Influenza B virus genome: assignment of viral polypeptides to RNA segments

Recent Progress in Recombinant Influenza Vaccine Development Toward Heterosubtypic Immune Response

Flu, a viral infection caused by the influenza virus, is still a global public health concern with potential to cause seasonal epidemics and pandemics. Vaccination is considered the most effective protective strategy against the infection. However, given the high plasticity of the virus and the suboptimal immunogenicity of existing influenza vaccines, scientists are moving toward the development of universal vaccines. An important property of universal vaccines is their ability to induce heterosubtypic immunity, i.e., a wide immune response coverage toward different influenza subtypes. With the increasing number of studies and mounting evidence on the safety and efficacy of recombinant influenza vaccines (RIVs), they have been proposed as promising platforms for the development of universal vaccines. This review highlights the current progress and advances in the development of RIVs in the context of heterosubtypic immunity induction toward universal vaccine production. In particular, this review discussed existing knowledge on influenza and vaccine development, current hemagglutinin-based RIVs in the market and in the pipeline, other potential vaccine targets for RIVs (neuraminidase, matrix 1 and 2, nucleoprotein, polymerase acidic, and basic 1 and 2 antigens), and deantigenization process. This review also provided discussion points and future perspectives in looking at RIVs as potential universal vaccine candidates for influenza.

FluB-RAM and FluB-RANS: Genome Rearrangement as Safe and Efficacious Live Attenuated Influenza B Virus Vaccines

Influenza B virus (IBV) is considered a major respiratory pathogen responsible for seasonal respiratory disease in humans, particularly severe in children and the elderly. Seasonal influenza vaccination is considered the most efficient strategy to prevent and control IBV infections. Live attenuated influenza virus vaccines (LAIVs) are thought to induce both humoral and cellular immune responses by mimicking a natural infection, but their effectiveness has recently come into question. Thus, the opportunity exists to find alternative approaches to improve overall influenza vaccine effectiveness. Two alternative IBV backbones were developed with rearranged genomes, rearranged M (FluB-RAM) and a rearranged NS (FluB-RANS). Both rearranged viruses showed temperature sensitivity in vitro compared with the WT type B/Bris strain, were genetically stable over multiple passages in embryonated chicken eggs and were attenuated in vivo in mice. In a prime-boost regime in naïve mice, both rearranged viruses induced antibodies against HA with hemagglutination inhibition titers considered of protective value. In addition, antibodies against NA and NP were readily detected with potential protective value. Upon lethal IBV challenge, mice previously vaccinated with either FluB-RAM or FluB-RANS were completely protected against clinical disease and mortality. In conclusion, genome re-arrangement renders efficacious LAIV candidates to protect mice against IBV.

Reverse genetics for influenza B viruses and recent advances in vaccine development

Influenza B virus is a respiratory pathogen that affects more severely the pediatric and elderly populations. There are two lineages of influenza B virus that seem to have differential predilection for age groups. Both lineages can co-circulate during the influenza season however one is usually more prominent than the other depending on the season. There are no defined indicators to predict which lineage will dominate in any given season. In recent years, the addition of viruses from both lineages to the seasonal influenza vaccine formulation has improved vaccine protection, although quadrivalent vaccines are not available worldwide. Reverse genetics has facilitated advancements in the field of vaccine development against influenza B virus. Different strategies have been explored showing promising results that could potentially lead to the development broadly protective influenza B virus vaccines.

Insights from the comparison of genomic variants from two influenza B viruses grown in the presence of human antibodies in cell culture

Understanding the extent and limitation of viral genome evolution can provide insight about potential drug and vaccine targets. Influenza B Viruses (IBVs) infect humans in a seasonal manner and causes significant morbidity and mortality. IBVs are negative-sense single-stranded RNA viruses with a segmented genome and can be divided into two antigenically distinct lineages. The two lineages have been circulating and further evolving for almost four decades. The immune response to IBV infection can lead to antibodies that target the strain causing the infection. Some antibodies are cross-reactive and are able to bind strains from both lineages but, because of antigenic drift and immunodominance, both lineages continue to evolve and challenge human health. Here we investigate changes in the genomes of an IBVs from each lineage after passage in tissue culture in the presence of human sera containing polyclonal antibodies directed toward antigenically and temporally distinct viruses. Our previous analysis of the fourth segment, which encodes the major surface protein HA, revealed a pattern of change in which signature sequences from one lineage mutated to the signature sequences of the other lineage. Here we analyze genes from the other genomic segments and observe that most of the quasispecies’ heterogeneity occurs at the same loci in each lineage. The nature of the variants at these loci are investigated and possible reasons for this pattern are discussed. This work expands our understanding of the extent and limitations of genomic change in IBV.

