Sequential passage of influenza virus in embryonated eggs or tissue culture: emergence of mutants

Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples

Viruses mutate rapidly, and recent studies of RNA viruses have shown that related viral variants can sometimes cooperate to improve each other’s growth. We previously described two variants of H3N2 influenza virus that cooperate in cell culture. The mutation responsible for cooperation is often observed when human samples of influenza virus are grown in the lab before sequencing, but it is unclear whether the mutation also exists in human infections or is exclusively the result of lab passage. We identified nine human isolates of influenza virus that had developed the cooperating mutation after being grown in the lab and performed highly sensitive deep sequencing of the unpassaged clinical samples to determine whether the mutation existed in the original human infections. We found no evidence of the cooperating mutation in the unpassaged samples, suggesting that the cooperation arises primarily under laboratory conditions.

The high mutation rates of RNA viruses lead to rapid genetic diversification, which can enable cooperative interactions between variants in a viral population. We previously described two distinct variants of H3N2 influenza virus that cooperate in cell culture. These variants differ by a single mutation, D151G, in the neuraminidase protein. The D151G mutation reaches a stable frequency of about 50% when virus is passaged in cell culture. However, it is unclear whether selection for the cooperative benefits of D151G is a cell culture phenomenon or whether the mutation is also sometimes present at appreciable frequency in virus populations sampled directly from infected humans. Prior work has not detected D151G in unpassaged clinical samples, but those studies have used methods like Sanger sequencing and pyrosequencing, which are relatively insensitive to low-frequency variation. We identified nine samples of human H3N2 influenza virus collected between 2013 and 2015 in which Sanger sequencing had detected a high frequency of the D151G mutation following one to three passages in cell culture. We deep sequenced the unpassaged clinical samples to identify low-frequency viral variants. The frequency of D151G did not exceed the frequency of library preparation and sequencing errors in any of the sequenced samples. We conclude that passage in cell culture is primarily responsible for the frequent observations of D151G in recent H3N2 influenza virus strains.

IMPORTANCE Viruses mutate rapidly, and recent studies of RNA viruses have shown that related viral variants can sometimes cooperate to improve each other’s growth. We previously described two variants of H3N2 influenza virus that cooperate in cell culture. The mutation responsible for cooperation is often observed when human samples of influenza virus are grown in the lab before sequencing, but it is unclear whether the mutation also exists in human infections or is exclusively the result of lab passage. We identified nine human isolates of influenza virus that had developed the cooperating mutation after being grown in the lab and performed highly sensitive deep sequencing of the unpassaged clinical samples to determine whether the mutation existed in the original human infections. We found no evidence of the cooperating mutation in the unpassaged samples, suggesting that the cooperation arises primarily under laboratory conditions.

Canine H3N8 influenza virus infection in dogs and mice

An H3N8 influenza virus closely related to equine influenza virus was identified in racing greyhound dogs with respiratory disease in 2004 and subsequently identified in shelter and pet dogs. Pathologic findings in dogs spontaneously infected with canine influenza virus were compared with lesions induced in beagle and mongrel dogs following experimental inoculation with influenza A/canine/Florida/43/2004. BALB/c mice were inoculated with canine influenza virus to assess their suitability as an experimental model for viral pathogenesis studies. All dogs inoculated with virus developed necrotizing and hyperplastic tracheitis and bronchitis with involvement of submucosal glands as well as mild bronchiolitis and pneumonia. Viral antigen was identified in bronchial and tracheal epithelial cells of all dogs and in alveolar macrophages of several dogs. Many dogs that were spontaneously infected with virus also developed bacterial pneumonia, and greyhound dogs with fatal spontaneous infection developed severe pulmonary hemorrhage with hemothorax. Virus-inoculated BALB/c mice developed tracheitis, bronchitis, bronchiolitis, and mild pneumonia in association with viral antigen in airway epithelial cells and in type 2 alveolar epithelial cells. Virus was not detected in extrarespiratory sites in any animals. The results indicate that canine influenza virus infection consistently induces acute tracheitis and bronchitis in dogs. Mice may be a useful model for some pathogenesis studies on canine influenza virus infection.

