Hemagglutinin of swine influenza virus: a single amino acid change pleiotropically affects viral antigenicity and replication

Antigenic mapping of the hemagglutinin of the H9 subtype influenza A viruses using sera from Japanese quail (Coturnix c. japonica)

IMPORTANCE

Determining the relevant amino acids involved in antigenic drift on the surface protein hemagglutinin (HA) is critical to understand influenza virus evolution and efficient assessment of vaccine strains relative to current circulating strains. We used antigenic cartography to generate an antigenic map of the H9 hemagglutinin (HA) using sera produced in one of the most relevant minor poultry species, Japanese quail. Key antigenic positions were identified and tested to confirm their impact on the antigenic profile. This work provides a better understanding of the antigenic diversity of the H9 HA as it relates to reactivity to quail sera and will facilitate a rational approach for selecting more efficacious vaccines against poultry-origin H9 influenza viruses in minor poultry species.

Genetic and antigenic evolution of H1 swine influenza A viruses isolated in Belgium and the Netherlands from 2014 through 2019

Surveillance of swine influenza A viruses (swIAV) allows timely detection and identification of new variants with potential zoonotic risks. In this study, we aimed to identify swIAV subtypes that circulated in pigs in Belgium and the Netherlands between 2014 and 2019, and characterize their genetic and antigenic evolution. We subtyped all isolates and analyzed hemagglutinin sequences and hemagglutination inhibition assay data for H1 swIAV, which were the dominant HA subtype. We also analyzed whole genome sequences (WGS) of selected isolates. Out of 200 samples, 89 tested positive for swIAV. swIAV of H1N1, H1N2 and H3N2 subtypes were detected. Analysis of WGS of 18 H1 swIAV isolates revealed three newly emerged genotypes. The European avian-like H1 swIAV (lineage 1C) were predominant and accounted for 47.2% of the total isolates. They were shown to evolve faster than the European human-like H1 (1B lineage) swIAV, which represented 27% of the isolates. The 2009 pandemic H1 swIAV (lineage 1A) accounted for only 5.6% of the isolates and showed divergence from their precursor virus. These results point to the increasing divergence of swIAV and stress the need for continuous surveillance of swIAV.

Genetic Characterization of Influenza A Viruses in Japanese Swine in 2015 to 2019

Understanding the current status of influenza A viruses of swine (IAVs-S) and their evolution at the farm level is important for controlling these pathogens. Efforts to monitor IAVs-S during 2015 to 2019 yielded H1N1, H1N2, and H3N2 viruses. H1 genes in Japanese swine formed a unique clade in the classical swine H1 lineage of 1A.1, and H3 genes originating from 1999–2000 human seasonal influenza viruses appear to have become established among Japanese swine. A(H1N1)pdm09-derived H1 genes became introduced repeatedly and reassorted with endemic IAVs-S, resulting in various combinations of surface and internal genes among pig populations in Japan. At the farm level, multiple introductions of IAVs-S with phylogenetically distinct HA sequences occurred, or IAVs-S derived from a single introduction have persisted for at least 3 years with only a single mutation at the antigenic site of the HA protein. Continued monitoring of IAVs-S is necessary to update and maximize control strategies.

To assess the current status of influenza A viruses of swine (IAVs-S) throughout Japan and to investigate how these viruses persisted and evolve on pig farms, we genetically characterized IAVs-S isolated during 2015 to 2019. Nasal swab samples collected through active surveillance and lung tissue samples collected for diagnosis yielded 424 IAVs-S, comprising 78 H1N1, 331 H1N2, and 15 H3N2 viruses, from farms in 21 sampled prefectures in Japan. Phylogenetic analyses of surface genes revealed that the 1A.1 classical swine H1 lineage has evolved uniquely since the late 1970s among pig populations in Japan. During 2015 to 2019, A(H1N1)pdm09 viruses repeatedly became introduced into farms and reassorted with endemic H1N2 and H3N2 IAVs-S. H3N2 IAVs-S isolated during 2015 to 2019 formed a clade that originated from 1999–2000 human seasonal influenza viruses; this situation differs from previous reports, in which H3N2 IAVs-S derived from human seasonal influenza viruses were transmitted sporadically from humans to swine but then disappeared without becoming established within the pig population. At farms where IAVs-S were frequently isolated for at least 3 years, multiple introductions of IAVs-S with phylogenetically distinct hemagglutinin (HA) genes occurred. In addition, at one farm, IAVs-S derived from a single introduction persisted for at least 3 years and carried no mutations at the deduced antigenic sites of the hemagglutinin protein, except for one at the antigenic site (Sa). Our results extend our understanding regarding the status of IAVs-S currently circulating in Japan and how they genetically evolve at the farm level.