Evolutionary dynamics of influenza B strains detected from paediatric acute respiratory infections in central Vietnam

Influenza virus B belongs to the family Orthomyxoviridae with segmented negative-sense RNA genomes. Since 1970s, influenza B has diverged intoVictoria and Yamagata, which differs in antigenic and evolutionary characteristics. Yet, molecular-epidemiological information of influenza B from developing nations is limited. In central Vietnam, influenza A subtype-specific circulation pattern and clinical characteristics were previously described. However, molecular evolutionary characteristics of influenza B has not been discussed to date. We utilized the influenza B positives obtained from paediatric ARI surveillance during 2007-2013. Influenza B HA and NA genes were amplified, sequenced, and phylogenetic/molecular evolutionary analysis was performed using Maximum Likelihood and Bayesian MCMC. Phylodynamics analysis was performed with Bayesian Skyline Plot (BSP). Furthermore, we performed selection pressure analysis and estimated N-glycosylation sites. In the current study, overall positive rate for influenza B was 3.0%, and Victoria lineage immediately became predominant in post-A/H1N1pdm09 period. The noticeable shift in Victoria lineage WHO Group occurred. With respect to the evolutionary rate (substitutions/site/year), Victoria lineage HA gene was evolving faster than Yamagata lineage (2.43 × 10^-3 vs 2.00 × 10^-3). Furthermore, the evolutionary rate of Victoria Group 5 was greater than Group 1. BSP presented the rapid growth in Effective Population Size (EPS) of Victoria lineage occurred soon after the 1st A/H1N1pdm09 case was detected whereas the EPS of Yamagata lineage was stable for both genes. N-glycosylation pattern between lineages and among WHO Groups were slightly different, and HA gene had a total of 6 amino acid substitutions under positive section pressure (4 for Victoria and 2 for Yamagata). The current results highlight the importance of Victoria lineage in post-A/H1N1pdm09 period. Difference in evolutionary characteristics and phylodynamics may indicate lineage and WHO Group-specific evolutionary dynamics. It is necessary to further continue the molecular-epidemiological surveillance in local setting to gain a better understanding of local evolutionary characteristics of influenza B strains.

Influenza B associated paediatric acute respiratory infection hospitalization in central vietnam

Background

Influenza B is one of the major etiologies for acute respiratory infections (ARI) among children worldwide; however, its clinical‐epidemiological information is limited. We aimed to investigate the hospitalization incidence and clinical‐epidemiological characteristics of influenza B‐associated paediatric ARIs in central Vietnam.

Methods

We collected clinical‐epidemiological information and nasopharyngeal swabs from ARI children hospitalized at Khanh Hoa General Hospital, Nha Trang, Vietnam from February 2007 through June 2013. Nasopharyngeal samples were screened for 13 respiratory viruses using Multiplex‐PCRs. Influenza B‐confirmed cases were genotyped by Haemagglutinin gene sequencing. We analyzed the clinical‐epidemiological characteristics of influenza B Lineages (Victoria/Yamagata) and WHO Groups.

Results

In the pre‐A/H1N1pdm09 period, influenza B‐associated ARI hospitalization incidence among children under five was low, ranging between 14.7 and 80.7 per 100 000 population. The incidence increased to between 51.4 and 330 in the post‐A/H1N1pdm09. Influenza B ARI cases were slightly older with milder symptoms. Both Victoria and Yamagata lineages were detected before the A/H1N1pdm09 outbreak; however, Victoria lineage became predominant in 2010‐2013 (84% Victoria vs 16% Yamagata). Victoria and Yamagata lineages did not differ in demographic and clinical characteristics. In Victoria lineage, Group1 ARI cases were clinically more severe compared to Group5, presenting a greater proportion of wheeze, tachypnea, and lower respiratory tract infection.

Conclusions

The current results highlight the increased incidence of influenza B‐related ARI hospitalization among children in central Vietnam in the post‐A/H1N1pdm09 era. Furthermore, the difference in clinical severity between Victoria lineage Group1 and 5 implies the importance of influenza B genetic variation on clinical presentation.

