Wave Genome Germany (WGG) is a network of German laboratories that send sequenced specimens directly to RKI for whole genome sequencing, in order to generate an unbiased sample set that detects emerging variants and allows comparative analysis.
Molecular phylogeny and Nextstrain-based mutation events indicate that during the transition from wave 1 to wave 2, several SARS-CoV-2 variants attempted to increase their transmissibility by adopting mutations to their spike protein.
Molecular Phylogeny
Molecular phylogeny analyses compare DNA sequences from various organisms to reconstruct their evolutionary histories, providing clues as to dates of divergence and the evolutionary origin of species. Closely related organisms tend to share similar genetic molecules like deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and proteins; this makes molecular phylogenetic analyses an accurate way of estimating time of divergence as mutation rates should remain similar across species sharing the same sequences.
Molecular systematics is an emerging discipline which utilizes molecular phylogenetic trees to classify taxa, predict morphological similarities and dissimilarities among them, and establish relationships with fossils. This approach is predicated upon the assumption that classifying any given taxon must correspond with its phylogenetic descent – however this method has its limitations; for example it requires large sample populations from each taxon which often is unobtainable; furthermore all valid taxa are monophyletic; this technique offers significant improvement over previous methods which relied solely upon morphological data alone.
An examination of Euphrasia genomes shows, for example, that at shallow phylogenetic scales postglacial colonization of North Western Europe was accomplished in multiple waves from distinct source populations. Furthermore, at deeper phylogenetic scales its phylogeny is structured by geography and ploidy; Euphrasia tetraploids form their own subgenus apart from Northern Hemisphere diploids.
Maximum likelihood is an excellent method for reconstructing phylogenetic trees, combining the likelihood of the tree topology and bootstrap calculation that assesses statistical confidence of individual nodes in the tree. Bootstrap values indicate how often an alignment was replicated randomly from its original state; high bootstrap values signify increased trust in tree topologies. This approach can provide useful data regarding relative timing of postglacial colonization events in a region as well as understanding patterns of disease transmission.
Deletion Events
Deletion events are a form of DNA mutation characterized by the removal of sections of DNA sequence. Deletions can range in size from one nucleotide to an entire chromosome. Most often, deletion events result from point mutations within genes themselves that are then repaired via recombination resulting in pseudogenes, or mutant versions with point mutations that lack their functional domain; Deletion mapping is one method that can help identify where deletion events have taken place; by comparing wild-type to mutant version of same genes then using mapping, you can identify its exact position on map as well.
As part of their genomDE project, researchers have identified many deletion events. These deletions alter the functions of many genes and proteins. One notable group of deleted genes involves those involved with anaerobic metabolism – including dehydrogenases involved with turning carbohydrates to energy. Another noteworthy group pertains to intermediary metabolism which helps plants survive in low oxygen environments.
Another intriguing finding from SARS-CoV-2 genome sequences was that wave-2 samples showed more deletion events than those collected during wave-1 samples, suggesting more active recombination during this second wave of pandemic transmission. This indicates that SARS-CoV-2 may quickly acquire its replication and transmission genes.
SARS-CoV-2 deletions may have come from previous infections. The pandemic of SARS-CoV-2 has greatly accelerated its evolution by allowing bacteria infected by it to acquire genetic mutations faster. This has resulted in faster rates of transmission of the virus, with earlier manifestation of disease symptoms.
Reconstructions of CHKs show they are ancient duplications of core angiosperm genes that occurred multiple times during WGDs in different lineages of Brassicaceae plants. Reconciliation trees support this hypothesis that ancient duplications may account for HPT amplification across monocot and dicot species.
Transversion Events
Transition and transversion mutations differ from deletion events in that they are the result of specific allele frequencies that reflect population-level genotypes. Furthermore, transitions and transversions represent the primary form of point mutation found in proteins which lead to amino acid substitutions; their abundance thus provides insights into where point mutations originated in protein coding sequences.
We find the frequency of parallel replacements significantly greater than expected from random events, suggesting an elevated sensitivity of genetic code evolution to parallel processes. More specifically, multiple alleles with similar amino acid changes increase the chances that one or both will be replaced by one having compatible sequence changes.
To measure these events, we developed a method that counts paths or events according to their likelihood of producing transitions or transversions in particular codon positions. By employing this approach, we found that four times more transition events occurred than expected while seven times more transversion events took place than expected.
These results demonstrate that mutational biases play a significant role in driving parallel adaptation observed across our sample of proteins, though its magnitude varies across species indicating its impact is complex and requires further study.
Phylogenetic analyses also revealed that pseudo-HPTs had evolved at least twice independently, consistent with the hypothesis that the cytokinin signaling pathway emerged through multiple WGD events (see GDB). Monocot pseudo-HPTs more frequently experienced gene loss after WGD events while dicot pseudo-HPTs tended to co-retain them.
SARS-CoV-2 Proteome
At Calu-3 human lung epithelial cells were infected at an MOI of 0.1 with SARS-CoV-2 isolate hCoV-19/Norway/Trondheim-S15/2020 at five time points (3, 6, 12, 24 and 48 hours postinfection) to assess host responses to SARS-CoV-2 infection. A comprehensive analysis was performed including transcriptomics, TMT-based quantitative temporal proteomics (QTP), phosphoproteomics and acetylomics data.
Transcriptomics has revealed early changes to protein levels associated with viral replication and entry, while the phosphoproteome data provided a glimpse into Hippo signaling, DNA/damage response pathways, protein ubiquitination processes, alternate splicing mechanisms as well as protein acetylation processes. Acetylomics analysis identified decreased protein acetylation at multiple sites – including one on vimentin LRR domain which plays an essential role in viral entry yet it remains to be established whether differential acetylation could play any part in virus-host interactions.
Proteomics experiments identified peptides which were then used to create a SARS-CoV-2-host contactome map and utilized molecular docking analysis to detect binding sites between SARS-CoV-2 spike glycoprotein RBD and the human ACE2 receptor; results demonstrated a highly conserved region on this receptor’s binding surface that likely accounts for its high binding affinity with RBD spike glycoprotein RBD.
At times of SARS-CoV-2 infection, other changes were noted in host cells, such as altered protein phosphorylation levels of those involved in cytoskeletal regulation being changed at multiple sites and DNA/damage/response and protein ubiquitination pathways being compromised.
Overall, the HuSCI virus-host contactome map demonstrated significant enrichment for host proteins known to be targets of other viruses or those that adapted their phosphorylation status in response to SARS-CoV-2 infection. It was also abundant with proteins known to directly interact with SARS-CoV-2 RNA. This suggests that it can serve as an invaluable resource in understanding interactions between viruses and hosts.
