VAERS data, Myocardial Infarction.

4,326 MIs in total.

Died after MI was listed as a symptom.

The chart on the left is # of MIs.

The chart on the right is # of deaths with MI listed as a symptom.

Putative host origins of RNA insertions in SARS-CoV-2 genomes

Naturally occurring insertions of foreign RNA into viral genomes are rare but can have high consequences. Coronaviruses have previously incorporated genes from their hosts or other viruses. For example, the phosphodiesterases, NS2a of the Embecovirus subgenus (which includes OC43, HKU1, and MHV), and NS4b of MERS-CoV, are thought to be two independent acquisitions of vertebrate AKAP7. Furthermore, Embecovirus Haemagglutinin-Esterase glycoproteins share a high degree of structural homology to the same proteins from Orthomyxoviridae. However, in both these examples, whole proteins or domains are used for a similar function to the host/other viruses. Flaviviridae and Orthomyxoviridae have been shown to acquire host RNA sequences that confer phenotypes unrelated to their original function, more like the insertions proposed in this study. Firstly, the Pestivirus bovine viral diarrhea virus (BVDV) has been shown to repeatedly insert host RNA into its NS2 coding region which can alter polyprotein cleavage and lead to a cytopathic phenotype in cell culture. Interestingly, some cytopathic BVDV achieved the same phenotype using viral-derived RNA sequences. Finally, and perhaps most relevant to the origin of SARS-CoV-2, is the example of the 2012 Mexican highly pathogenic avian influenza H7N3 outbreak (Maurer-Stroh, Lee et al. 2013). Avian influenza viruses of the H7 and H5 subtypes can exist as either low or high pathogenicity depending on the presence or absence of a polybasic furin cleavage site in their haemagglutinin proteins. It has been proposed that the 2013 Mexican H7N3 virus gained its furin cleavage site from heterologous recombination with host 28S ribosomal RNA, thought to be possible due to genomic RNA replication in the host nucleus/nucleolus where nascent rRNA is synthesized.

Insertions in the SARS-CoV-2 genome are also of particular interest as they may have the potential for much greater phenotypic change than mutation or deletion alone - a prime example being the original insertion generating the furin cleavage site, which likely contributed to the pandemic potential of the virus. However, insertion of additional loops in the Spike NTD, or further insertions at the S1/S2 site may have the ability to change the antigenicity or cleavability of these regions, respectively, and alter the phenotype of the viruses that emerge. These types of mutations therefore can act as ‘wildcard’ mutations that are hard to predict, and special care should be taken so they can accurately be identified and characterized.

https://virological.org/t/putative-host-origins-of-rna-insertions-in-sars-cov-2-genomes/761

A structural explanation for the low effectiveness of the seasonal influenza H3N2 vaccine

Abstract

The effectiveness of the annual influenza vaccine has declined in recent years, especially for the H3N2 component, and is a concern for global public health. A major cause for this lack in effectiveness has been attributed to the egg-based vaccine production process. Substitutions on the hemagglutinin glycoprotein (HA) often arise during virus passaging that change its antigenicity and hence vaccine effectiveness. Here, we characterize the effect of a prevalent substitution, L194P, in egg-passaged H3N2 viruses. X-ray structural analysis reveals that this substitution surprisingly increases the mobility of the 190-helix and neighboring regions in antigenic site B, which forms one side of the receptor-binding site (RBS) and is immunodominant in recent human H3N2 viruses. Importantly, the L194P substitution decreases binding and neutralization by an RBS-targeted broadly neutralizing antibody by three orders of magnitude and significantly changes the HA antigenicity as measured by binding of human serum antibodies. The receptor binding mode and specificity are also altered to adapt to avian receptors during egg passage. Overall, these findings help explain the low effectiveness of the seasonal vaccine against H3N2 viruses, and suggest that alternative approaches should be accelerated for producing influenza vaccines as well as isolating clinical isolates.

Discussion

It should be noted that the receptor specificity changes conferred by the L194P substitution differ from the traditional ones that facilitate avian-to-human transmission where substantial diminishment in binding to avian receptors is accompanied by a large affinity gain towards human receptors [33, 34]. The atypical receptor specificity change observed in L194P is likely due to the glycan content in embryonated chicken eggs. Firstly, sialylated glycans in eggs are short and are predominantly α2–3 linkage [12], whereas recent human H3N2 viruses have a receptor specificity favoring long α2–6 sialylated glycans with several LacNAc repeats [35]. Therefore, passaging human H3N2 viruses in eggs would result in a strong selection against α2–6 sialylated glycans. Secondly, there may be a high surface density of sialylated glycans in eggs, as suggested by the fact that eggs can support a wild-type-level growth of an RBS mutant Y98F that has a low receptor-binding affinity and is attenuated in vivo [36, 37]. These observations, along with the results from our study, indicate that a slight increase in binding towards avian receptors is sufficient to improve the replication efficiency of human H3N2 viruses in eggs.

Change in antigenicity caused by egg-adaptive substitutions is common for the influenza virus [17–20, 22]. Such an antigenic effect was expected to only impact the epitopes that contain the substitution of interest [22]. However, we demonstrate here that the egg-adaptive substitution L194P in H3 subtype disrupts a larger region spanning the 190-helix and part of the 150-loop in the HA RBS. In fact, such conformational dynamics have been shown to influence antigenicity in several other pathogens [38–40]. While this type of effect caused by the L194P substitution may not be as applicable to other egg-adaptive substitutions, it may have profound implications for vaccine effectiveness. The prevalence of the L194P substitution from egg-passaged H3N2 viruses will likely hinder the ability of the influenza vaccine to induce an antibody response that effectively protects against circulating seasonal H3N2 viruses, especially for responses against antigenic site B and surrounding epitope regions. Importantly, antigenic site B has been shown to be immunodominant in recent human H3N2 viruses [20, 27] and hence such a substitution would have a more profound effect on the antibody response. The extensive usage of chicken eggs for passaging clinical isolates and for vaccine production suggests that the egg-adaptive substitution L194P may contribute to the low vaccine effectiveness against the H3N2 subtype [8]. A recent study indeed demonstrated that an egg-adaptive substitution Q226R in the H1N1 vaccine elicits an immune response that preferentially targets the vaccine strain, but not its circulating counterpart [22]. As annual vaccination remains the major preventive measure against the influenza virus, it may be beneficial to accelerate consideration of alternative approaches for influenza vaccine production [41] to optimize the protective effect of the vaccine [22].

https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1006682

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