Genetic analysis of influenza B viruses isolated in Uganda during the 2009-2010 seasons

Background

Influenza B viruses can cause morbidity and mortality in humans but due to the lack of an animal reservoir are not associated with pandemics. Because of this, there is relatively limited genetic sequences available for influenza B viruses, especially from developing countries. Complete genome analysis of one influenza B virus and several gene segments of other influenza B viruses isolated from Uganda from May 2009 through December 2010 was therefore undertaken in this study.

Methods

Samples were collected from patients showing influenza like illness and screened for influenza A and B by PCR. Influenza B viruses were isolated on Madin-Darby Canine Kidney cells and selected isolates were subsequently sequenced and analyzed phylogenetically.

Findings

Of the 2,089 samples collected during the period, 292 were positive by PCR for influenza A or B; 12.3% of the PCR positives were influenza B. Thirty influenza B viruses were recovered and of these 25 that grew well consistently on subculture were subjected to further analysis. All the isolates belonged to the B/Victoria-lineage as identified by hemagglutination inhibition assay and genetic analysis except one isolate that grouped with the B-Yamagata-lineage. The Ugandan B/Victoria-lineage isolates grouped in clade 1 which was defined by the N75K, N165K and S172P substitutions in hemagglutinin (HA) protein clustered together with the B/Brisbane/60/2008 vaccine strain. The Yamagata-like Ugandan strain, B/Uganda/MUWRP-053/2009, clustered with clade 3 Yamagata viruses such as B/Bangladesh/3333/2007 which is characterized by S150I and N166Y substitutions in HA.

Conclusion

In general there was limited variation among the Ugandan isolates but they were interestingly closer to viruses from West and North Africa than from neighboring Kenya. Our isolates closely matched the World Health Organization recommended vaccines for the seasons.

Influenza B and C virus NEP (NS2) proteins possess nuclear export activities

Nucleocytoplasmic transport of viral ribonucleoproteins (vRNPs) is an essential aspect of the replication cycle for influenza A, B, and C viruses. These viruses replicate and transcribe their genomes in the nuclei of infected cells. During the late stages of infection, vRNPs must be exported from the nucleus to the cytoplasm prior to transport to viral assembly sites on the cellular plasma membrane. Previously, we demonstrated that the influenza A virus nuclear export protein (NEP, formerly referred to as the NS2 protein) mediates the export of vRNPs. In this report, we suggest that for influenza B and C viruses the nuclear export function is also performed by the orthologous NEP proteins (formerly referred to as the NS2 protein). The influenza virus B and C NEP proteins interact in the yeast two-hybrid assay with a subset of nucleoporins and with the Crm1 nuclear export factor and can functionally replace the effector domain from the human immunodeficiency virus type 1 Rev protein. We established a plasmid transfection system for the generation of virus-like particles (VLPs) in which a functional viral RNA-like chloramphenicol acetyltransferase (CAT) gene is delivered to a new cell. VLPs generated in the absence of the influenza B virus NEP protein were unable to transfer the viral RNA-like CAT gene to a new cell. From these data, we suggest that the nuclear export of the influenza B and C vRNPs are mediated through interaction between NEP proteins and the cellular nucleocytoplasmic export machinery.

Influenza B viruses with site-specific mutations introduced into the HA gene

We have succeeded in engineering changes into the genome of influenza B virus. First, model RNAs containing the chloramphenicol acetyltransferase gene flanked by the noncoding sequences of the HA or NS genes of influenza B virus were transfected into cells which were previously infected with an influenza B helper virus. Like those of the influenza A viruses, the termini of influenza B virus genes contain cis-acting signals which are sufficient to direct replication, expression, and packaging of the RNA. Next, a full-length copy of the HA gene from influenza B/Maryland/59 virus was cloned. Following transfection of this RNA, we rescued transfectant influenza B viruses which contain a point mutation introduced into the original cDNA. A series of mutants which bear deletions or changes in the 5' noncoding region of the influenza B/Maryland/59 virus HA gene were constructed. We were able to rescue viruses which contained deletions of 10 or 33 nucleotides at the 5' noncoding region of the HA gene. The viability of these viruses implies that this region of the genome is flexible in sequence and length.

The hemagglutinating glycoproteins of influenza B and C viruses are acylated with different fatty acids

We present evidence that the hemagglutinin (HA) of influenza B virus and the glycoprotein of influenza C virus (HEF) are acylated. The fatty acid linkage is sensitive to treatment with hydroxylamine and mercaptoethanol, which points to a labile thioester-type linkage. The HA of influenza B virus contains mainly palmitic acid, whereas the HEF glycoprotein of influenza C virus is acylated with stearic acid which has not been observed before as the prevailing fatty acid in viral or cellular acyl proteins.