IMPORTANCE Understanding the current status of influenza A viruses of swine (IAVs-S) and their evolution at the farm level is important for controlling these pathogens. Efforts to monitor IAVs-S during 2015 to 2019 yielded H1N1, H1N2, and H3N2 viruses. H1 genes in Japanese swine formed a unique clade in the classical swine H1 lineage of 1A.1, and H3 genes originating from 1999–2000 human seasonal influenza viruses appear to have become established among Japanese swine. A(H1N1)pdm09-derived H1 genes became introduced repeatedly and reassorted with endemic IAVs-S, resulting in various combinations of surface and internal genes among pig populations in Japan. At the farm level, multiple introductions of IAVs-S with phylogenetically distinct HA sequences occurred, or IAVs-S derived from a single introduction have persisted for at least 3 years with only a single mutation at the antigenic site of the HA protein. Continued monitoring of IAVs-S is necessary to update and maximize control strategies.

Antigenically Diverse Swine Origin H1N1 Variant Influenza Viruses Exhibit Differential Ferret Pathogenesis and Transmission Phenotypes

Influenza A(H1) viruses circulating in swine represent an emerging virus threat, as zoonotic infections occur sporadically following exposure to swine. A fatal infection caused by an H1N1 variant (H1N1v) virus was detected in a patient with reported exposure to swine and who presented with pneumonia, respiratory failure, and cardiac arrest. To understand the genetic and phenotypic characteristics of the virus, genome sequence analysis, antigenic characterization, and ferret pathogenesis and transmissibility experiments were performed. Antigenic analysis of the virus isolated from the fatal case, A/Ohio/09/2015, demonstrated significant antigenic drift away from the classical swine H1N1 variant viruses and H1N1 pandemic 2009 viruses. A substitution in the H1 hemagglutinin (G155E) was identified that likely impacted antigenicity, and reverse genetics was employed to understand the molecular mechanism of antibody escape. Reversion of the substitution to 155G, in a reverse genetics A/Ohio/09/2015 virus, showed that this residue was central to the loss of hemagglutination inhibition by ferret antisera raised against a prototypical H1N1 pandemic 2009 virus (A/California/07/2009), as well as gamma lineage classical swine H1N1 viruses, demonstrating the importance of this residue for antibody recognition of this H1 lineage. When analyzed in the ferret model, A/Ohio/09/2015 and another H1N1v virus, A/Iowa/39/2015, as well as A/California/07/2009, replicated efficiently in the respiratory tract of ferrets. The two H1N1v viruses transmitted efficiently among cohoused ferrets, but respiratory droplet transmission studies showed that A/California/07/2009 transmitted through the air more efficiently. Preexisting immunity to A/California/07/2009 did not fully protect ferrets from challenge with A/Ohio/09/2015.IMPORTANCE Human infections with classical swine influenza A(H1N1) viruses that circulate in pigs continue to occur in the United States following exposure to swine. To understand the genetic and virologic characteristics of a virus (A/Ohio/09/2015) associated with a fatal infection and a virus associated with a nonfatal infection (A/Iowa/39/2015), we performed genome sequence analysis, antigenic testing, and pathogenicity and transmission studies in a ferret model. Reverse genetics was employed to identify a single antigenic site substitution (HA G155E) responsible for antigenic variation of A/Ohio/09/2015 compared to related classical swine influenza A(H1N1) viruses. Ferrets with preexisting immunity to the pandemic A(H1N1) virus were challenged with A/Ohio/09/2015, demonstrating decreased protection. These data illustrate the potential for currently circulating swine influenza viruses to infect and cause illness in humans with preexisting immunity to H1N1 pandemic 2009 viruses and a need for ongoing risk assessment and development of candidate vaccine viruses for improved pandemic preparedness.