Heterogeneity of the mutation rates of influenza A viruses: isolation of mutator mutants

The rates of mutation to the mar (monoclonal antibody-resistant) genotype of individual influenza virus plaque isolates, obtained from a stock generated after two successive cloning steps, have been determined by the fluctuation test. When a random sample of 60 clones was analyzed, 7 contained a proportion of mar mutants significantly higher than the average, and among them, 2 showed a mutation rate two to three times higher than the average value obtained for the virus population when the hemagglutinin-specific monoclonal antibody 2G10 was used. In order to look for mutants with higher mutation rates, a systematic search was carried out with a nonmutagenized virus stock, and several clones with increased mutation rates were isolated. One of them (mut43) was characterized further and was shown to have a mutation rate three to four times higher than that of the virus population at the sites defined by two nonoverlapping, hemagglutinin-specific monoclonal antibodies as well as at the site defined by a neuraminidase-specific monoclonal antibody. These results indicate that the mutation rate of an influenza virus is a weighted average of the contributions of a heterogeneous population. The consequences of this fact for the adaptive evolution of influenza viruses are discussed.

Polymerase errors accumulating during natural evolution of the glycoprotein gene of vesicular stomatitis virus Indiana serotype isolates

We report the entire glycoprotein (G) gene nucleotide sequences of 26 vesicular stomatitis virus Indiana serotype (VSV IND) type 1 isolates from North and Central America. These sequences are also compared with partial G gene sequences of VSV IND type 2 (Cocal) and type 3 (Alagoas) viruses and the complete G gene sequences of the more distantly related VSV New Jersey (NJ) and Chandipura viruses. Phylogenetic analysis of the G gene sequences by maximum parsimony revealed four major lineages or subtypes within the classical VSV IND (type 1) viruses, each with a distinct geographic distribution. A high degree of VSV genetic diversity was found in Central America, with several virus subtypes of both VSV IND and NJ serotypes existing in this mainly enzootic disease region. Nineteen percent sequence variation but no deletions or insertions were evident within the 5' noncoding and the coding regions of the VSV IND type 1 G genes. In addition to numerous base substitutions, the 3' noncoding regions of these viruses also contained numerous base insertions and deletions. This resulted in striking variation in G gene sizes, with gene lengths ranging from 1,652 to 1,868 nucleotides. As the VSV IND type 1 subtypes have diverged from the common ancestor with the NJ subtypes, their G mRNAs have accumulated more 3' noncoding sequence inserts, ranging up to 303 nucleotides in length. These primarily consist of an imprecise reiteration of the sequence UUUUUAA, apparently generated by a unique polymerase stuttering error. Analysis of the deduced amino acid sequence differences among VSV IND type 1 viruses revealed numerous substitutions within defined antigenic epitopes, suggesting that immune selection may play a role in the evolution of these viruses.

Genetic heterogeneity of the RNA genome population of the plant virus U5-TMV

The genetic heterogeneity in a population of the U5 strain of tobacco mosaic virus (U5-TMV) was studied. The T1 fingerprint characterizing a cloned population did not vary after a new cloning step in the local lesion host Nicotiana tabacum Xanthi-nc, nor during four series of 20 passages in the systemic host N. tabacum Samsum. No heterogeneity was observed among 10 clones derived from the cloned populations, while 1 of 18 clones derived from a 20-fold passaged population differed from the rest in 1 of 55 oligonucleotides. A higher heterogeneity was found in an uncloned field isolate in which 2 of 10 clones differed in type in 1 and 2 oligonucleotides, respectively. These data agree with those reported for bacterial and animal RNA viruses and are compatible with the quasi-species model for RNA populations. On the other hand, the intrapopulational heterogeneities found for U5-TMV are considerably smaller than those reported for other RNA viruses, our data showing a high genetic stability for U5-TMV.