Genetics of cold-adapted B/Ann Arbor/1/66 influenza virus reassortants: the acidic polymerase (PA) protein gene confers temperature sensitivity and attenuated virulence

The cold-adapted B/Ann Arbor/1/66 influenza virus (ca B/AA/1/66) expresses temperature-sensitive (ts), cold-adapted (ca) and attenuation phenotypes. Reassortants which inherit one or more genes from ca B/AA/1/66 and all other genes from a virulent, wild-type influenza virus, B/Houston/1732/76, were produced and evaluated in order to identify the gene(s) responsible for the ts, ca and attenuation phenotypes. Only reassortants which inherited the PA gene from ca B/AA/1/66 expressed the ts phenotype in MDCK cells at 39 degrees C. None of the reassortants tested expressed the ca phenotype in embryonated eggs at 25 degrees C. The virulence of several reassortants was evaluated in ferrets. Inheritance of the PA gene from ca B/AA/1/66 was correlated with significant febrile attenuation and the apparent restriction of viral replication in the lower respiratory tract. Isolation of a virulent, non-ts revertant virus inheriting only the PA gene from ca B/AA/1/66 established a direct relationship between expression of the ts phenotype and attenuated virulence. Evidence for the contribution of at least one other gene from ca B/AA/1/66 to attenuation was observed. Thus, based on the methods used to determine reassortant gene compositions, these results indicate that the PA gene is primarily responsible for attenuation of ca B/AA/1/66 and its reassortants.

Primary structure of the polymerase acidic (PA) gene of an influenza B virus (B/Sing/222/79)

A DNA copy of influenza B/Singapore/222/79 viral RNA segment 3 containing the gene coding for the polymerase acidic (PA) protein has been cloned in Escherichia coli plasmid pBR322, and its nucleotide sequence has been determined. The cDNA clone was incomplete and contained 1810 nucleotides (nt 396 to 2205). The remaining nucleotide sequence at both 5' and 3' ends of B PA gene was obtained by sequencing the viral RNA (minus sense) and messenger RNA (plus sense) using oligonucleotide primers. The influenza B PA gene contains 2304 nucleotides and codes for a protein of 725 amino acids with a molecular weight of 83,000. The predicted influenza B PA protein is less acidic than the influenza A PA protein. Computer alignment of the influenza B PA amino acid sequence with that of influenza A PA (A/PR/8/34) revealed an overall 38% direct homology which increases to 45% in the carboxyl terminus half of the protein. In addition, comparison of the secondary structural elements, hydropathy profile, and isofunctional amino acid changes between B PA and A PA proteins demonstrated a strong structural and possibly functional conservation between these two proteins. These data suggest that PA genes of influenza A and B viruses arose from a common ancestor gene.

Influenza B virus PB1 protein; nucleotide sequence of the genome RNA segment predicts a high degree of structural homology with the corresponding influenza A virus polymerase protein

The complete nucleotide sequence of a cloned cDNA copy of the genome RNA segment encoding the influenza B/Lee/40 virus PB1 polymerase protein has been determined. The genome RNA segment is 2368 nucleotides in length and is capable of encoding a polymerase (PB1) protein of 752 amino acids with a calculated mol mass of 84,407 Da. As expected, the protein is highly basic with a net charge of +20 at pH 7.0. Sequence comparison between the influenza A and B virus PB1 proteins reveals that they share 61% amino acid homology. An internal hydrophobic domain and 90% of the proline residues found within the influenza A virus PB1 protein are conserved in the influenza B virus molecule. The influenza A and B virus PB1 proteins share the highest homology yet seen between proteins encoded by these disparate viruses. This remarkable conservation of primary structure argues for severe functional constraint on the evolution of this influenza virus polymerase protein.