Antigenic and genetic evolution of contemporary swine H1 influenza viruses in the United States

Several lineages of influenza A viruses (IAV) currently circulate in North American pigs. Genetic diversity is further increased by transmission of IAV between swine and humans and subsequent evolution. Here, we characterized the genetic and antigenic evolution of contemporary swine H1N1 and H1N2 viruses representing clusters H1-α (1A.1), H1-β (1A.2), H1pdm (1A.3.3.2), H1-γ (1A.3.3.3), H1-δ1 (1B.2.2), and H1-δ2 (1B.2.1) currently circulating in pigs in the United States. The δ1-viruses diversified into two new genetic clades, H1-δ1a (1B.2.2.1) and H1-δ1b (1B.2.2.2), which were also antigenically distinct from the earlier H1-δ1-viruses. Further characterization revealed that a few key amino acid changes were associated with antigenic divergence in these groups. The continued genetic and antigenic evolution of contemporary H1 viruses might lead to loss of vaccine cross-protection that could lead to significant economic impact to the swine industry, and represents a challenge to public health initiatives that attempt to minimize swine-to-human IAV transmission.

A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses

The H1 subtype of influenza A viruses (IAVs) has been circulating in swine since the 1918 human influenza pandemic. Over time, and aided by further introductions from nonswine hosts, swine H1 viruses have diversified into three genetic lineages. Due to limited global data, these H1 lineages were named based on colloquial context, leading to a proliferation of inconsistent regional naming conventions. In this study, we propose rigorous phylogenetic criteria to establish a globally consistent nomenclature of swine H1 virus hemagglutinin (HA) evolution. These criteria applied to a data set of 7,070 H1 HA sequences led to 28 distinct clades as the basis for the nomenclature. We developed and implemented a web-accessible annotation tool that can assign these biologically informative categories to new sequence data. The annotation tool assigned the combined data set of 7,070 H1 sequences to the correct clade more than 99% of the time. Our analyses indicated that 87% of the swine H1 viruses from 2010 to the present had HAs that belonged to 7 contemporary cocirculating clades. Our nomenclature and web-accessible classification tool provide an accurate method for researchers, diagnosticians, and health officials to assign clade designations to HA sequences. The tool can be updated readily to track evolving nomenclature as new clades emerge, ensuring continued relevance. A common global nomenclature facilitates comparisons of IAVs infecting humans and pigs, within and between regions, and can provide insight into the diversity of swine H1 influenza virus and its impact on vaccine strain selection, diagnostic reagents, and test performance, thereby simplifying communication of such data. IMPORTANCE A fundamental goal in the biological sciences is the definition of groups of organisms based on evolutionary history and the naming of those groups. For influenza A viruses (IAVs) in swine, understanding the hemagglutinin (HA) genetic lineage of a circulating strain aids in vaccine antigen selection and allows for inferences about vaccine efficacy. Previous reporting of H1 virus HA in swine relied on colloquial names, frequently with incriminating and stigmatizing geographic toponyms, making comparisons between studies challenging. To overcome this, we developed an adaptable nomenclature using measurable criteria for historical and contemporary evolutionary patterns of H1 global swine IAVs. We also developed a web-accessible tool that classifies viruses according to this nomenclature. This classification system will aid agricultural production and pandemic preparedness through the identification of important changes in swine IAVs and provides terminology enabling discussion of swine IAVs in a common context among animal and human health initiatives.

Pleiotropic effects of amino acid substitutions in H5 hemagglutinin of influenza A escape mutants

We believe that the monitoring of pleiotropic effects of the hemagglutinin (HA) mutations found in H5 escape mutants is essential for accurate prediction of mutants with pandemic potential. In the present study, we assessed multiple characteristics of antibody-selected HA mutations. We examined the pH optimum of fusion, HA heat inactivation, affinity to sialyl receptors, and in vitro and in vivo replication kinetics of various influenza H5 escape mutants. Several amino acid substitutions, including T108I, K152E, R162G, and K218N, reduced the stability of HA as determined by heat inactivation, whereas S128L and T215A substitutions were associated with significant increases in HA thermostability compared to the respective wild-type viruses. HA mutations at positions 108, 113, 115, 121, 123, 128, 162, and 190 and substitutions at positions 123, 199, and 215 affected the replicative ability of H5 escape mutants in vitro and in vivo, respectively. The T108I substitution lowered the pH optimum of fusion and HA temperature stability while increasing viral replicative ability. Taken together, a co-variation between antigenic specificity and different HA phenotypic properties has been demonstrated.

