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

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.

Variant analysis of SARS-CoV-2 strains with phylogenetic analysis and the Coronavirus Antiviral and Resistance Database

Aims: This study determined SARS-CoV-2 variations by phylogenetic and virtual phenotyping analyses. Materials & methods: Strains isolated from 143 COVID-19 cases in Turkey in April 2021 were assessed. Illumina NexteraXT library preparation kits were processed for next-generation ]sequencing. Phylogenetic (neighbor-joining method) and virtual phenotyping analyses (Coronavirus Antiviral and Resistance Database [CoV-RDB] by Stanford University) were used for variant analysis. Results: B.1.1.7–1/2 (n = 103, 72%), B.1.351 (n = 5, 3%) and B.1.525 (n = 1, 1%) were identified among 109 SARS-CoV-2 variations by phylogenetic analysis and B.1.1.7 (n = 95, 66%), B.1.351 (n = 5, 4%), B.1.617 (n = 4, 3%), B.1.525 (n = 2, 1.4%), B.1.526-1 (n = 1, 0.6%) and missense mutations (n = 15, 10%) were reported by CoV-RDB. The two methods were 85% compatible and B.1.1.7 (alpha) was the most frequent SARS-CoV-2 variation in Turkey in April 2021. Conclusion: The Stanford CoV-RDB analysis method appears useful for SARS-CoV-2 lineage surveillance.

First DNA Barcoding Based Record of Lysiosquillina Maculata (Fabricius, 1793) (Crustacea: Stomatopoda) From Chennai Coast, Tamil Nadu, India

Taxonomic identification of mantis shrimp Lysiosquillina maculata through DNA barcoding analysis collected from Kasimedu fisheries harbour, Chennai coast, Tamil Nadu, India. The mitochondrial cytochrome oxidase sub unit I gene (mtcoI) with 650 bp region was sequenced for phylogenetic analysis. The present record, mitochondrial gene sequences were used to identify the mantis shrimp Lysiosquillina maculata. This is the first confirmed record of Indian waters and the mt COI sequence was deposited in GenBank. The neighbor joining method was used for phylogenetic analysis. The pair wise genetic distance calculated with 08 closely related species varied form 0.03-0.404%. Phylogenetic tree based on 13 protein coding genes shows that Lysiosquillina maculata has a closer phylogenetic relationship to Harpiosquilla harpax.

Characterization and Biological Activity of a Novel Exopolysaccharide Produced by Pediococcus pentosaceus SSC–12 from Silage

In this study, 22 strains of exopolysaccharides-producing lactic acid bacteria were isolated from silage, and the strain SSC–12 with the highest exopolysaccharide (EPS) production was used as the test strain. The SSC–12 was identified as Pediococcus pentosaceus, based upon 16S rDNA gene sequencing and Neighbor Joining (NJ) phylogenetic analysis. The analysis of the kinetic results of EPS generation of SSC–12 showed that the EPS generation reached the maximum value at 20 h of culture. The characterization study showed the EPS produced by SSC–12 was a homogeneous heteropolysaccharide comprising glucose (42.6%), mannose (28.9%), galactose (16.2%), arabinose (9.4%), and rhamnose (2.9%). The EPS had good antioxidant activity, especially the activity of scavenging hydroxyl free radicals. At the same time, the EPS also had strong antibacterial ability and could completely inhibit the growth of Staphylococcus aureus. The EPS produced by the Pediococcus pentosaceus SSC–12 can be used as a biologically active product with potential application prospects in the feed, food, and pharmaceutical industries.

Molecular phylogeny of Lytorhynchus diadema (Reptilia, Colubridae) populations in Saudi Arabia

This study presents the molecular phylogenetic relationships among Lytorhynchus diadema (Duméril, Bibron & Duméril, 1854) populations in Saudi Arabia relative to populations from Africa and Asia. This phylogenetic analysis was based on mitochondrial 16S and 12S rRNA partial gene fragments using Neighbor-joining, Maximum Parsimony, and Bayesian methods. The results strongly support the monophyly of Lytorhynchus based on two concatenated genes and the 12S rRNA gene separately. Also, a significant separation is observed between the Arabian samples from Saudi Arabia, Yemen, and Oman, and the African populations from Egypt, Tunisia, and Morocco.

Power and Weakness of Repetition – Evaluating the Phylogenetic Signal From Repeatomes in the Family Rosaceae With Two Case Studies From Genera Prone to Polyploidy and Hybridization (Rosa and Fragaria)

Plant genomes consist, to a considerable extent, of non-coding repetitive DNA. Several studies showed that phylogenetic signals can be extracted from such repeatome data by using among-species dissimilarities from the RepeatExplorer2 pipeline as distance measures. Here, we advanced this approach by adjusting the read input for comparative clustering indirectly proportional to genome size and by summarizing all clusters into a main distance matrix subjected to Neighbor Joining algorithms and Principal Coordinate Analyses. Thus, our multivariate statistical method works as a “repeatomic fingerprint,” and we proved its power and limitations by exemplarily applying it to the family Rosaceae at intrafamilial and, in the genera Fragaria and Rosa, at the intrageneric level. Since both taxa are prone to hybridization events, we wanted to show whether repeatome data are suitable to unravel the origin of natural and synthetic hybrids. In addition, we compared the results based on complete repeatomes with those from ribosomal DNA clusters only, because they represent one of the most widely used barcoding markers. Our results demonstrated that repeatome data contained a clear phylogenetic signal supporting the current subfamilial classification within Rosaceae. Accordingly, the well-accepted major evolutionary lineages within Fragaria were distinguished, and hybrids showed intermediate positions between parental species in data sets retrieved from both complete repeatomes and rDNA clusters. Within the taxonomically more complicated and particularly frequently hybridizing genus Rosa, we detected rather weak phylogenetic signals but surprisingly found a geographic pattern at a population scale. In sum, our method revealed promising results at larger taxonomic scales as well as within taxa with manageable levels of reticulation, but success remained rather taxon specific. Since repeatomes can be technically easy and comparably inexpensively retrieved even from samples of rather poor DNA quality, our phylogenomic method serves as a valuable alternative when high-quality genomes are unavailable, for example, in the case of old museum specimens.

