The genome of the influenza virus

The Neuraminidase Stalk Deletion Serves as Major Virulence Determinant of H5N1 Highly Pathogenic Avian Influenza Viruses in Chicken

Highly pathogenic avian influenza viruses (HPAIV) cause devastating losses in gallinaceous poultry world-wide and raised concerns of a novel pandemic. HPAIV develop from low-pathogenic precursors by acquisition of a polybasic HA cleavage site (HACS), the prime virulence determinant. Beside that HACS, other adaptive changes accumulate in those precursors prior to transformation into an HPAIV. Here, we aimed to unravel such virulence determinants in addition to the HA gene. Stepwise reduction of HPAIV genes revealed that the HPAIV HA and NA form a minimum set of virulence determinants, sufficient for a lethal phenotype in chicken. Abolishing the NA stalk deletion considerably reduced lethality and prevented transmission. Conversely, the analogous stalk deletion reconstructed in the NA of an LPAIV reassortant carrying only the HPAIV HA resulted in 100% lethality both after primary and contact infection. Remarkably, the unmodified LPAIV NA with its long stalk, when exclusively introduced into the H5N1 HPAIV, still enabled high virulence and efficient transmission. Therefore, irrespective of an NA stalk deletion, minor virulence determinants in addition to the essential polybasic HACS contribute to high virulence, whereas the NA stalk deletion alone may serve as major virulence determinant.

Definition of the minimal viral components required for the initiation of unprimed RNA synthesis by influenza virus RNA polymerase

The first 11 nt at the 5' end of influenza virus genomic RNA were shown to be both necessary and sufficient for specific binding by the influenza virus polymerase. A novel in vitro transcription assay, in which the polymerase was bound to paramagnetic beads via a biotinylated 5'-vRNA oligonucleotide, was used to study the activities of different forms of the polymerase. Complexes composed of co-expressed PB1/PB2/PA proteins and a sub-complex composed of PB1/PA bound to the 5'-vRNA oligonucleotide, whereas PB1 expressed alone did not. The enriched 5'-vRNA/PB1/PB2/PA complex was highly active for ApG and globin mRNA primed transcription on a model 3'-vRNA template. RNA synthesis in the absence of added primers produced products with 5'-terminal tri- or diphosphate groups, indicating that genuine unprimed initiation of transcription also occurred. No transcriptase activity was detected for the PB1/PA complex. These results demonstrate a role for PA in the enhancement of 5' end binding activity of PB1, a role for PB2 in the assembly of a polymerase complex able to perform both cap-dependent and -independent synthesis and that NP is not required for the initiation of replicative transcription.

Temperature-sensitive lesions in two influenza A viruses defective for replicative transcription disrupt RNA binding by the nucleoprotein

The negative-sense segmented RNA genome of influenza virus is transcribed into capped and polyadenylated mRNAs, as well as full-length replicative intermediates (cRNAs). The mechanism that regulates the two forms of transcription remains unclear, although several lines of evidence imply a role for the viral nucleoprotein (NP). In particular, temperature-shift and biochemical analyses of the temperature-sensitive viruses A/WSN/33 ts56 and A/FPV/Rostock/34/Giessen tsG81 containing point mutations within the NP coding region have indicated specific defects in replicative transcription at the nonpermissive temperature. To identify the functional defect, we introduced the relevant mutations into the NP of influenza virus strain A/PR/8/34. Both mutants were temperature sensitive for influenza virus gene expression in transient-transfection experiments but localized and accumulated normally in transfected cells. Similarly, the mutants retained the ability to self-associate and interact with the virus polymerase complex whether synthesized at the permissive or the nonpermissive temperatures. In contrast, the mutant NPs were defective for RNA binding when expressed at the nonpermissive temperature but not when expressed at 30 degrees C. This suggests that the RNA-binding activity of NP is required for replicative transcription.

Mutants and revertants of an avian influenza A virus with temperature-sensitive defects in the nucleoprotein and PB2

ts19 is a temperature-sensitive (ts) mutant of the influenza A fowl plague virus with a defect in the nucleoprotein (NP). In ts19-infected chicken embryo cells all viral components are synthesized in normal yields at the nonpermissive temperature, but infectious virus is not formed. Under these conditions the migration of the NP and M of ts19 from the cell nucleus to the cytoplasm is affected. This ts defect is due to a single amino acid replacement (R162K) in a completely conserved region of the NP. Another mutant with a different defect in the NP is ts81. After infection with ts81 at 40 degrees no vRNA is being synthesized. By backcross of a revertant derived from ts81 many isolates with a ts defect in the PB2 protein were obtained. This ts defect seems to extragenically suppress the ts defect in the NP gene and to be dominant in a wild-type background.