Genome rearrangements of bovine rotavirus after serial passage at high multiplicity of infection

After serial passage at high multiplicity of infection of standard bovine rotavirus in MA104 cells, different genome rearrangements occurred in which segment 5 was lost from the RNA profile and distinct additional bands of double-stranded (ds) RNA were found in positions on gels between segments 1 and 6. It was shown that some of the additional RNA bands contained segment 5-specific sequences. The additional RNA bands were transcribed in vitro to apparent full length. Analysis of the proteins synthesized in cells infected with viruses possessing rearranged genomes showed that in all cases the product of RNA segment 5, VP5, was missing; however, in one case an abnormal protein was observed which corresponded in size to the coding capacity of the mRNA transcribed from the additional genomic RNA band. Viruses with rearranged genomes could be plaque purified, and they grew in the absence of standard virus to titers comparable to those obtained from standard virus. In mixed infections of standard virus and virus possessing genome rearrangements, standard virus overgrew during passage at low multiplicity of infection whereas virus possessing genome rearrangements overgrew during passage at high multiplicity of infection.

Influenza B virus genome: complete nucleotide sequence of the influenza B/lee/40 virus genome RNA segment 5 encoding the nucleoprotein and comparison with the B/Singapore/222/79 nucleoprotein

The complete nucleotide sequence of a cloned full-length DNA copy of genome RNA segment 5 of influenza B/Lee/40 virus has been determined. The genome segment is 1841 nucleotides in length and is capable of coding for a nucleoprotein (NP) of 560 amino acids. Comparison with the only other known sequence of an influenza B virus nucleoprotein gene (B/Singapore/222/79) indicates striking homology. Only 113 nucleotide substitutions are present between the two strains in their protein coding region and these lead to only 22 amino acid substitutions between nucleoproteins of identical polypeptide chain length. Assuming a common lineage, this reflects a calculated rate of amino acid sequence divergence of 0.1% per year. Like its influenza A virus counterpart, the influenza B/Lee/40 nucleoprotein is a basic protein with a relatively even distribution of its charged residues. The remarkable conservation of nucleoprotein primary structure over a 39-year period probably reflects both selection for performance of specific functions and protection from antigenic selection by the host immune system.

Biochemical and serological studies of influenza B viruses: comparisons of historical and recent isolates

The genetic characteristics of 24 representative influenza B viruses isolated in widely different geographical areas of the world between 1940 and 1980 were analysed using either RNA:RNA hybridisation or oligonucleotide mapping. Additional biochemical characterisation included electrophoretic analysis of virus-induced polypeptides and virion RNAs. A panel of monoclonal antibodies to virus HA was used to investigate serological relationships between the viruses. The influenza B viruses examined constituted a genetically and serologically related group but mutational changes were detected in all eight genes of the viruses isolated in different eras and also in genes of viruses isolated in the same epidemic year. Regardless of the overall and dominating similarities, at a higher level of discrimination it was clear that certain genetic and serological relationships were more complex than expected and, for example, some recently circulating field viruses were apparently more closely related antigenically and genetically to viruses isolated five to twelve years previously than to other viruses isolated concurrently. No evidence of recombination with hitherto undescribed influenza B viruses and with genes coding for internal proteins was detected.

Complete nucleotide sequence of the nucleoprotein gene of influenza B virus

A DNA copy of influenza B/Singapore/222/79 viral RNA segment 5, containing the gene coding for the nucleoprotein (NP), has been cloned in Escherichia coli plasmid pBR322, and its nucleotide sequence has been determined. The influenza B NP gene contains 1,839 nucleotides and codes for a protein of 560 amino acids with a molecular weight of 61,593. Comparison of the influenza B NP amino acid sequence with that of influenza A NP (A/PR/8/34) reveals 37% direct homology in the aligned regions, indicating a common ancestor. However, influenza B NP has an additional 50 amino acids at its N-terminal end. As is the case with influenza A NP, influenza B NP is a basic protein, with its charged residues relatively evenly distributed rather than clustered. The structural homology suggests functional similarity between the NP of influenza A and B viruses.

A previously unrecognized influenza B virus glycoprotein from a bicistronic mRNA that also encodes the viral neuraminidase

RNA segment 6 of the influenza B virus genome codes for a previously unidentified polypeptide designated NB. The reading frame for this polypeptide begins with the first AUG codon on the mRNA and overlaps the reading frame for the viral neuraminidase by 292 nucleotides. The amino acid sequence of polypeptide NB deduced from the nucleotide sequence of the B/Lee/40 strain consists of 100 amino acids with a molecular weight of 11,242. The sequence contains four potential glycosylation sites, and the protein has been found to be glycosylated in infected cells. NB has not been found in virions. Sucrose gradient sedimentation and analysis of the structure of the mRNA by nuclease S1 mapping and sequence analysis by the primer extension method indicated that polypeptide NB and the neuraminidase are translated from a single bicistronic mRNA. A protein analogous to NB has not been found with influenza A virus, and this represents a major difference between the two virus types.