Pleiotropic effects of hemagglutinin amino acid substitutions of H5 influenza escape mutants

In the present study we assessed pleiotropic characteristics of the antibody-selected mutations. We examined pH optimum of fusion, temperatures of HA heat inactivation, and in vitro and in vivo replication kinetics of the previously obtained influenza H5 escape mutants. Our results showed that HA1 N142K mutation significantly lowered the pH of fusion optimum. Mutations of the escape mutants located in the HA lateral loop significantly affected H5 HA thermostability (P<0.05). HA changes at positions 131, 144, 145, and 156 and substitutions at positions 131, 142, 145, and 156 affected the replicative ability of H5 escape mutants in vitro and in vivo, respectively. Overall, a co-variation between antigenic specificity and different HA phenotypic properties has been demonstrated. We believe that the monitoring of pleiotropic effects of the HA mutations found in H5 escape mutants is essential for accurate prediction of mutants with pandemic potential.

Influenza type A virus: an outstandingly protean pathogen and a potent modular weapon

A remarkable debate recently arose on a global scale, about bioethics, biohazard, bioweaponry and bioterrorism issues related to scientific research concerning the induced transition of the highly lethal H5N1 avian flu virus from a non-pandemic to a tentatively pandemic strain, which might fall into malevolent hands. Appreciable ecogenetic complexity marks the main attributes of influenza type A viruses, namely infectivity, virulence, antigenicity, transmissibility, host range, endemicity, and epidemicity. They all shape, conjunctively, the outstanding protean nature of this pathogen, hence the modularity of the latter as a potent weapon. The present analysis inquires into those attributes, so as to profile and gauge threat, usability, impact and coping, particularly that the dimension of genetic engineering of this virus largely amplifies its potential. Within that context, various human interventions and misuses, including human experimental infections, undesirable vaccinations, as well as unauthorized and unskillful operations, led to bad corollaries and are also discussed in the present study. Altogether, a variety of interrelated properties underlying the complicatedness of and menaces posed by influenza A virus as a grave medical challenge, a dually explorable pathogen, and a modular biological warfare agent, are thereby illuminated, alongside with their scientific, strategic and practical implications.

Escape mutants of pandemic influenza A/H1N1 2009 virus: variations in antigenic specificity and receptor affinity of the hemagglutinin

A panel of 6 neutralizing monoclonal antibodies (MAbs) raised against A/Moscow/IIV01/2009 (H1N1) virus isolated during the 2009 pandemic was used for the selection of 26 escape mutants. The mutants were characterized in immune cross-reactions with the panel of MAbs. The sequencing of the mutant HA genes revealed 5 amino acid positions recognized by monoclonal antibodies: 129, 156, 158, 159, and 190 (H3 numbering). The amino acid positions were distributed in two epitopes belonging to antigenic sites Sa and Sb. The mutant HAs exhibited variations in the affinity to synthetic high molecular mass sialic acid-containing receptor analogues. Results are discussed in connection with the antigenic drift potential of the "swine-like" pandemic 2009 influenza virus.

The modes of evolutionary emergence of primal and late pandemic influenza virus strains from viral reservoir in animals: an interdisciplinary analysis

Based on a wealth of recent findings, in conjunction with earliest chronologies pertaining to evolutionary emergences of ancestral RNA viruses, ducks, Influenzavirus A (assumingly within ducks), and hominids, as well as to the initial domestication of mallard duck (Anas platyrhynchos), jungle fowl (Gallus gallus), wild turkey (Meleagris gallopavo), wild boar (Sus scrofa), and wild horse (Equus ferus), presumed genesis modes of primordial pandemic influenza strains have multidisciplinarily been configured. The virological fundamentality of domestication and farming of those various avian and mammalian species has thereby been demonstrated and broadly elucidated, within distinctive coevolutionary paradigms. The mentioned viral genesis modes were then analyzed, compatibly with common denominators and flexibility that mark the geographic profile of the last 18 pandemic strains, which reputedly emerged since 1510, the antigenic profile of the last 10 pandemic strains since 1847, and the genomic profile of the last 5 pandemic strains since 1918, until present. Related ecophylogenetic and biogeographic aspects have been enlightened, alongside with the crucial role of spatial virus gene dissemination by avian hosts. A fairly coherent picture of primary and late evolutionary and genomic courses of pandemic strains has thus been attained, tentatively. Specific patterns underlying complexes prone to generate past and future pandemic strains from viral reservoir in animals are consequentially derived.