Influenza virus RNA replication in vitro: synthesis of viral template RNAs and virion RNAs in the absence of an added primer

The two steps in influenza virus RNA replication are (i) the synthesis of template RNAs, i.e., full-length copies of the virion RNAs, and (ii) the copying of these template RNAs into new virion RNAs. We prepared nuclear extracts from infected HeLa cells that catalyzed both template RNA and virion RNA synthesis in vitro in the absence of an added primer. Antibody depletion experiments implicated nucleocapsid protein molecules not associated with nucleocapsids in template RNA synthesis for antitermination at the polyadenylation site used during viral mRNA synthesis. Experiments with the WSN influenza virus temperature-sensitive mutant ts56 containing a defect in the nucleocapsid protein proved that the nucleocapsid protein was indeed required for template RNA synthesis both in vivo and in vitro. Nuclear extracts prepared from mutant virus-infected cells synthesized template RNA at the permissive temperature but not at the nonpermissive temperature, whereas the synthesis of mRNA-size transcripts was not decreased at the nonpermissive temperature. Antibody depletion experiments showed that nucleocapsid protein molecules not associated with nucleocapsids were also required for the copying of template RNA into virion RNA. In contrast to the situation with the synthesis of transcripts complementary to virion RNA, no discrete termination product(s) were made during virion RNA synthesis in vitro in the absence of nucleocapsid protein molecules.

Molecular aspects of the epidemiology of virus disease

With regard to molecular epidemiology, influenza A viruses belong to the best-studied virus systems. At least two large reservoirs of influenza A viruses have been built up in nature, one in humans and another one in water fowls. The latter one is very heterogenous, consisting of viruses belonging to 13 hemagglutinin (HA) and 9 neuraminidase (NA) subtypes in almost all possible combinations. The segmented structure of the influenza virus genome allows the creation of new influenza strains by reassortment. By replacement of the HA gene of human strains new pandemic viruses can be generated (antigenic shift). The particular structure of the HA enables the human influenza A-viruses to create variants which can escape the immune response of the host (antigenic drift). The nucleoprotein is responsible for keeping those two large reservoirs apart. Mixing of genes of viruses from these two reservoirs seems to happen predominantly by double infection of pigs, which apparently are tolerant for infection by either human or avian influenza viruses. The molecular mechanisms described for influenza viruses can be explained by the particular structure of their genome and their components and cannot be generalized. Each virus has developed its own strategy to multiply and to spread.

Extragenic and intragenic suppression of a transport mutation in the hemagglutinin gene of an influenza A virus as revealed by backcross and sequence determination

Cooperation of viral proteins, or functional domains within a protein, can be studied by analyzing temperature-sensitive (ts) mutants and revertants carrying suppressor mutations. Accordingly, we have sequenced the hemagglutinin (HA) genes of a ts mutant of fowl plague virus (FPV), with a transport defect in the HA, and of five independent ts+ revertants (R1, R3, R4, R5, and R9). The amino acid replacement in position 480 from Thr to Ile, leading to the loss of a complex carbohydrate side chain, is responsible for the ts phenotype. R3, R4, and R5 are true revertants in that they have Thr in position 480, while R1 and R9 have kept Ile. The sequence of the HA of R1 is exactly the same as that of the ts mutant, while the R9 HA has two additional amino acid replacements in positions 91 (Lys-Thr) and 104 (Gly-Val). By doing a backcross with wild-type virus, it was shown that R1 carries an extragenic suppressor mutation, while R9 is intragenically suppressed. We conclude that the HA is transported from the site of its synthesis in the rough endoplasmic reticulum (RER) to the plasma membrane along with another viral gene product, which by mutation can complement the ts defect. An alternative interpretation is that the ts mutation results from a change in HA which allows an interacting protein to bind HA too soon, holding it back in the RER. The suppressor mutation may remove this premature interaction.

Evolution of the influenza virus neuraminidase gene during drift of the N2 subtype

The complete genetic information for the neuraminidase (NA) gene of influenza virus A/Bangkok/1/79 has been cloned by in vitro synthesis of dsDNA, insertion into pBR322 plasmid, and transformation of Escherichia coli. The nucleotide sequence of the NA gene has been determined by the Maxam and Gilbert method. It is 1466 nucleotides long and contains a single open reading frame with a coding capacity for 469 amino acids. When compared to the NA genes of the N2 strains A/Victoria/3/75, A/Udorn/72, A/NT/60/68, and A/RI/5-/57, 90% of the nucleotide positions and 87% of the amino acid positions remained invariant. Forty-two nucleotide changes and 14 amino acid changes accumulated in the period 1975-1979, but the general structure of the protein appeared to remain constant.