Preparation of influenza virus subviral particles lacking the HA1 subunit of hemagglutinin: unmasking of cross-reactive HA2 determinants

Acid treatment of influenza A and B virus preparations followed by addition of dithiothreitol (DTT) and centrifugation through a sucrose cushion removes the HA1 subunit of hemagglutinin from virus. Rabbit sera made against these subviral particles and untreated virus were tested in a radioimmune precipitation assay using [35S]cysteine-labeled virus. Conditions of the assay permitted discrimination of discrete HA1- and HA2-specific antibody populations. It was found that (a) sera raised to intact influenza A virus preparations contained both HA1- and HA-2 specific antibodies, (b) sera made to subviral particles of influenza A virus contained HA2-specific antibody but had little or no detectable HA1-specific antibody. (c) the HA2-specific antibodies were partially cross-reactive with the HA2 of an influenza A virus of a different subtype, and (d) sera raised against two strains of untreated influenza B viruses contained antibodies which were cross-reactive with the HA2 as well as the NP of influenza A viruses.

Temperature-sensitive influenza A virus clones originated by a cross between A/Aichi/2/68 (H3N2) and B/Yamagata/1/73

A genetic cross was performed between influenza viruses B/Yamagata/1/73 and clone 6-10, an A type influenza virus derived from a cross between A/Aichi/2/68 (H3N2) and B/Yamagata. Efficiency of plating of B/Yamagata at 39.5 degrees C was less than 10(-3) in MDCK cells, while that of clone 6-10 or A/Aichi was higher than 10(-1). Four of the 15 clones selected for HA of Aichi serotype from the mixed yield, where type B virus was predominant over type A, were temperature-sensitive (ts), with efficiency of plating at 39.5 degrees C less than 10(-2), exceeding the frequency of spontaneous ts mutants among clone 6-10 progeny. Thus, co-existing type B virus not only interfered with the replication of type A, but also rendered it temperature-sensitive. Genetic analysis of the 4ts clones using a set of ts mutants of influenza virus A/WSN (H0N1) revealed that these clones, in contrast with the spontaneous ts mutant of clone 6-10, with ts defect only in NP gene, possessed ts lesions in multiple genes including a common ts defect in M. Polyacrylamide gel electrophoresis of viral RNA and proteins of these clones showed an identical gel pattern to that of clone 6-10, although the rate of synthesis of individual viral polypeptide was variable from clone to clone.

[Influenza]

Influenza is the last great uncontrolled plague of mankind. Pandemics and epidemics occur at regular time intervals. The influenza viruses are divided into the types A, B and C and show unique variability of their surface antigens (hemagglutinin and neuraminidase). Influenza viruses of type A show the largest degree of antigenic variation which, in turn, resulted in the definition of a number of subtypes, each comprising many strains. By comparison, influenza viruses of types B and C exhibit much less variation of their surface antigens. As a consequence, no subtypes but many different strains have been recognized. The degree of antigenic variation correlates with the epidemiologic significance of the virus types, type A being the most and type C the least important. Two different kinds of antigenic variation have been recognized: In the case of minor variation of one or both surface antigens, the term "antigenic drift" is employed. Antigenic drift occurs with all three types of virus, it is caused by point mutations which increase the chance of survival of mutants in the diseased host. In addition, influenza A viruses show sudden and complete changes of their surface antigens in regular time intervals, resulting in the appearance of new subtypes. This event is called "antigenic shift". The mechanisms responsible for antigenic shift are poorly understood, only. In addition to the recycling of preceding subtypes, reassortment resulting from double infection of cells with strains of human and animal origin are considered possible explanations. By use of modern DNA recombinant technology, the base sequences of a series of virus genes and, as a consequence, the amino acid sequence of the corresponding antigens have been determined. By means of monoclonal antibodies, the antigenic structure of many influenza antigens has been further elucidated. It can be expected that further research on the molecular basis of antigenic variation could finally result in an understanding of the causal mechanisms. It is an outstanding feature of the epidemiology of influenza A viruses that a family of related strains prevails for a certain period of time and disappears abruptly as a new subtype emerges.(ABSTRACT TRUNCATED AT 400 WORDS)

