Corona Virus (CoVid19) Genome: Genomic and Evolutionary Analysis Point Towards Its Possible Synthetic Origin

The Severe acute respiratory syndrome (SARS) corona virus (CoV) 2 SARS-CoV-2 mediated epidemic is a global pandemic. The first genome sequence data of SARS-CoV-2 (CoVid19) concluded that it has a bat reservoir and bat was the immediate donor. Andersen et al., (2020) has reported that it is improbable to do laboratory manipulation of SARS CoV [1]. But, Lau et al., (2010) has already reported the generation of recombinant bat SARS CoV and they had reported three recombinant genotypes. Hence laboratory based manipulation has already completed long before[2]. A deep comparative study of bat SARS CoV with other SARS CoVs (including human SARS CoV of German isolate) revealed, human SARS CoV-2 genomes (isolates of China, India, Italy, Nepal, and the United States of America) had sequence similarity of 79-80% only with bat SARS CoV and it has sequence similarity of approximately 60% with the human SARS CoV (German isolate). The presence of large genomic dissimilarity of bat SARS CoV genome with human SARS CoV-2 cannot be considered as an immediate donor to human SARS CoV-2. However, the genomic sequence similarity within the SARS CoV-2 isolates of China, India, Italy, Nepal, and USA shared 99-100% similarity. This suggests that human SARS CoV-2 did not undergo heavy mutation to generate immediate new genotype. If the SARS CoV-2 infection happened to the human through the SARS CoV of bat from Wuhan meat market, it should have sequence similarity of more than 99% which was not found in the study. Phylogenetic analysis revealed, bat SARS CoV did not fall with the group of SARS CoV-2 of China, India, Italy, Nepal, and USA isolates. This suggests that bat SARS CoV has genomic and evolutionary dissimilarity and cannot be considered as immediate and direct donor of human SARS CoV-2. The natural selection of bat genome before transfer to the zoonotic organism is a time-consuming process and natural selection in human post zoonotic transfer is also time-consuming event. Therefore, concept mentioned by Andersen et al., (2020)[1] regarding its transfer from a bat of Wuhan meat market is irrefutably incorrect. Sequence alignment revealed the presence of inserted codons in human SARS CoV-2 and synteny analysis corroborated with the presence of extra nucleotides/codons in the human SARS CoV-2. Relative time tree analysis revealed it origin before 0.00 million year ago, suggesting its recent synthetic/modified origin.

Corona virus (CoVid19) genome: genomic and biochemical analysis revealed its possible synthetic origin

The Severe acute respiratory syndrome (SARS) corona virus 2 SARS-CoV-2 mediated epidemic is a global pandemic. It has evolved as a curse to the human civilization and at the present situation, where most of the cities in the world are on lockdown. The first genome sequence data of SARS-CoV-2 (CoVid19) and their reports that followed concluded that it was a member of the genus Betacoronavirus and has a bat reservoir. To understand its origin and evolution, we conducted a deep comparative study by comparing the genomes of bat SARS CoV and other SARS CoVs (including human SARS CoV of German isolate). Results revealed that CoVid19 genomes from isolates of China, India, Italy, Nepal, and the United States of America has sequence similarity of 79-80% only with the bat SARS CoV and it has sequence similarity of approximately 60% with the human SARS CoV of German isolate. Whereas, the sequence similarity within the CoVid19 genomes of these countries was 99-100%. If the SARS CoV infection happened to human through the SARS CoV of bat origin, it should have sequence similarity of more than 99% which was absent in this case. Phylogenetic analysis revealed, bat SARS CoV did not fall with the group of SARS CoV of China, India, Italy, Nepal, and USA isolates. The genome analysis revealed the presence of multiple microsatellite repeats sequences. Proteome analysis revealed, the melting temperature (Tm) of surface glycoprotein was less than 55oC, suggesting the steam treatment can be an ideal preventative measure to destabilize the CoVid19, and thus it’s spreading

First Identification and Genomic Characterization of a Porcine Sapelovirus from Corsica, France, 2017

We report the isolation and genomic characterization of a Sapelovirus A strain, or porcine sapelovirus (PSV), from a diarrheic Corsican piglet in France. It shares 87% nucleotide identity with a 2014 German isolate.