Partial RNA sequencing of eight supposed derivatives of type 3 poliovirus/USA/Saukett/50 reveals remarkable differences between three apparent substrains

Eight supposed derivatives of type 3 poliovirus/USA/Saukett/50 could be divided in three subgroups differing from each other as much as from the independent P3/Sabin strain as judged by partial genomic sequences covering about 25% of the portion of RNA coding for the structural proteins. This suggests that strains designated as Saukett in different laboratories are derived from three separate but related American isolates of type 3 poliovirus. Deduced amino acid sequence of the "Saukett" strains revealed amino acid substitutions at all known major antigenic sites compared with P3/Sabin or P3/Finland/23127/84 strain, but also between individual Saukett strains. These substitutions may be responsible for the known antigenic differences between the studied strains.

Extreme heterogeneity in populations of vesicular stomatitis virus

Vesicular stomatitis virus (VSV) sequence evolution and population heterogeneity were examined by T1 oligonucleotide mapping. Individual clones isolated from clonal pools of wild-type Indiana serotype VSV displayed identical T1 maps. This was observed even after one passage at high concentrations of the potent viral mutagen 5-fluorouracil. Under low-multiplicity passage conditions, the consensus T1 fingerprint of this virus remained unchanged after 523 passages. Interestingly, however, individual clones from this population (passage 523) differed significantly from each other and from consensus sequence. When virus population equilibria were disrupted by high-multiplicity passage (in which defective interfering particle interference is maximized) or passage in the presence of mutagenic levels of 5-fluorouracil, rapid consensus sequence evolution occurred and extreme population heterogeneity was observed (with some members of these population differing from others at hundreds of genome positions). A limited sampling of clones at one stage during high-multiplicity passages suggested the presence of at least several distinct master sequences, the related subpopulations of which exhibit at least transient competitive fitness within the total virus population (M. Eigen and C.K. Biebricher, p. 211-245, in E. Domingo, J.J. Holland, P. Ahlquist, ed., RNA Genetics, vol. 3, 1988). These studies further demonstrate the important role of selective pressure in determining the genetic composition of RNA virus populations. This is true under equilibrium conditions in which little consensus sequence evolution is observed owing to stabilizing selection as well as under conditions in which selective pressure is driving rapid RNA virus genome evolution.

The E3 protein of bovine coronavirus is a receptor-destroying enzyme with acetylesterase activity

In addition to members of the Orthomyxoviridae and Paramyxoviridae, several coronaviruses have been shown to possess receptor-destroying activities. Purified bovine coronavirus (BCV) preparations have an esterase activity which inactivates O-acetylsialic acid-containing receptors on erythrocytes. Diisopropyl fluorophosphate (DFP) completely inhibits this receptor-destroying activity of BCV, suggesting that the viral enzyme is a serine esterase. Treatment of purified BCV with [3H]DFP and subsequent sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the proteins revealed that the E3 protein was specifically phosphorylated. This finding suggests that the esterase/receptor-destroying activity of BCV is associated with the E3 protein. Furthermore, treatment of BCV with DFP dramatically reduced its infectivity in a plaque assay. It is assumed that the esterase activity of BCV is required in an early step of virus replication, possibly during virus entry or uncoating.