Complete nucleotide sequence of the neuraminidase gene of influenza B virus

The complete nucleotide sequence of the neuraminidase gene of influenza virus B/Lee/40 was derived from a cloned cDNA copy of virion RNA segment 6 and its corresponding mRNA. The RNA segment contains 1,557 virus-specific nucleotides, and the protein encoded by the longest open reading frame has a total of 466 amino acids with a molecular weight of 51,721. As is the case with the influenza A virus neuraminidases, the deduced amino acid sequence of the influenza B protein includes a single hydrophobic region near the amino terminus which would be capable of spanning the lipid bilayer of the viral or cell membrane. There are four potential glycosylation sites in the protein, two of which are near the amino-terminal hydrophobic region. Comparisons of the nucleotide and amino acid sequences with those of influenza A virus neuraminidases revealed seven regions of extensive homology within the central portion of the molecules, including 12 conserved cysteine residues. Five other cysteine residues in the terminal portions were also conserved.

Intrinsic interference between influenza A and B viruses

Reproduction and synthesis of virus-specific macromolecules were studied in chick embryo fibroblast cultures co-infected with influenza viruses type A (FPV) and B (B/Japan/73). When a multiplicity of infection (MOI) of B/Japan/73 virus (10 EID50/cell and higher) was equal to, or exceeded that of FPV, formation of infectious FPV virions in coinfected cells was suppressed significantly. At equal MOI of FPV and B/Japan/73 synthesis of all proteins of one partner and some proteins of the other was observed. However, when a MOI of one virus was 10 times higher than that of the other, proteins of the virus used at a higher MOI were formed. Studies of the synthesis of virus-specific cRNAs formed in the presence of cycloheximide have shown that at equal MOI. cRNAs were detected that corresponded only to one of the partners involved in the reproduction. The data obtained suggest that intrinsic interference between A and B viruses occurs at a stage of primary transcription.

Evolution of influenza A and B viruses: conservation of structural features in the hemagglutinin genes

The complete nucleotide sequence of the hemagglutinin (HA) gene of a type B influenza virus (B/Lee/40) was obtained by using cloned cDNA derived from the RNA segment. The gene is 1,882 nucleotides long and can code for a protein precursor of 584 amino acids. Structural features common to type A virus HAs are also conserved in the B virus HA. These include a hydrophobic signal peptide, hydrophobic NH2 and COOH termini of the HA2 subunit, and a HA1/HA2 cleavage site involving an arginine residue. The sequence of the B HA gene and its deduced amino acid sequence were compared to those of a type A influenza virus (A/PR/8/34). When these two genes were aligned, it was found that 24% of the amino acids in the HA1 subunits and 39% of the amino acids in the HA2 subunits are conserved. This degree of relatedness between type B virus and type A virus HAs (intertypic comparison) is similar to the homologies observed among certain type A virus HAs (intratypic comparison). A close evolutionary relationship is therefore suggested between the HAs of type A and type B influenza viruses.

Influenza B virus genome: sequences and structural organization of RNA segment 8 and the mRNAs coding for the NS1 and NS2 proteins

Double-stranded DNA derived from influenza B virus genome RNA segment 8, which codes for the NS1 and NS2 proteins, was constructed by hybridization of full-length cDNA copies of RNA segment 8 and of the NS1 mRNA. This DNA was cloned in plasmid pBR322 and sequenced. The NS1 mRNA (approximately 1,080 viral nucleotides) contains nonviral nucleotides at its 5' end and is capable of coding for a protein of 281 amino acids. Sequencing of the NS2 mRNA has shown that it contains an interrupted sequence of 655 nucleotides and is most likely synthesized by a splicing mechanism. The first approximately 75 virus-specific nucleotides at the 5' end of the NS2 mRNA are the same as are found at the 5' -end of the NS1 mRNA. This region contains the initiation codon for protein synthesis and coding information for 10 amino acids common to the two proteins. The approximately 350-nucleotide body region of the NS2 mRNA can be translated in the +1 reading frame, and the sequence indicates that the NS1 and NS2 protein-coding regions overlap by 52 amino acids translated from different reading frames. Thus, between the influenza A and B viruses, the organization of the NS1 and NS2 mRNAs and the sizes of the NS2 mRNA and protein are conserved despite the larger size of the influenza B virus RNA segment, NS1 mRNA, and NS1 protein.

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.