Toxoplasma gondii Genotypes Circulating in Serbia—Insight into the Population Structure and Diversity of the Species in Southeastern Europe, a Region of Intercontinental Strain Exchange

In Europe, Toxoplasma gondii lineage II is dominant, and ToxoDB#1 the most frequently occurring genotype. The abundance of lineage III genotypes varies geographically and lineage I are rare, yet present in several regions of the continent. Data on the T. gondii population structure in southeastern Europe (SEE) are scarce, yet necessary to appreciate the diversity of the species in Europe. To help fill this gap, we genotyped 67 strains from nine species of intermediate hosts in Serbia by MnPCR-RFLP, determined the population structure, and identified the genotypes using ToxoDB. A neighbor-joining tree was also constructed from the isolates genotyped on nine loci. While 42% of the total genotype population consisted of ToxoDB#1 and ToxoDB#2, variant genotypes of both lineages comprised 46% of the population in wildlife and 28% in domestic animals and humans. One genotype of Africa 4 lineage was detected in a human sample. Interestingly, the findings include one lineage III variant and one II/III recombinant isolate with intercontinental distribution, which appear to be moderately related to South American genotypes. Based on these findings, SEE is a region of underappreciated T. gondii genetic diversity and possible strain exchange between Europe and Africa.

Genetic structure and phylogenetic relationships of Phyllidiellapustulosa species from Seribu Islands, North Sulawesi, Halmahera, and West Papua

Phyllidiella pustulosa are brightly coloured gastropod molluscs frequently found in coral reefs of the tropical Indo-Pacific. Phyllidiella pustulosa is widely distributed in Indonesia, such as Seribu Island, North Sulawesi, West Papua, and Halmahera. Based on the genetic characteristics of an individual’s DNA sequence, differences between species can be identified. In this paper, we would like to provide the molecular analysis and phylogenetic relationship among nudibranchs from Indonesian waters. Identification was made by measuring the genetic distance between species. The phylogenetic tree reconstruction was made using the Kimura 2-parameter model with 1000 times bootstrap with neighbor-joining and maximum likelihood method. There is 46 DNA Sequence obtained from 4 different regions (Seribu Island, Halmahera, North Sulawesi, and West Papua). The genetic distance of West Papua and Halmahera has the smallest value among other populations, which is between 0.0051-1.4629, compared to the population in Halmahera. The phylogenetic tree also shows populations from West Papua and Halmahera are on the same lineage, indicating that the population in West Papua and Halmahera had the closest relation. The study suggested that North Sulawesi, Halmahera and West Papua have genetic mixing of the same region, which is distinctive from Seribu Island.

S-D614G Mutation Reveals the Euro-America and East-Asia Origin SARS-CoV-2 Virus Spread in Indonesia

COVID-19 is a pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. The first case was found in the city of Wuhan, Hubei province, China. The first case in Indonesia was reported in March 2020 and currently there are 0.5 million cases with a death rate of 3.1%. This rapid increase in cases is thought to due to presence of the mutant strain S-D614G, which causes a faster rate of infection and spread. The purpose of this study was to determine the presence of S-D614G mutations in Indonesian samples in order to find the origin of COVID-19 which was spread in Indonesia based on the Spike gene sequences and the RdRp genes from 25 countries, and one control sequence China/Wuhan-Hu-1 obtained from the NCBI and GISAID databases. Mutation analysis was carried out through multiple alignments using BioEdit software. Phylogenetic tree reconstruction using MEGA6 software with the Neighbor Joining method. This study found mutation of S-D614G in one Indonesian sample, namely the Indonesian/SBY9 sample along with 23 samples from Europe, America, and Africa. The phylogenetic tree reconstruction confirmed these findings; the mutated samples were closely related to samples from these continents, while the non-mutated Indonesian samples were closely related to sample from East Asia. These findings indicate that the origin of the SARS-CoV-2 virus in Indonesia possibly came from the East Asia cluster and the European-American cluster.

Biosorption of Chromium from Spent Semi-Chrome Liquor: Part 1 Effective Pollution Abatement using Bacillus cerus

The current study focuses on the isolation of Bacillus cerus from mangrove rhizosphere and its ability to treat semi-chrome process liquor of upper leathers. This strain has been identified by its molecular characteristics (16s rRNA sequencing) and confirmation has been obtained from neighbor joining tree. Minimum inhibitory concentration of the strain has been found to be 50 ppm. The growth pattern of this organism has been investigated in the presence of chromium, which showed the bacterial strain can grow luxuriantly at 50 and 100 ppm concentration of chromium. Biosorption study has been conducted at different concentrations (50, 100, 150, 200 and 250 ppm) of chromium. The biosorption capability of Bacillus cerus has been found to be 80.78, 73.19, 65.86, 59.44 and 39.27% for 50, 100, 150, 200 and 250 ppm respectively. Chromium sorption from the semi-chrome process liquor by Bacillus cerus has also been investigated, which showed a reduction of 76.15, 68.56, 61.63, 56.29 and 36.51% against 50, 100, 150, 200 and 250 ppm of chromium. Sorption characterization has been carried out by FTIR (Fourier Transform Infra-Red spectroscopy) and SEM (Scanning Electron Microscopy) analyses and the results confirmed the presence of sorption of chromium in Bacillus cerus.