Measurement of antibodies to influenza virus neuraminidase by an enzyme-linked immunosorbent assay

The contribution of influenza A neuraminidase antibodies to the reaction with whole virus in an enzyme-linked immunosorbent assay (ELISA) was assessed by specific absorption of rabbit hyperimmune sera. Although measurable and independent, the effect of neuraminidase antibodies was less than that of hemagglutinin antibodies. Recombinants with an irrelevant hemagglutinin were used successfully as antigens in an ELISA test for measuring neuraminidase antibodies in rabbit hyperimmune sera, but a low cross-reaction between N1 and N2 subtypes was observed. However, for the measurement of N2 antibody rises in human sera, ELISA was highly specific and compared favorably with two other methods, neuraminidase inhibition and single radial hemolysis.

Cloning and sequence of UK bovine rotavirus gene segment 7: marked sequence homology with simian rotavirus gene segment 8

The genome of the UK bovine rotavirus, which consists of eleven segments of dsRNA was polyadenylated and reverse-transcribed into cDNA. Complementary cDNA strands were annealed and the termini of the duplexes completed using DNA polymerase I. Full-length DNA copies of RNA segments 7, 8 and 9 were cloned into the Pst I site of pBR322 and a clone containing the entire gene 7 was identified and sequenced. Gene 7 is 1059 nucleotides in length and contains a single long open reading frame capable of coding for a protein of 317 amino-acids. The known gene product of segment 7 is a protein with an estimated molecular weight of 33,000 daltons. When the UK bovine rotavirus gene 7 sequence was compared with the published data for the homologous gene (segment 8) of the simian rotavirus SA11, it was found to be identical to it in size and the arrangement of the proposed coding and non-coding regions, and very similar in nucleotide sequence (88% homology). Most of the base changes are silent and the predicted amino-acid sequences are almost identical (96% homology).

Neuraminidase gene from the early Asian strain of human influenza virus, A/RI/5-/57 (H2N2)

The complete structure of the neuraminidase gene from the A/RI/5-/57 strain of influenza virus has been determined. It is 1467 nucleotides long and codes for a protein of 469 amino acid residues. Comparison with the gene sequence for the N1 strains A/WSN/33 and A/PR/8/34, the N2 strain A/Udorn/72 and the protein sequence for the N2 strain A/Tokyo/3/67 shows the amino acid sequence changes that have occurred during antigenic shift (60%) and drift (7-9%).

Sequence analysis of the polymerase 1 gene and the secondary structure prediction of polymerase 1 protein of human influenza virus A/WSN/33

The nucleotide sequence of polymerase 1 (P1) gene of a human influenza virus (A/WSN/33) has been determined by using cDNA clones, except for the last 83 nucleotides, which were obtained by primer extension. The WSN P1 gene contains 2,341 nucleotides and codes for a protein of 757 amino acids (Mr = 86,500). P1 gene possesses a striking tandem repeat of 12 nucleotides (nucleotide position 2,188 to 2,199, 2,200 to 2,211) and a corresponding tandem repeat of tetrapeptide in the P1 protein. The deduced sequence of P1 protein is enriched in basic amino acids, particularly arginine. In addition, it also contains clusters of basic amino acids which may provide sites for the interaction with the template virion RNA capped primer as well as with other proteins involved in viral replication and transcription. A secondary structure prediction, using Chou and Fasman analyses (Annu. Rev. Biochem. 47:251-276, 1978), shows that the P1 protein possesses some unique features, viz., one "four-helical supersecondary structure" and four "polypeptide double helices" (antiparallel beta-pleated sheets) which are considered important in RNA binding.

Complete nucleotide sequence of the polymerase 3 gene of human influenza virus A/WSN/33

The complete nucleotide sequence of polymerase 3 (P3) gene of a human influenza virus (A/WSN/33) has been determined using cDNA clones except for the last 11 nucleotides which were obtained by direct RNA sequencing. The WSN P3 gene contains 2,341 nucleotides and codes for a protein of 759 amino acids (molecular weight 85,800). The WSN P3 protein, as deduced from the plus-strand DNA sequence, is basic and enriched in positively charged amino acids. In addition, it contains clusters of basic amino acids which may provide sites for the interaction of P3 protein with the capped primer, template, and/or other polymerase proteins during the transcriptive and replicative processes of influenza viral RNA.

