Novel Negative Sense Genes in the RNA Genome of Coronaviruses.

The coronavirus family consists of lipid-containing envelope viruses that have a single-stranded RNA genome that encodes 25-30 proteins in different viruses by the mechanism of positive-polarity strategy. In addition, extended open reading trnslation frames (ORFs, genes) located in a negative-sense orientation were found in the genomes of coronaviruses. The size of negative-sense genes varies in the range of 150-450 nt, which corresponds to polypeptides encoded by negative-polarity genes (negative gene proteins, NGP) with m. m. 5-30 × 103 kDa. Coronaviruses show marked differences from virus to virus in the number of negative genes detected. These negative-sense genes in the coronavirus genome allow this family to be considered as viruses developing an ambisense genome strategy.

Structural and evolutionary characteristics of HA, NA, NS and M genes of clinical influenza A/H3N2 viruses passaged in human and canine cells.

BACKGROUND: Canine (MDCK) cells and chicken eggs are usually used for isolation of human influenza viruses. Viruses isolated by these procedures often differ from those present in the clinical specimens, since adaptive changes occur during virus transmission from the human host to cells of heterologous origin. OBJECTIVES: To minimize these species-dependent changes, CACO-2 cells derived from human intestinal epithelium were used to isolate virus from influenza patients. STUDY DESIGN: Influenza A viruses of subtype H3N2 were primarily isolated in CACO-2 and then passaged in parallel in CACO-2 and MDCK cells. Structural properties of passaged virus variants were compared and analyzed for evolutionary relationships. RESULTS: Influenza viruses were isolated in CACO-2 with higher efficiency than in MDCK and chicken eggs. The following observations were made: (i) recent isolates showed an about 2-fold increase in the number of glycosylation sites of HA and NA when compared to isolates from 1968 to 1970; (ii) during passages of clinical strains in CACO-2 and MDCK cells HA and NA mutated cooperatively with strain-specific variations implying that functioning of the HA-NA complex varied from strain to strain in one influenza outbreak; (iii) there were no amino acid exchanges in the HA receptor binding site although the viruses acquired the ability to agglutinate avian erythrocytes after passage in MDCK cells, suggesting that virus adsorption is regulated by several factors; (iv) quasispecies characterized by deletion of 66 nucleotides (22 amino acids) in the stalk region of the NA gene was dominant in naso-pharyngeal washes of all patients whereas during passaging in CACO-2 cells this deleted genotype in isolates from different patients was either stably retained as prevalent quasispecies or rapidly replaced for that one containing full length NA gene; (v) the M2 protein of clinical viruses was sensitive to amantadine; (vi) the NS segment of human viruses, unlike the most of avian ones, contained an additional positive-sense open reading frame encoding a hypothetical 25kD polypeptide (negative strand protein, NSP). CONCLUSIONS: The data suggest that (i) clinical influenza viruses can be isolated from respiratory tract of humans more effectively in human than in canine cells; (ii) heterologous virus population circulates during one influenza outbreak; (iii) increasing numbers of glycosylation sites on HA and NA and stalk shortening of NA take place during virus evolution in humans.