Global variation in the SARS-CoV-2 proteome reveals the mutational hotspots in the drug and vaccine candidates

ABSTRACTTo accelerate the drug and vaccine development against the severe acute respiratory syndrome virus 2 (SARS-CoV-2), a comparative analysis of SARS-CoV-2 proteome has been performed in two phases by considering manually curated 31389 whole genome sequences from 84 countries. Among the 9 mutations that occur at a high significance (T85I-NPS2, L37F-NSP6, P323L-NSP12, D614G-spike, Q57H-ORF3a, G251V-ORF3a, L84S-ORF8, R203K-nucleocapsid and G204R-nucleocapsid), R203K-nucleocapsid and G204R-nucleocapsid are co-occurring (dependent) mutations and P323L-NSP12 and D614G-spike often appear simultaneously. Other notable variations that appear with a moderate to low significance are, M85-NSP1 deletion, D268-NSP2 deletion, 112 amino acids deletion in ORF8, a phenylalanine insertion amidst F34-F36 (NSP6) and several co-existing (dependent) substitution/deletion (I559V & P585S in NSP2, P504L & Y541C in NSP13, G82 & H83 deletions in NSP1 and K141, S142 & F143 deletions in NSP2) mutations. P323L-NSP12, D614G-spike, L37F-NSP6, L84S-ORF8 and the sequences deficient of the high significant mutations have led to 4 major SARS-CoV-2 clades. The top 5 countries bearing all the high significant and majority of the moderate significant mutations are: USA, England, Wales, Australia and Scotland. Further, the majority of the significant mutations have evolved in the first phase and have already transmitted around the globe indicating the positive selection pressure. Among the 26 SARS-CoV-2 proteins, nucleocapsid protein, ORF3a, ORF8, RNA dependent RNA polymerase and spike exhibit a higher heterogeneity compared with the rest of the proteins. However, NSP9, NSP10, NSP8, the envelope protein and NSP4 are highly resistant to mutations and can be exploited for drug/vaccine development.

Diversity analysis of amp gene sequences in the ‘Candidatus Phytoplasma meliae’

Phytoplasmas are plant pathogenic bacteria transmitted by insects. As endosymbiotic bacteria that lack a cell wall, their membrane proteins are in direct contact with host cytoplasm. In phytoplasmas the immunodominant membrane proteins (IDPs), are the most abundant proteins of the cell membrane. The antigenic membrane protein (Amp), one of the three types of IDPs, is characterized by a positive selection pressure acting in their extracellular domain. In South America, the ‘Candidatus Phytoplasma meliae’ has been associated to chinaberry yellows disease. In the present work, we describe for the first time the structure, phylogeny and selection pressure of amp gene in sixteen ‘Candidatus Phytoplasma meliae’ isolates. Our results indicate that amp gene sequences preserve the structure, large extracellular domain flanked by to hydrophobic domains in the N- (signal peptide) and C-termini (transmembrane), previously described in its orthologues and high divergence in the amino acids residues from extracellular domain. Moreover, a positive selection pressure was detected predominantly in this region confirming previous reports.

Insights into molecular evolution recombination of pandemic SARS-CoV-2 using Saudi Arabian sequences

ABSTRACTThe recently emerged SARS-CoV-2 (Coronaviridae; Betacoronavirus) is the underlying cause of COVID-19 disease. Here we assessed SARS-CoV2 from the Kingdom of Saudi Arabia alongside sequences of SARS-CoV, bat SARS-like CoVs and MERS-CoV, the latter currently detected in this region. Phylogenetic analysis, natural selection investigation and genome recombination analysis were performed. Our analysis showed that all Saudi SARS-CoV-2 sequences are of the same origin and closer proximity to bat SARS-like CoVs, followed by SARS-CoVs, however quite distant to MERS-CoV. Moreover, genome recombination analysis revealed two recombination events between SARS-CoV-2 and bat SARS-like CoVs. This was further assessed by S gene recombination analysis. These recombination events may be relevant to the emergence of this novel virus. Moreover, positive selection pressure was detected between SARS-CoV-2, bat SL-CoV isolates and human SARS-CoV isolates. However, the highest positive selection occurred between SARS-CoV-2 isolates and 2 bat-SL-CoV isolates (Bat-SL-RsSHC014 and Bat-SL-CoVZC45). This further indicates that SARS-CoV-2 isolates were adaptively evolved from bat SARS-like isolates, and that a virus with originating from bats triggered this pandemic. This study thuds sheds further light on the origin of this virus.AUTHOR SUMMARYThe emergence and subsequent pandemic of SARS-CoV-2 is a unique challenge to countries all over the world, including Saudi Arabia where cases of the related MERS are still being reported. Saudi SARS-CoV-2 sequences were found to be likely of the same or similar origin. In our analysis, SARS-CoV-2 were more closely related to bat SARS-like CoVs rather than to MERS-CoV (which originated in Saudi Arabia) or SARS-CoV, confirming other phylogenetic efforts on this pathogen. Recombination and positive selection analysis further suggest that bat coronaviruses may be at the origin of SARS-CoV-2 sequences. The data shown here give hints on the origin of this virus and may inform efforts on transmissibility, host adaptation and other biological aspects of this virus.