Nucleotide sequence of human influenza A/PR/8/34 segment 2

The nucleotide sequence of RNA segment 2 of human influenza strain A/PR/8/34 has been determined. Segment 2 in 2341 nucleotides long and encodes a protein of 757 amino acids (86,500 daltons molecular weight) which is involved in RNA synthesis. Although segment 2 is identical in size to segment 1, which encodes a protein of related function, neither the nucleotide sequences of these two RNA segments nor the amino acid sequences of the encoded proteins appear to be homologous. The sequence of segment 2 completes the sequence of the virus (total 13,588 nucleotides).

The sequence of the nucleoprotein gene of human influenza A virus, strain A/NT/60/68

The nucleotide sequence of the nucleoprotein gene of influenza A/NT/60/68 was established after using improved cloning methods to obtain full length cDNA clones in pBr322. The gene is 1565 residues long and codes for a basic protein of 498 amino acids. There are only 30 amino acid differences between it and the homologous sequence in A/PR/8/35, all occurring as point mutations. Assuming a common lineage, the evolutionary rate of divergence of the two strains is 0.18% amino acid per year. This confirms there is a slow but significant rate of evolution.

Comparisons of rotavirus polypeptides by limited proteolysis: close similarity of certain polypeptides of different strains

The polypeptides of SA11 rotavirus produced in virus-infected cells were analyzed by limited proteolysis, using Staphylococcus aureus V8 protease. This clearly distinguished between all the known primary gene products of the virus and allowed relationships between other infected-cell proteins, and between infected-cell and virus structural proteins, to be ascertained. A comparison of the proteolysis cleavage patterns between SA11 rotavirus and the human rotavirus Wa was also performed which demonstrated a marked conservation in the digestion patterns among nonstructural and inner-shell structural proteins, but a marked variation in the digestion patterns among outer-shell structural proteins.

Isolation of an influenza A virus from seals

Influenza A virus of serotype Hav1 Neq1 (H7N7 by the 1980 revised influenza typing system proposed by WHO experts) was repeatedly isolated from lung and brain tissues taken from harbor seals (Phoca vitulina) found suffering from pneumonia on Cape Cod Peninsula (U.S.A.) in the winter of 1979-1980. The seal isolates, although of a serotype identical to some fowl plaque virus strains, were harmless to chickens and turkeys in transmission experiments. An earlier human infection by a Hav1 Neq1 influenza virus and the serologic relatedness of this avian serotype with the equine 1 serotype are cited in support of the view that influenza viruses with these antigenic characteristics seem to have a facility to pass from birds to mammals.

Complete nucleotide sequence of the nucleoprotein gene from the human influenza strain A/PR/8/34 (HON1)

The complete nucleotide sequence of the influenza A/PR/8/34 nucleoprotein gene was determined after cloning for dsDNA copy in pBR322. The nucleoprotein gene is 1517 nucleotides long of which 1446 nucleotides code for 482 amino acids. The calculated amino acid composition is in good agreement with those published for influenza A nucleoprotein genes. The amino acid sequence of the nucleoprotein contains clusters of basic amino acids and proline, a property shared with other nucleic-acid-associated proteins like Semliki forest virus nucleocapsid protein, VP1 protein of polyoma virus and Simian virus 40, and the core antigen of hepatitis B virus. The described nucleoprotein structure brings the number of sequenced genes of influenza A/PR/8/34 to five out of eight genes.

Variation in nucleotide sequences coding for the N-terminal regions of the matrix and nonstructural proteins of influenza A viruses

Nucleotide sequences have been determined for complementary DNA transcribed from the 3' ends of RNA segments 7 (matrix gene) and 8 (nonstructural gene) from a number of human influenza A viruses isolated over a period of 43 years and representing H0N1, H1N1, H2N2, and H3N2 subtypes. The pattern of nucleotide variation in both genes suggests that RNA segments 7 and 8 were conserved during the reassortment events which were responsible for the antigenic shifts H1N1 leads to H2N2 and H2N2 leads to H3N2. During the 23-year period between the isolation of A/PR/8/34(H0N1) and A/RI/5-/57(H2N2), substitutions have occurred at 7 of 230 nucleotides in RNA segment 7 and 13 of 220 nucleotides in RNA segment 8, and in 20 years A/RI/5-/57(H2N2) to A/Canberra Grammar/77(H3N2) substitutions have occurred at 5 of 230 nucleotides in RNA segment 7 and 12 of 220 nucleotides in RNA segment 8. These give rise to 2 of 67, 5 of 64, 1 of 67, and 5 of 64 amino acid changes, respectively. The number of nucleotide and amino acid changes observed is of the same order of magnitude as that which occurs over a comparable period of drift in RNA segments 4 and 6, which code for the variable antigenic determinants hemagglutinin and neuraminidase.