Gene constellation of influenza A virus reassortants with high growth phenotype prepared as seed candidates for vaccine production

Background

Influenza A virus vaccines undergo yearly reformulations due to the antigenic variability of the virus caused by antigenic drift and shift. It is critical to the vaccine manufacturing process to obtain influenza A seed virus that is antigenically identical to circulating wild type (wt) virus and grows to high titers in embryonated chicken eggs. Inactivated influenza A seasonal vaccines are generated by classical reassortment. The classical method takes advantage of the ability of the influenza virus to reassort based on the segmented nature of its genome. In ovo co-inoculation of a high growth or yield (hy) donor virus and a low yield wt virus with antibody selection against the donor surface antigens results in progeny viruses that grow to high titers in ovo with wt origin hemagglutinin (HA) and neuraminidase (NA) glycoproteins. In this report we determined the parental origin of the remaining six genes encoding the internal proteins that contribute to the hy phenotype in ovo.

Methodology

The genetic analysis was conducted using reverse transcription-polymerase chain reaction (RT-PCR) and restriction fragment length polymorphism (RFLP). The characterization was conducted to determine the parental origin of the gene segments (hy donor virus or wt virus), gene segment ratios and constellations. Fold increase in growth of reassortant viruses compared to respective parent wt viruses was determined by hemagglutination assay titers.

Significance

In this study fifty-seven influenza A vaccine candidate reassortants were analyzed for the presence or absence of correlations between specific gene segment ratios, gene constellations and hy reassortant phenotype. We found two gene ratios, 6∶2 and 5∶3, to be the most prevalent among the hy reassortants analyzed, although other gene ratios also conferred hy in certain reassortants.

A single-amino-acid substitution in the HA protein changes the replication and pathogenicity of the 2009 pandemic A (H1N1) influenza viruses in vitro and in vivo

Background

The novel pandemic A (H1N1) virus was first identified in Mexico in April 2009 and since then it spread world wide over a short period of time. Although the virus infection is generally associated with mild disease and a relatively low mortality, it is projected that mutations in specific regions of the viral genome, especially within the receptor binding domain of the hemagglutinin (HA) protein could result in more virulent virus stains, leading to a more severe pandemic.

Results

Here, we found that a single amino acid substitution of Asp-to-Gly at position 222 in the HA protein of the A (H1N1) virus occurred after two passage propagation in the allantoic cavities of chicken embryonated eggs, and this single residue variation dramatically increased the viral replication ability in MDCK cells and pathogenicity in BALB/c mice.

Conclusions

A substitution of Asp-to-Gly at position 222 in the HA protein was prone to occur under positive selection pressures, and this single amino acid mutation could dramatically increase the virus replication ability in vitro and pathogenicity in vivo. Our finding offers a better understanding of the transmission and evolution of the 2009 pandemic A (H1N1) virus and brings attention to further potentially severe influenza pandemic that may result from cross-host evolution of the influenza viruses.

Strain identification of commercial influenza vaccines by mass spectrometry

Current influenza vaccine manufacturing and testing timelines require that the constituent hemagglutinin (HA) and neuraminidase (NA) strains be selected each year approximately 10 months before the vaccine becomes available. The threat of a pandemic influenza outbreak requires that more rapid testing methods be found. We have developed a specialized on-filter sample preparation method that uses both trypsin and chymotrypsin to enzymatically digest peptide-N-glycosidase F (PNGase F)-deglycosylated proteins in vaccines. In tandem with replicate liquid chromatography-mass spectrometry (LC-MS) analyses, this approach yields sufficient protein sequencing data (>85% sequence coverage on average) for strain identification of HA and NA components. This has allowed the confirmation, and in some cases the correction, of the identity of the influenza strains in recent commercial vaccines as well as the correction of some ambiguous HA sequence annotations in available databases. This method also allows the identification of low-level contaminant egg proteins produced during the manufacturing process.