Genetic diversity of enzootic isolates of vesicular stomatitis virus New Jersey

The RNA genomes of 43 vesicular stomatitis virus (VSV) isolates of the New Jersey (NJ) serotype were T1-ribonuclease fingerprinted to compare the extent of genetic diversity of virus from regions of epizootic and enzootic disease activity. Forty of these viruses were obtained from Central America during 1982 to 1985. The other three were older isolates, including a 1970 isolate from Culex nigripalpus mosquitos in Guatemala, a 1960 bovine isolate from Panama, and a 1976 isolate from mosquitos (Mansonia indubitans) in Ecuador. The data indicate that extensive genetic diversity exists among virus isolates from this predominantly enzootic disease zone. Six distinct T1 fingerprint groups were identified for the Central American VSV NJ isolates from 1982 to 1985. The 1960 VSV NJ isolate from Panama and the 1976 isolate from Ecuador formed two additional distinct fingerprint groups. This finding is in sharp contrast to the relatively close genetic relationship existing among VSV NJ isolates obtained from predominantly epizootic disease areas of the United States and Mexico during the same period (S. T. Nichol, J. Virol. 61:1029-1036, 1987). In this previous study, RNA genome T1 fingerprint differences were observed among isolates from different epizootics; however, the isolates were all clearly members of one large T1 fingerprint group. The eight T1 fingerprint groups described here for Central American and Ecuadorian viruses are distinct from those characterized earlier for virus isolates from the United States and Mexico and for the common laboratory virus strains Ogden and Hazelhurst. Despite being isolated 14 years earlier, the 1970 insect isolate from Guatemala is clearly a member of one of the 1982 to 1985 Central American virus fingerprint groups. This indicates that although virus genetic diversity in the region is extensive, under certain natural conditions particular virus genotypes can be relatively stably maintained for an extended period. The implications of these findings for the evolution of VSV NJ and epizootiology of the disease are discussed.

Measurement of the mutation rates of animal viruses: influenza A virus and poliovirus type 1

Epidemiologic and genetic evidence suggests that influenza A viruses evolve more rapidly than other viruses in humans. Although the high mutation rate of the virus is often cited as the cause of the extensive variation, direct measurement of this parameter has not been obtained in vivo. In this study, the rate of mutation in tissue culture for the nonstructural (NS) gene of influenza A virus and for the VP1 gene in poliovirus type 1 was assayed by direct sequence analysis. Each gene was repeatedly sequenced in over 100 viral clones which were descended from a single virion in one plaque generation. A total of 108 NS genes of influenza virus were sequenced, and in the 91,708 nucleotides analyzed, seven point changes were observed. A total of 105 VP1 genes of poliovirus were sequenced, and in the 95,688 nucleotides analyzed, no mutations were observed. We then calculated mutation rates of 1.5 X 10(-5) and less than 2.1 X 10(-6) mutations per nucleotide per infectious cycle for influenza virus and poliovirus, respectively. We suggest that the higher mutation rate of influenza A virus may promote the rapid evolution of this virus in nature.

Comparative studies of wild-type and cold-mutant (temperature-sensitive) influenza virus: detection of mutations in all genes of the A/Ann Arbor/6/60 (H2N2) mutant vaccine donor strain

Direct biochemical evidence has been obtained for the existence of mutations in all eight RNA segments of the A/Ann Arbor/6/60 cold-adapted (ca) mutant influenza virus strain as compared with its wild-type (wt) progenitor. Polyacrylamide gel electrophoresis (PAGE) of viral RNA revealed a change in the electrophoretic migration of RNA 2 (PB1). T1 oligonucleotide mapping revealed changes in two polymerase genes (the PB2 and PA genes), the hemagglutinin (HA) gene and the nucleoprotein (NP) gene. Analysis of S1 nuclease-treated RNA hybrids on polyacrylamide gels detected changes in the HA and neuraminidase (NA) genes. Partial DNA sequence analysis demonstrated a base sequence change in the matrix (M) protein gene that predicts an amino acid change in the M2 protein and a silent mutation in the non-structural (NS) protein gene. In addition, analysis of viral polypeptides by PAGE has so far revealed changes in the viral protein, PA. These findings directly demonstrate the existence of multiple mutations in the ca vaccine strain, a property that may provide reliably and stably attenuated vaccines that derive their six internal genes from the ca A/Ann Arbor/6/60 donor strain.