Nucleotide sequence of influenza virus RNA segment 8 indicates that coding regions for NS1 and NS2 proteins overlap

The smallest RNA segment of influenza A viruses (vRNA segment 8) has recently been shown to code for two unrelated nonstructural proteins (NS1 and NS2) translated from separate mRNAs. Molecular weight considerations indicated that there might not be enough space on vRNA segment 8 for the two coding regions unless they overlap. We have recently cloned in bacterial plasmids several genes of an avian influenza A virus, fowl plague virus (EPV), and now present the complete nucleotide sequence of FPV RNA segment 8 largely determined from the cloned DNA. The DNA sequence predicts two open protein synthesis reading frames that can be translated into polypeptides of sizes similar to those of NS1 and NS2. The coding regions for these polypeptides overlap by the equivalent of 43-60 amino acids, the exact amount depending on which of several possible methionines initiates the synthesis of NS2.

Secondary structures of influenza and Sendai Virus RNAs

The secondary structures of influenza and Sendai virus RNAs were investigated by thermal denaturation, circular dichroism and proflavine binding methods. In 0.1 M NaCl about 60% of the bases of both RNAs were involved in secondary structure. The melting temperatures (Tm) of both viral RNAs were linear functions of the logarithm of the sodium ion concentration in solution, but under all ionic conditions the melting temperatures of Sendai virus RNA were higher than those of influenza virus RNA. At all ionic strengths the melting range of Sendai virus RNA was less than influenza virus RNA, indicating that the helical regions in Sendai virus RNA were longer than those in influenza virus RNA. Although Sendai virus RNA had a higher thermal stability than influenza virus RNA, hyperchromicity and circular dichroism data showed that Sendai virus RNA had less G+C content (34%) within the double stranded regions than influenza virus RNA (48%). The binding isotherms of Sendai and influenza virus RNA-proflavine complexes were studied at different ionic strengths. The number of binding sites of proflavine with influenza virus RNA were significantly lower than those with Sendai virus RNA. These results demonstrate the essential difference between the secondary and tertiary structures of the RNAs under study.

Complete nucleotide sequence of the haemagglutinin gene from a human influenza virus of the Hong Kong subtype

The complete nucleotide sequence has been determined for a cloned double-stranded DNA copy of the haemagglutinin gene from the human influenza strain A/NT/60/68/29C, a laboratory-isolated variant of A/NT/60/68, an early strain of the Hong Kong subtype. The gene is 1765 nucleotides long and contains information sufficient to code for a protein of 566 amino acids, which includes a hydrophobic leader peptide (16 residues), HA1 (328), HA2 (221) and an arginine residue which joins the HA subunits. Comparison of the predicted amino acid sequence for 29C haemagglutinin with protein sequence data available for HA from other influenza strains shows that no potential coding information is lost by processing of the mRNA. A comparison of the amino acid sequences predicted from the gene sequences for 29C and fowl plague virus haemagglutinins, (1) indicates the extent to which changes can occur in the primary sequence of different regions of the protein, while maintaining essential structure and function.

Host range mutants of an influenza A virus

Temperature-sensitive (ts) mutants of fowl plague virus with a ts-lesion in segment 1 (ts 3, polymerase 1 gene) or segment 2 (ts 90, transport gene) do not form plaques on MDCK cells at the permissive temperature, while the wild type and ts-mutants of other groups are able to do so. This property is correlated with the ts-lesion, since revertants for the ts-lesion of ts 3 and ts 90 again form plaques on MDCK cells. The block on MDCK cells--at least for ts3--may be located in a late function, since viral RNA polymerase and hemagglutinin are formed in almost normal yields. MDCK cells infected with ts 3 or ts 90 exhibit a retarded cytopathic effect at 33 degrees C, but no cytopathic effect at 39 degrees C, at which temperature the infected cells can be passaged and super-infected with the wild type strain. Cells surviving the infection with ts 90 at 33 degrees C sometimes grow out again to a normal monolayer. It is suggested that the spread of virus is inhibited under these conditions.