees. The population of Bali seems to form new subpopulations. The data obtained in this study will be very useful for the management of H. squamata abalone genetic resources related to their sustainability and utilization.


2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Shabarni Gaffar ◽  
◽  
Syifa Al Fauziah Rahmani ◽  
Ari Hardianto

Coronavirus disease-2019 (COVID-19) is an infectious acute respiratory disease caused by SARS-CoV-2. The protein that plays a role in the entry of SARS-CoV-2 into human cells is the surface protein, or the Spike, which is thought to be the effective vaccine target to prevent SARS-CoV-2 infection. Until December 2020, Indonesia has reported 106 SARS-CoV-2 genome sequences identified from COVID-19 positive patients. The purpose of this study was to analyze the phylogenetic relationship of the Spike protein of the Indonesian isolates of SARS-CoV-2 Indonesian, as well as the virus mutations and their effects on changes in the amino acid. The 106 Indonesian SARS-CoV-2 genomes were downloaded from GISAID and the Spike nucleotide and amino acid sequences were analyzed by multiple sequence alignment (MSA) and mutation analysis using the ClustalW method. Phylogenetic trees were created using the Neighbor-Joining method in MEGA-X software. The results showed that 30 of the 106 Indonesian isolate SARS-CoV-2 Spike were 100% identical to the Wuhan-Hu-1, while the remaining 76 had experienced mutations at 1-4 sites. There were 43-point mutations in the Spike gene, 27 of which led to amino acid changes and four had not been reported in other countries. The global mutation D614G was found in 60 Indonesian isolates , of which West Java was the province with the most reports. The phylogenetic of Spike showed that the Indonesian samples have been divided into several branches that are far from Wuhan-Hu-1. This study indicates the possibility of differences in the protein structure of Indonesian isolate SARS-CoV-2 Spike that need to be further studied to manufacture a vaccine against the Indonesian strain of SARS-CoV-2.


Parasitology ◽  
2006 ◽  
Vol 134 (5) ◽  
pp. 695-703 ◽  
Author(s):  
Q. GAO ◽  
M. X. CHEN ◽  
W. J. YAO ◽  
Y. GAO ◽  
Y. SONG ◽  
...  

SUMMARYThe phylogenetic relationship of 5 genera, i.e. Diplozoon Nordmann, 1832, ParadiplozoonAchmerov, 1974, InustiatusKhotenovsky, 1978, SindiplozoonKhotenovsky, 1981, and EudiplozoonKhotenovsky, 1985 in the subfamily Diplozoinae Palombi, 1949 (Monogenea, Polyopisthocotylea) was inferred from rDNA ITS-2 region using neighbour-joining (NJ), maximum likelihood (ML) and Bayesian methods. The phylogenetic trees produced by using NJ, ML and Bayesian methods exhibit essentially the same topology. Surprisingly, freshwater species of Paradiplozoon from Europe clustered together with species of Diplozoon, but separated from Chinese Paradiplozoon species. The results of molecular phylogeny and lower level of divergence (4·1–15·7%) in ITS-2 rDNA among Paradiplozoon from Europe and Diplozoon and, on the other hand, high level of divergence (45·3–53·7%) among Paradiplozoon species from Europe and China might indicate the non-monophyletic origin of the genus Paradiplozoon. Also, the generic status of European Paradiplozoon needs to be revised. The species of Paradiplozoon in China is a basal group in Diplozoinae as revealed by NJ and Bayesian methods, and Sindiplozoon appears to be closely related to European Paradiplozoon and Diplozoon with their relationship to Eudiplozoon and Inustiatus being unresolved.


2020 ◽  
Author(s):  
Agnieszka Wykowska ◽  
Jairo Pérez-Osorio ◽  
Stefan Kopp

This booklet is a collection of the position statements accepted for the HRI’20 conference workshop “Social Cognition for HRI: Exploring the relationship between mindreading and social attunement in human-robot interaction” (Wykowska, Perez-Osorio & Kopp, 2020). Unfortunately, due to the rapid unfolding of the novel coronavirus at the beginning of the present year, the conference and consequently our workshop, were canceled. On the light of these events, we decided to put together the positions statements accepted for the workshop. The contributions collected in these pages highlight the role of attribution of mental states to artificial agents in human-robot interaction, and precisely the quality and presence of social attunement mechanisms that are known to make human interaction smooth, efficient, and robust. These papers also accentuate the importance of the multidisciplinary approach to advance the understanding of the factors and the consequences of social interactions with artificial agents.


