A 32% Human-Derived Mosaic in the In Silico-Assembled SARS-CoV-2 Spike Protein: Accidental Contaminant Misincorporation or Intentional Functional Chimeric Design?

ABSTRACT

The SARS-CoV-2 spike glycoprotein (YP_009724390.1) was not isolated from a physical virion but was computationally assembled in silico from fragmented RNA in bronchoalveolar lavage fluid (BALF) of a single patient (Wu et al., Nature, 2020). This in silico-derived sequence serves as the antigen in mRNA vaccines administered to over five billion individuals. Here, we report that 32% (416 amino acids) of this spike exhibits significant local similarity to human endogenous retroviral (HERV) elements and cellular proteins across six functional domains: membrane fusion, receptor binding, immune modulation, intracellular trafficking, structural rigidity, and metabolic interference. These alignments, identified via six reproducible NCBI BLASTp searches (RIDs: H2C3P344014, H2PYZ3WV016, H3XRGFXY014, H47XDWV7014, H48U4FWY016, H498WK63016), involve over 150 independent human loci and are absent in bat or pangolin coronaviruses. The in silico origin of the spike is established; the critical unresolved question is whether the 32% human mosaic reflects (1) accidental misincorporation of host contaminants during metagenomic assembly or (2) intentional inclusion of human-derived sequences for chimeric functional enhancement. The precision of motif placement, statistical improbability of random convergence (< 10⁻²⁰), and functional coherence of the domains—independently validated by HERV-K/W upregulation in nasal mucosa as early predictors of hospitalization and respiratory failure (Petrone et al., 2023), severe COVID-19 lungs (Temerozo et al., 2022), blood with IFN-I induction (Guo et al., 2022), pulmonary arterial hypertension (Wang et al., 2023), pediatric MIS-C/KD (Balestrieri et al., 2023), MSH3 homology in the furin site (Ambati et al., 2022), and SARS-CoV-2-triggered HERV transactivation driving inflammaging, senescence, and neurodegeneration (Wu et al., 2025)—support the need for independent re-assembly of the raw data using human-excluded reference databases.

Keywords: SARS-CoV-2, in silico assembly, spike protein, human endogenous retrovirus, sequence homology, chimeric, chimera, mosaic, mRNA vaccine, inflammaging, accidental vs. intentional design