Influenza H1N1 A/Solomon Island/3/06 virus receptor binding specificity correlates with virus pathogenicity, antigenicity, and immunogenicity in ferrets

Influenza viruses attach to cells via a sialic acid moiety (sialic acid receptor) that is alpha2-3 linked or alpha2-6 linked to galactose (alpha2-3SAL or alpha2-6SAL); sialic acid acts as a receptor for the virus. Using lectin staining, we demonstrated that the alpha2-6SAL configuration is predominant in the respiratory tract of ferrets, including trachea, bronchus, and lung alveolus tissues. Recombinant wild-type (rWT) influenza A/Solomon Island/3/06 (SI06) (H1N1) viruses were constructed to assess the impact of the hemagglutinin (HA) variations (amino acids 190 or 226) identified in natural variants on virus replication in the upper and lower respiratory tract of ferrets, as well as virus antigenicity and immunogenicity. A single amino acid change at residue 226 (from Gln to Arg) in the HA of SI06 resulted in the complete loss of binding to alpha2-6SAL and a concomitant loss of the virus's ability to replicate in the lower respiratory tract of ferrets. In contrast, the virus with Gln226 in the HA protein has a receptor binding preference for alpha2-6SAL and replicates efficiently in the lungs. There was a good correlation between viral replication in the lungs of ferrets and disease symptoms. In addition, we also showed that the 190 and 226 residues affected viral antigenicity and immunogenicity. Our data emphasize the necessity of thoroughly assessing wild-type influenza viruses for their suitability as reference strains and for carefully selecting the HA antigen for vaccine production during annual influenza vaccine evaluation processes.

Generation of live attenuated novel influenza virus A/California/7/09 (H1N1) vaccines with high yield in embryonated chicken eggs

Several live attenuated influenza virus A/California/7/09 (H1N1) (CA09) candidate vaccine variants that possess the hemagglutinin (HA) and neuraminidase (NA) gene segments from the CA09 virus and six internal protein gene segments from the cold-adapted influenza virus A/Ann Arbor/6/60 (H2N2) virus were generated by reverse genetics. The reassortant viruses replicated relatively poorly in embryonated chicken eggs. To improve virus growth in eggs, reassortants expressing the HA and NA of CA09 were passaged in MDCK cells and variants exhibiting large-plaque morphology were isolated. These variants replicated at levels approximately 10-fold higher than the rate of replication of the parental strains in embryonated chicken eggs. Sequence analysis indicated that single amino acid changes at positions 119, 153, 154, and 186 were responsible for the improved growth properties in MDCK cells and eggs. In addition, the introduction of a mutation at residue 155 that was previously shown to enhance the replication of a 1976 swine influenza virus also significantly improved the replication of the CA09 virus in eggs. Each variant was further evaluated for receptor binding preference, antigenicity, attenuation phenotype, and immunogenicity. Mutations at residues 153, 154, and 155 drastically reduced viral antigenicity, which made these mutants unsuitable as vaccine candidates. However, changes at residues 119 and 186 did not affect virus antigenicity or immunogenicity, justifying their inclusion in live attenuated vaccine candidates to protect against the currently circulating 2009 swine origin H1N1 viruses.

Efficacy of commercial swine influenza vaccines against challenge with a recent European H1N1 field isolate

This study examines the immunogenicity and efficacy of four commercial swine influenza (SI) vaccines against challenge with a recent European H1N1 virus, Sw/Gent/112/07. The vaccines contained different H1N1 strains showing between 77% and 95% genetic homology with the haemagglutinin (HA) of the challenge virus. Four groups of 10 pigs each received a double vaccination, with a 4-week interval, with one of the vaccines; a fifth group served as unvaccinated controls. All pigs were challenged 3 weeks after the second vaccination intratracheally with 10(5.0)EID(50) of Sw/Gent/112/07. Sera were examined in haemagglutination inhibition (HI) tests against the homologous vaccine H1N1 strains, the challenge virus and a panel of five recent H1N1 isolates. Pigs were euthanized at 24 or 72h post-challenge and virus titres were determined in right and left lung halves. Two vaccines, in which the H1N1 strains showed a genetic homology of 93% and 89% to Sw/Gent/112/07, significantly reduced virus replication. The vaccine containing an H1N1 strain with 95% homology to Sw/Gent/112/07, did not offer significant protection, neither did it induce the highest HI titres. In general, pigs with HI antibody titres >or=20 against Sw/Gent/112/07 were virologically protected against challenge. HI titres against other viruses, however, differed compared to the challenge virus and between viruses. Our data clearly show that the genetic homology with the challenge virus is not the ultimate predictor for SI vaccine performance. The true reason for the differences in vaccine potency remains obscure because other factors, such as the antigen dose and/or the adjuvant, also differed between the vaccines.