2020 ◽  
Vol 18 ◽  
Author(s):  
Yin Yueqi ◽  
Zhou Ying ◽  
Lu Jing ◽  
Guo Hongxiong ◽  
Chen Jianshuang ◽  
...  

Background: CRF01_AE and CRF07_BC are the two major HIV-1 virus strains circulating in China. The proportion of dominant subtypes (CRF01_AE and CRF07_BC) among MSM in Jiangsu province was over 80%. A large number of URFs have been found in China in recently years. Objective: This study aimed to report on novel HIV-1 recombinants. Method: We constructed Phylogenetic trees using the maximum likelihood (ML) method with 1000 bootstrap replicates in IQ-TREE 1.6.8 software and determined recombination break points using SimPlot 3.5.1. Results: We identified a novel, second-generation HIV-1 recombinant (JS020202) between CRF01_AE and CRF07_BC. The analysis of near full-length genome (NFLG) showed there were at least 8 breakpoints inner virus, which differed from any previously identified CRF and URF around the world. Conclusion: Novel diverse CRF01_AE/07_BC suggested the complexity trends of HIV-1 genetics. The emergency situation of diverse recombinant strains should be monitored continuously.


Author(s):  
Anupama M. Gudadappanavar ◽  
Jyoti Benni

AbstractA novel coronavirus infection coronavirus disease 2019 (COVID-19) emerged from Wuhan, Hubei Province of China, in December 2019 caused by SARS-CoV-2 is believed to be originated from bats in the local wet markets. Later, animal to human and human-to-human transmission of the virus began and resulting in widespread respiratory illness worldwide to around more than 180 countries. The World Health Organization declared this disease as a pandemic in March 2020. There is no clinically approved antiviral drug or vaccine available to be used against COVID-19. Nevertheless, few broad-spectrum antiviral drugs have been studied against COVID-19 in clinical trials with clinical recovery. In the current review, we summarize the morphology and pathogenesis of COVID-19 infection. A strong rational groundwork was made keeping the focus on current development of therapeutic agents and vaccines for SARS-CoV-2. Among the proposed therapeutic regimen, hydroxychloroquine, chloroquine, remdisevir, azithromycin, toclizumab and cromostat mesylate have shown promising results, and limited benefit was seen with lopinavir–ritonavir treatment in hospitalized adult patients with severe COVID-19. Early development of SARS-CoV-2 vaccine started based on the full-length genome analysis of severe acute respiratory syndrome coronavirus. Several subunit vaccines, peptides, nucleic acids, plant-derived, recombinant vaccines are under pipeline. This article concludes and highlights ongoing advances in drug repurposing, therapeutics and vaccines to counter COVID-19, which collectively could enable efforts to halt the pandemic virus infection.


Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 764
Author(s):  
Bohu Pan ◽  
Zuowei Ji ◽  
Sugunadevi Sakkiah ◽  
Wenjing Guo ◽  
Jie Liu ◽  
...  

Severe acute respiratory syndrome coronavirus 2 (SARS−CoV−2) has caused the ongoing global COVID-19 pandemic that began in late December 2019. The rapid spread of SARS−CoV−2 is primarily due to person-to-person transmission. To understand the epidemiological traits of SARS−CoV−2 transmission, we conducted phylogenetic analysis on genome sequences from >54K SARS−CoV−2 cases obtained from two public databases. Hierarchical clustering analysis on geographic patterns in the resulting phylogenetic trees revealed a co-expansion tendency of the virus among neighboring countries with diverse sources and transmission routes for SARS−CoV−2. Pairwise sequence similarity analysis demonstrated that SARS−CoV−2 is transmitted locally and evolves during transmission. However, no significant differences were seen among SARS−CoV−2 genomes grouped by host age or sex. Here, our identified epidemiological traits provide information to better prevent transmission of SARS−CoV−2 and to facilitate the development of effective vaccines and therapeutics against the virus.


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