Oligonucleotide mapping of viral ribonucleic acid as an aid in identifying laboratory contaminants of influenza virus

Influenza viruses that were suspected to be laboratory contaminants of clinical specimens because they had antigenic properties identical to standard laboratory strains were examined by T1 oligonucleotide mapping of virion ribonucleic acid. For the three instances reported herein involving thirteen viruses, it was concluded that laboratory contamination had occurred, since in each instance, a standard laboratory strain that had been used in the clinical laboratory before the isolation, had an oligonucleotide map that was either identical to or very similar to those of the "isolates," there was no evidence of spread of these viruses, and in cases where serum samples were available, no serologic evidence existed of infection by these virus strains.

Biochemical and antigenic analysis using monoclonal antibodies of a series of of influenza A (H3N2) and (H1N1) virus reassortants

Reassortant influenza A viruses with high growth capacity in eggs and suitable as candidate vaccine strains or as standard reagents for influenza HA quantification were prepared using the high yielding A/PR/8/34 (H1N1) as one parent and a number of 'wild' strains of influenza A (H1N1) or (H3N2) viruses as the other parent. The genetic and antigenic composition of the reassortants was determined. The parental derivation of genes in the reassortants was established by electrophoretic analysis of virus RNA and virus induced polypeptides. The haemagglutinin (HA) antigens of the three H1N1 viruses (NIB-6, NIB-7 NIB-12) were found to resemble those of the parental viruses when tested against a panel of monoclonal antibodies and using the HI test. A similar correspondence between the antigenic characteristics of the HA of the influenza A (H3N2) reassortants (NIB-1, NIB-4, NIB-5, NIB-8 and NIB-11) and parental viruses was noted. Therefore laboratory manipulations to produce the reassortants did not result in the selection of significant antigenic variants.

Direct method for quantitation of extreme polymerase error frequencies at selected single base sites in viral RNA

Methods are described which allow direct quantitation and sequence analysis of base substitution levels at predetermined single nucleotide positions in cloned pools of an RNA virus genome or in its RNA transcripts in vitro. Base substitution frequencies for vesicular stomatitis virus (VSV) at one highly conserved site examined were reproducible and extremely high, averaging between 10(-4) and 4 X 10(-4) substitutions per base incorporated at this single site. If polymerase error frequencies averaged as high at all other sites in the 11-kilobase VSV genome, then every member of a cloned VSV population would differ from most other genomes in that clone at a number of different nucleotide positions. The preservation of a consensus sequence in such variable RNA virus genomes then could only result from strong biological selection (in a single host or multihost environment) for the most fit and competitive representatives of extremely heterogeneous virus populations.

Oriented synthesis and cloning of influenza virus nucleoprotein cDNA that leads to its expression in mammalian cells

The influenza virus nucleoprotein gene has been cloned by a procedure that involves direct cDNA synthesis onto the primer-vector pBSV9, a pBR322-SV40 recombinant plasmid. dT-tailed pBSV9 was used to prime the synthesis of cDNA on a template of in vitro synthesized viral mRNA. The synthesis of ds-cDNA was initiated by a specific oligodeoxynucleotide and the resulting recombinant was circularized by intramolecular ligation. Recombinant pSVa963 contained the viral nucleoprotein gene directly fused to the SV40 early promoter region included in pBSV9 and followed by a dA:dT tail and the SV40 polyadenylation signal. When pSVa963 was used to transfect COS-1 cells, the presence of three NP-specific mRNAs of 1600, 1900 and 2500 nucleotides in length could be detected. Pulse labelling experiments of COS-1 transfected cells and immunobinding to a nucleoprotein monoclonal antibody indicated the synthesis of nucleoprotein. This nucleoprotein accumulated in the nucleus of transfected cells at a level similar to that found in infected cells. The vector and method described may be useful for the specific cloning and expression of any mRNA for which a 5'-terminal sequence is known.