Morphological and Genetic Analyses of the Invasive Forest Pathogen Phytophthora austrocedri Reveal that Two Clonal Lineages Colonized Britain and Argentina from a Common Ancestral Population

Phytophthora austrocedri is causing widespread mortality of Austrocedrus chilensis in Argentina and Juniperus communis in Britain. The pathogen has also been isolated from J. horizontalis in Germany. Isolates from Britain, Argentina, and Germany are homothallic, with no clear differences in the dimensions of sporangia, oogonia, or oospores. Argentinian and German isolates grew faster than British isolates across a range of media and had a higher temperature tolerance, although most isolates, regardless of origin, grew best at 15°C and all isolates were killed at 25°C. Argentinian and British isolates caused lesions when inoculated onto both A. chilensis and J. communis; however, the Argentinian isolate caused longer lesions on A. chilensis than on J. communis and vice versa for the British isolate. Genetic analyses of nuclear and mitochondrial loci showed that all British isolates are identical. Argentinian isolates and the German isolate are also identical but differ from the British isolates. Single-nucleotide polymorphisms are shared between the British and Argentinian isolates. We concluded that British isolates and Argentinian isolates conform to two distinct clonal lineages of P. austrocedri founded from the same as-yet-unidentified source population. These lineages should be recognized and treated as separate risks by international plant health legislation.

Incidence of Garlic common latent virus in Argentina, and phylogenetic and recombination analyses of isolates

The objective of this work was to estimate the incidence and prevalence of Garlic common latent virus (GarCLV) in the main production regions of garlic (Allium sativum) in Argentina, and to perform phylogenetic and recombination analyses in isolates from these regions. Leaf samples (3,050) were taken from four garlic commercial types, in 13 departments of the four main garlic-producing provinces of Argentina, in a 1,175-ha sampling area. Virus infection was evaluated with DAS-Elisa test using specific antiserum, and the phylogenetic and recombination analyses were done with capsid protein (CP) nucleotide sequence of seven GarCLV isolates from the provinces. The incidence of GarCLV in the evaluated provinces varied between 6.7 and 22% of the samples, whereas the prevalence varied between 52.6 and 70%. In the analysis of garlic commercial types, Morado showed the highest incidence of the virus, in the province of San Juan, whereas Rosado Paraguayo had the lowest incidence, in the province of Cordoba. Nucleotide identity in the CP sequences ranged between 80.3 and 97.6%. The phylogenetic analysis shows the presence of two main groups of GarCLV and of a possible third group that would include only a German isolate. The recombination analysis between isolates from different parts of the world evidences the presence of recombinant isolates from Poland and Australia.

Molecular Characterization of Pseudomonas fluorescens Isolates Involved in the Italian “Blue Mozzarella” Event

Between June and September 2010, widespread Italian consumer reports of unusual blue spoilage on fresh dairy products were publicized, resulting in the so-called blue mozzarella event. An inordinately high number of samples from mozzarella and whey cheese products of Italian and German production subsequently tested positive for Pseudomonas fluorescens. The aim of this study was to verify whether a selected P. fluorescens strain was responsible for this apparently unusual event. Molecular characterization of 181 isolated P. fluorescens strains was conducted using a newly optimized pulsed-field gel electrophoresis protocol. Although a high number of pulsotypes was found (132), only four pulsotypes were associated with more than one production plant, and only one German isolate had the same pulsotype as was detected in two Italian plants. This is the only evidence of possible cross-contamination among cheeses from the two countries. The overall results did not support the spread of contamination from German to Italian plants or the presence of one environmental strain that spread in both countries.