Sequence similarity of SARS-CoV-2 and humans: Implications for SARS-CoV-2 detection

Host-similar fragments in the African swine fever virus genome: distribution, functions, and evolution

African swine fever virus (ASFV) predominantly infects Argasidae and suids, resulting in high morbidity and mortality in pigs. Despite the crucial role that viral sequences resembling those of the host play in the virus's survival, there are limited comprehensive studies on the genomic similarities between ASFV and its hosts. Consequently, this study employs homology analysis to construct a similarity network between ASFV and its hosts (Argasidae and suids), investigating the distribution, function, evolution, and origins of these similar sequences in ASFV. Our findings indicate that the host-similar fragments are mainly distributed between positions 70000 and 180000 of the ASFV genome, primarily within non-coding regions. Notably, these non-coding fragments are often associated with promoter functions. Furthermore, the analysis of suid proteins that share similarities with ASFV proteins reveals that they predominantly exhibit RNA polymerase activity and are involved in metabolic processes. Evolutionary analysis indicates that pan-similar sequences of ASFV exist in an open state, highlighting the diversity of these analogous sequences. Additionally, a positive correlation was identified between the occurrence of recombination breakpoints and similar sequences, indicating that homologous recombination may serve as a crucial mechanism driving the formation of these analogous sequences.

Global genomic diversity and conservation of SARS-CoV-2 since the COVID-19 outbreak

IMPORTANCE

Our results indicate that most severe acute respiratory syndrome coronavirus 2 genomes sampled from patients had a mutation rate ≤1.07 ‰ and genome-tail proteins (including S protein) were the main sources of genetic polymorphism. The analysis of the virus-host interaction network of genome-tail proteins showed that they shared some antiviral signaling pathways, especially the intracellular protein transport pathway.