Noncumulative sequence changes in the hemagglutinin genes of influenza C virus isolates

Sequence analysis and comparison of hemagglutinin (HA) genes of different influenza C viruses isolated between 1947 and 1983 reveals that (1) the extent of difference among the HA genes is independent of the year in which these viruses were isolated and that (2) changes in the HA genes do not appear to accumulate with time. These results suggest that epidemiologically dominant variants of influenza C viruses do not emerge successively with time and that C virus variants derived from multiple evolutionary pathways cocirculate at any one time. Thus the epidemiology of influenza C viruses differs markedly from that of influenza A viruses, which is characterized by the emergence of successive variants. Based on the nucleotide sequence data, we propose different evolutionary models for influenza A and influenza C viruses.

Morphology and antigenicity studies on reassortant influenza (H3N2) viruses for use in inactivated vaccines

Three influenza A (H3N2) reassortant whole virus vaccine strains with differing antibody-inducing capacities in hamsters were investigated morphologically and antigenically. Although initial measurements of virion circumference, from electron micrographs of vaccine preparations, suggested a relationship of small virion size with low immunogenicity, subsequent immunization with, and morphological investigation of, vaccine virions separated on sucrose gradients, failed to obtain populations whose antibody-inducing capacity clearly correlated with constituent virion density, size, morphology or integrity. However, antigenic investigation using single radial haemolysis (SRH) and monoclonal antibodies revealed significant differences in antigenic specificity between the strains. Furthermore, a series of H3N2 isolates, derived using standard reassortment procedures, also showed differences in antigenic specificity in their haemagglutination-inhibition (HI) reactions with monoclonal antibodies after five passages in allantois-on-shell cultures. Variation between these isolates and their A/Victoria parent virus could be detected using SRH and hamster sera raised against each isolate. These results demonstrate variation between candidate influenza A virus vaccine strains, all possessing the same surface (H3N2) glycoproteins, expressed as a consequence of the reassortant system used for their production.

Interferon induction by viruses. XIV. Development of interferon inducibility and its inhibition in chick embryo cells "aged" in vitro

Studies with a number of viruses revealed a time-dependent acquisition of interferon (IFN) inducibility in primary chick embryo cells as they "aged" in vitro for 2-12 days at a confluent cell density without a medium change. The time-course for the development of IFN inducibility was established by generating and analyzing a family of dose (multiplicity)-response (IFN yield) curves, using Newcastle disease virus (NDV, strain LaSota) as the inducer. Cells produced little or no IFN for the first 4-5 days. Between 5 and 6 days the cells gradually developed the capacity to respond to NDV (and other viruses). Maximal yields of IFN were inducible by day 10. This time-dependent development of IFN inducibility was abrogated almost completely when "aging" was carried out in the presence of drugs that inhibited the synthesis of cyclic derivatives of C20 oxygenated unsaturated fatty acids, i.e., inhibitors of prostaglandin/leukotriene synthesis and the arachidonic acid cascade. Of the prostaglandin synthesis inhibitors, indomethacin was particularly effective. Cells treated on day 0 with 10 micrograms/ml of indomethacin produced 100- to 1000-fold less IFN than controls when induced on day 8. To prevent maximally the development of IFN inducibility, indomethacin must be added within the first 2 days of seeding. After about 2 days, the cells begin to escape the action of the drug. Indomethacin added at the time of induction had no effect on the yield of IFN. IFN inducibility was partially restored when indomethacin was removed during the aging process. "Aging" chick cells in low concentrations of cycloheximide (0.5 micrograms/ml) produced results comparable to incubation with indomethacin. Neither reagent had any marked effect on the rate of total protein or RNA synthesis, nor did their action prevent the induction of stress (heat shock) proteins. Cells "aged" in indomethacin were threefold less efficient in responding to the action of IFN, whereas aging in cycloheximide had no effect on IFN's action. Plaque formation on drug-treated cells was normal for viruses that were poor inducers of IFN. However, both the plaquing efficiency and plaque size of Sindbis virus (an excellent IFN inducer) were enhanced markedly on cells treated with indomethacin or low concentrations of cycloheximide during the aging process. These data implicate a family of fatty acid derivatives of arachadonic acid, including prostaglandins and leukotrienes, in the development of IFN inducibility in primary chick embryo cells "aged" in vitro.