Differences in the electrophoretic migration rates of polypeptides and RNAs of recent isolates of influenza B viruses

The electrophoretic migration rates of structural and non-structural polypeptides of 38 influenza B viruses isolated in epidemics in 1978-1980 and antigenically closely related to B/Singapore/222/79 virus were compared using high resolution SDS polyacrylamide gels. Thirty of the viruses could be distinguished from the prototype B/Singapore/222/79 virus by electrophoretic migration rate differences in HA, 17 by differences in NP and 27 by differences in mobility of the NS 1 polypeptide. Mobility differences of NP, NS 1 and HA polypeptides was noted in influenza B viruses isolated in the UK in the same year. In addition, electrophoretic mobility of 32P labeled virus RNAs varied for certain UK isolates and indicated heterogeneity in genes 2, 3, 4 and 8 coding for polymerase proteins 2 and 1, nucleoprotein (NP) and non-structural protein (NS 1) respectively.

Antigenic variation of influenza A virus nucleoprotein detected with monoclonal antibodies

Monoclonal antibodies were used to study antigenic variation in the nucleoprotein of influenza A viruses. We found that the nucleoprotein molecule of the WSN/33 strain possesses at least five different determinants. Viruses of other influenza A virus subtypes showed antigenic variation in these nucleoprotein determinants, although changes in only one determinant were detected in H0N1 and animal strains. The nucleoprotein of human strains isolated from 1933 through 1979 could be divided into six groups, based on their reactivities with monoclonal antibodies; these groups did not correlate with any particular hemagglutinin or neuraminidase subtype. Our results indicate that antigenic variation in the nucleoproteins of influenza A viruses proceeds independently of changes in the viral surface antigens and suggest that point mutations and genetic reassortment may account for nucleoprotein variability.

Influenza B virus: alpha-amanitin sensitivity of replication and primer-dependence of in vitro transcription

The replication of influenza B/Lee/40 virus in MDCK (canine kidney) cells was sensitive to alpha-amanitin and actinomycin D. In vitro, virion transcriptase activity was stimulated by dinucleotide primers such as ApG. The above characteristics are shared by A/WSN virus.

The 3' and 5'-terminal sequences of influenza A, B and C virus RNA segments are highly conserved and show partial inverted complementarity

The 3'- and 5'-terminal nucleotides of the genome segments of an influenza A, B, and C virus were identified by directly sequencing viral RNA using two different sequencing techniques. A high degree of conservation at the 3' ends as well as at the 5' ends was observed among the genome segments of each virus and among the segments of the three different virus types. A uridine-rich region was observed from positions 17 through 22 at the 5' end of each segment. Moreover, the conserved 3' and 5'-terminal sequences showed partial and inverted complementarity. This feature results in very similar sequences at the 3' ends of the plus and minus strand RNAs and may also enable single-strand RNAs of influenza virus to form "panhandle" structures. Inverted complementary repeats may play an important role in initiation of viral RNA replication.

Evolution of human influenza A viruses in nature: recombination contributes to genetic variation of H1N1 strains

In June of 1977, a new influenza A pandemic was started by strains of the H1N1 serotype. Oligonucleotide fingerprint analysis of the RNA from viruses isolated during the early stage of this pandemic demonstrated that genetic variation among these 1977 strains could be attributed to sequential mutation [Young, J.F., Desselberger, U. & Palese, P. (1979) Cell, 18, 73-83]. Examination of more recent strains revealed that the H1N1 variants that were isolated in the winter of 1978-1979 differed considerably from the H1N1 viruses isolated the previous year. Oligonucleotide and peptide map analysis of the new prototype strain (A/Cal/10/78) suggested that it arose by recombination. It appears that only the HA, NA, M, and NS genes of this virus are derived from the earlier H1N1 viruses and that the P1, P2, P3, and NP genes most likely originate from an H3N2 parent. These data suggest that genetic variation in influenza virus strains of the same serotype is not restricted to mutation alone, but can also involve recombination (reassortment).

Isolation of influenza C virus recombinants

Recombinants between two different influenza C viruses were isolated. In MDCK (canine kidney) cells, one strain, C/JJ/50, caused lytic plaques, whereas C/JHG/66 virus did not produce clear plaques. From a mixed infection of MDCK cells with C/JHG/66 virus and UV-inactivated C/JJ/50 virus, clones were isolated which possessed the clear-plaque phenotype. Fingerprint analyses indicated that the RNAs of parent viruses had different oligonucleotide patterns and that one of the clones derived from the mixed infection was formed by reassortment of parental genes. This recombinant clone most likely inherited RNAs 1, 2, 3, 6, and 7 from C/JGH/66 virus and RNAs 4 and 5 from C/JJ/50 virus.