Structures of virus-like capsids formed by the Drosophila neuronal Arc proteins

The neuronal protein Arc is a critical mediator of synaptic plasticity. Arc originated in tetrapods and flies through domestication of retrotransposon Gag genes. Recent studies have suggested that Arc mediates intercellular mRNA transfer and like Gag, can form capsid-like structures. Here we report that Drosophila proteins dArc1 and dArc2 assemble virus-like capsids. We determine the capsid structures to 2.8 Å and 3.7 Å resolution, respectively, finding similarity to capsids of retroviruses and retrotransposons. Differences between dArc1 and dArc2 capsids, including the presence of a structured zinc-finger pair in dArc1, are consistent with differential RNA-binding specificity. Our data support a model in which ancestral capsid-forming and RNA-binding properties of Arc remain under positive selection pressure and have been repurposed to function in neuronal signalling.

New Insights into Long Terminal Repeat Retrotransposons in Mulberry Species

The evolutionary dynamics of long terminal repeat (LTR) retrotransposons in tree genomes has remained largely unknown. The availability of the complete genome sequences of the mulberry tree (Morus notabilis) has offered an unprecedented opportunity for us to characterize these retrotransposon elements. We investigated 202 and 114 families of Copia and Gypsy superfamilies, respectively, comprising 2916 intact elements in the mulberry genome. The tRNAMet was the most frequently used type of tRNA in both superfamilies. Phylogenetic analysis suggested that Copia and Gypsy from mulberry can be grouped into eight and six lineages, respectively. All previously characterized families of such elements could also be found in the mulberry genome. About 95% of the identified Copia and Gypsy full elements were estimated to have been inserted into the mulberry genome within the past 2–3 million years. Meanwhile, the estimated insertion times of members of the three most abundant families of the Copia superfamily (908 members from the three most abundant families) and Gypsy superfamily (783 members from the three most abundant families) revealed divergent life histories. Compared with the situation in Gypsy elements, three families of Copia elements are under positive selection pressure, which suggested that Copia elements may have a dominant influence in the evolution of mulberry genes. Analysis of insertion and deletion dynamics suggested that Copia and Gypsy elements exhibited a very long half-life in the mulberry genome. The present work provides new insights into the insertion and deletion dynamics of LTR retrotransposons, and it will greatly improve our understanding of the important roles transposable elements play in the architecture of the mulberry genome.

Selective sweep and phylogenetic models for the emergence and spread of pyrimethamine resistance mutations in Plasmodium vivax

Pyrimethamine resistance is a major concern for the control of human haemoprotozoa, especially Plasmodium species. Currently, there is little understanding of how pyrimethamine resistance developed in Plasmodium vivax in the natural field conditions. Here, we present first time the evidence of positive selection pressure on a dihydrofolate reductase locus and its consequences on the emergence and the spread of pyrimethamine resistance in P. vivax in the Punjab province of Pakistan. First, we examined the pyrimethamine resistance locus in 38 P. vivax populations to look for evidence of positive selection pressure in human patients. The S58R (AGA)/S117N (AAC) double mutation was most common, being detected in 10/38 populations. Single mutation S117N (AAC), I173L (CTT) and S58R (AGA) SNPs were detected in 8/38, 2/38 and 1/38 populations, respectively. The F57L/I (TTA/ATA) and T61M (ATG) SNPs were not detected in any population examined. Although both soft and hard selective sweeps have occurred with striking differences between populations, there was a predominance of hard sweeps. A single resistance haplotype was present at high frequency in 9/14 populations, providing a strong evidence for the single emergence of these mutations. In contrast, 5/14 populations carried multiple resistance haplotypes at high frequencies, providing an evidence of the emergence of resistance by recurrent mutations, characteristics of soft selective sweeps. Our phylogenetic relationship analysis suggests that S58R (AGA)/S117N (AAC) and S117N (AAC) mutations arose multiple times from a single origin and spread to multiple different cities in the Punjab province through gene flow. Interestingly, the I173L (CTT) mutation was present on a single haplotype, suggesting that it arises rarely and has not spread between cities. Our work shows the need for responsible use of exiting and new antimicrobial drugs and their combinations, control the movement of infected patients and mosquito vector control strategies.