Multiple genetic variants arise in the course of replication of foot-and-mouth disease virus in cell culture

The genetic heterogeneity generated upon passage of foot-and-mouth disease virus (FMDV) in cell culture has been evaluated by T1-oligonucleotide fingerprinting of genomic RNA. Plaque-purified FMDV O-S7 and C-S8 were propagated by serial low multiplicity infections of BHK-21 (c-13) or IBRS-2 (c-26) cells. In independent parallel passage of the same virus, different oligonucleotide variations were fixed in the RNAs. T1-oligonucleotide fingerprinting of RNA from 34 individual viral clones derived from two passaged populations shows an extensive heterogeneity, with some mutations present in only one of the cloned genomes analyzed. Some FMDV variants are phenotypically distinct in that they yield increased progeny in infections of cell monolayers. From the number of variant sequences it can be estimated that each infectious RNA in the population differs in two to eight mutations from the average parental sequence. Thus, passaged FMDV populations consist of a pool of variants, an observation previously made with phage Q beta (E. Domingo, D. Sabo, T. Taniguchi, and C. Weissmann, Cell 13, 735-744, 1978). The FMDV genome must be described as a fluctuating distribution of sequences due to its high mutability. This may be the basis of the extensive genetic and antigenic diversity of this virus in nature.

Sequential mutations in the NS genes of influenza virus field strains

The complete nucleotide sequences of the NS genes from three human influenza viruses, A/FM/1/47 (H1N1), A/FW/1/50 (H1N1), and A/USSR/90/77 (H1N1), were determined. Only five single-base differences were found within the sequences of the A/FW/1/50 and A/USSR/90/77 NS genes, thus confirming earlier data suggesting that the 1977 H1N1 viruses are closely related to virus strains that were circulating around 1950. Comparison of all three sequences with those from A/PR/8/34 and A/Udorn/72 viruses illustrates that these genes (with the exception of that of the A/USSR/90/77 strain) evolve through cumulative base changes along a single common lineage. A nucleotide sequence variation of approximately 2.2 to 3.4% per 10 years was determined for the NS gene segments. Extensive size variation was also observed among the NS1 proteins of the various human viruses. The A/FM/1/47 NS1 protein, which consists of 202 amino acids, is 15% shorter than the A/Udorn/72 NS1 protein, which consists of 237 amino acids.

Plaquing characteristics of influenza A virus recombinants of defined genetic composition. Brief report

The plaque size and morphology of twenty-two influenza A virus recombinants representing seven distinct families were analyzed on MDCK cells. By examination of the genetic composition of the recombinants no relationship could be established between any gene, including those coding for the surface antigens, and the plaque size and morphology.

Rapid evolution of RNA genomes

RNA viruses show high mutation frequencies partly because of a lack of the proofreading enzymes that assure fidelity of DNA replication. This high mutation frequency is coupled with high rates of replication reflected in rates of RNA genome evolution which can be more than a millionfold greater than the rates of the DNA chromosome evolution of their hosts. There are some disease implications for the DNA-based biosphere of this rapidly evolving RNA biosphere.

Variation of influenza A, B, and C viruses

Influenza is caused by highly variable RNA viruses belonging to the orthomyxovirus group. These viruses are capable of constantly changing the genes coding for their surface proteins as well as for their nonsurface proteins. The mechanisms responsible for these changes in type A influenza viruses include recombination (reassortment) of genes among strains, deletions and insertions in genes, and, frequently, point mutations. In addition, old strains may reappear in the population. Influenza viruses of types B and C appear to vary to a lesser degree. The mechanisms responsible for changes in these viruses are not well characterized.

Antigenicity in hamsters of inactivated vaccines prepared from recombinant influenza viruses

Inactivated vaccines prepared form influenza virus strains obtained by the recombination of A/PR/8/34 (H1N1) or A/FM/1/47 (H1N1) viruses with A/Victoria/3/75 (H3N2) virus, were tested for their antigenicity in hamsters. The parental origin of the genes of each cloned recombinant virus was determined by polyacrylamide gel electrophoresis, and vaccines prepared from each strain by concentration, purification on sucrose density gradients and inactivation with formalin. All the recombinant strains used in these studies possessed surface haemagglutinin and neuraminidase antigens derived from the A/Victoria/75 parent strain. On inoculation into hamsters, at equivalent concentrations, these vaccines varied in their ability to induce haemagglutination-inhibiting (HI) antibodies in the serum. This variation was not dependent on concentration and was observed using neutralization and single radial haemolysis, as well as HI. The possible reasons for the findings are discussed.

src Genes of ten Rous sarcoma virus strains, including two reportedly transduced from the cell, are completely allelic; putative markers of transduction are not detected

The src genes of different Rous sarcoma virus (RSV) strains have been reported to be highly conserved by some investigators using RNA-cDNA hybridization, whereas others using oligonucleotide, peptide, and serological analyses have judged src genes to be variable in 30 to 50% of the respective markers. Moreover, distinctive src oligonucleotides and peptides of so-called recovered RSVs (rRSV's) whose src genes were reported to be experimentally transduced from the cell are thought to represent specific markers of host-derived src sequences. By contrast, we have pointed out previously that these markers may represent point mutations of parental equivalents. Here we have compared the src-specific sequences of eight RSV strains and of two rRSV's to each other and to a molecular clone of the src-related chicken locus. Our comparisons are based on RNase T(1)-resistant oligonucleotides of RNA hybridized to src-specific cDNA, which was prepared by hybridizing RSV cDNA with RNA of isogenic src deletion mutants, or to a cloned cellular src-related DNA. All of the approximately 20 src-oligonucleotides of a given RSV strain were recovered by src-specific cDNA's of all other RSV strains or by cellular src-related DNA. The number of oligonucleotides varied slightly with the length of the src deletion used to prepare src-specific cDNA, thus providing a measure for src deletion mutants. Our data indicate that the src genes of all RSV strains tested, including the two reportedly transduced from the cell, are about 98% conserved and completely allelic with only scattered single nucleotide differences in certain variable regions which are subject to point mutations. Hence, based on the src oligonucleotide markers analyzed by us and others, we cannot distinguish between a cellular and viral origin of rRSV's. However, the following are not compatible with a cellular origin of rRSV's. (i) The only putative oligonucleotide marker which is exclusively shared by the two rRSV's studied and which differs from a parental counterpart in a single base was not detectable in cellular src-related DNA. (ii) The number of different allelic src markers observed by us and others in rRSV's was too large to derive from one or two known cellular src-related loci. (iii) The known absence of linkage of the cellular src-related locus with other virion sequences was extended to all non-src oligonucleotides, including some mapping directly adjacent to src. This is difficult to reconcile with the claim that transformation-defective, partial src deletion mutants of RSV which contain both, one, or, as we show here, possibly no src termini nevertheless transduce at the same frequencies, even though homologous, single or double illegitimate recombinations would be involved. Given (i) our evidence that src genes are subject to point mutation under selective conditions similar to those prevailing when rRSV's were generated and (ii) the lack of absolute evidence for the clonal purity of the transformation-defective, partial src deletion mutants of RSV used to generate rRSV's, we submit that the src genes of rRSV's could have been generated by cross-reactivation of nonoverlapping src deletions or mutation of src variants possibly present in transformation-defective, partial src deletion mutants of RSV. To prove experimental transduction, unambiguous markers need to be identified, or it would be necessary to generate rRSV's with molecularly cloned transformation-defective, partial src deletion mutants of RSV. Although our evidence casts doubt on the idea that specific src sequences of rRSV's originated by transduction, the close relationship between viral src and cellular src-related sequences argues that src genes originated at one time in evolution from the cell by events that involved illegitimate recombination and deletion of non-src sequences that interrupt the cellular src locus.