The total influenza vaccine failure of 1947 revisited: major intrasubtypic antigenic change can explain failure of vaccine in a post-World War II epidemic

Although vaccine-induced immunity to influenza A virus is continually challenged by progressively selected mutations in the virus's major antigens (antigenic drift), virus strains within a subtype (e.g., H1N1) are antigenically cross-reactive. Although cross-immunity diminishes as further mutations accumulate, necessitating frequent changes in vaccine strains, older vaccines are usually partially protective. The post-World War II epidemic of 1947 is notable for the total failure of a vaccine previously effective in the 1943-44 and 1944-45 seasons. We have combined extensive antigenic characterization of the hemagglutinin and neuraminidase antigens of the 1943 and 1947 viruses with analysis of their nucleotide and amino acid sequences and have found marked antigenic and amino acid differences in viruses of the two years. Furthermore, in a mouse model, vaccination with the 1943 vaccine had no effect on infection with the 1947 strain. These findings are important, because complete lack of cross-immunogenicity has been found previously only with antigenic shift, in which antigenically novel antigens have been captured by reassortment of human and animal strains, sometimes leading to pandemics. Although the 1947 epidemic lacked the usual hallmarks of pandemic disease, including an extensive increase in mortality, it warns of the possibility that extreme intrasubtypic antigenic variation (if coupled with an increase in disease severity) could produce pandemic disease without the introduction of animal virus antigens.

Rapid confirmation by RFLP of transfer to vaccine candidate reassortment viruses of the principal 'high yield' gene of influenza A viruses

Influenza vaccines must be revised constantly on almost a yearly basis because of the sequential mutations (antigenic drift) that occur as the virus responds to immunologic pressure. New, high yield (hy) reassortant viruses have proved essential to meet production needs for the supply of new vaccines. We have devised a method for simple, rapid and precise identification of the principal influenza A virus RNA segment (RNA 7) associated with hy and transferred from the hy donor virus, A/PR/8/34 (H1N1). The method entails the use of a single restriction enzyme, Bsgl, in analysis by restriction fragment length polymorphism (RFLP) of reverse transcriptase-polymerase chain reaction (RT-PCR)-generated DNA amplicons. The method clearly distinguishes the RNA coding for the M proteins of the donor virus from that of representative and epidemiologically significant human wild type viruses of the past 60 years. In the course of this methodological study further evidence has been found of the variability of the so-called 'invariant' and stable M1 and M2 proteins of the virus. Another finding of potentially basic significance that merits further study is the occurrence of a consistent change at the same amino acid (aa) site of the donated RNA 7 upon its transfer to reassortant viruses.

Genomic analysis of matrix gene and antigenic studies of its gene product (M1) of a swine influenza virus (H1N1) causing chronic respiratory disease in pigs

The nucleotide sequence of gene coding for the matrix protein (M1 and M2) of swine influenza (H1N1) virus, A/Sw/Quebec/5393/91 (SwQc91), associated with chronic respiratory disease in pigs, was determined. The deduced amino acid (aa) sequence was compared with the other North American swine strains including the A/Sw/Quebec/192/81 (SwQc81) strain associated with the chronic and acute respiratory disease in pigs. Separate analysis of the M1 and M2 gene products showed different evolutions. M1 had 2 aas changes among 252 aas and these were at positions 4 and 205. The mutation rate was 0.08%, aa changes per residue per year, and its homology with other strains was 99.2%. The M2 protein (97 aas) was relatively more variable than M1 with 5 substitutions. Differences observed were at positions 4, 16, 21, 54 and 95. The mutation rate was 0.51% and its homology with other strains was 94.8%. The M1 gene was cloned in the procaryotic plasmid pET21a and the recombinant plasmid was expressed in Escherichia coli under pre-determined optimal conditions. The recombinant M1 protein (RM1P) (approximately 28 kDa) comigrated as a single band on SDS-PAGE. RM1P was antigenic and reacted with polyclonal sera and 5 monoclonal antibodies (MAbs) spanning 4 epitopes including the membrane binding site and the transcription inhibition activity site. RM1P was immunogenic. The mouse anti-RM1P ELISA antibodies reacted with the purified viral M1 protein and the whole virus.

Molecular basis for the generation in pigs of influenza A viruses with pandemic potential

Genetic and biologic observations suggest that pigs may serve as "mixing vessels" for the generation of human-avian influenza A virus reassortants, similar to those responsible for the 1957 and 1968 pandemics. Here we demonstrate a structural basis for this hypothesis. Cell surface receptors for both human and avian influenza viruses were identified in the pig trachea, providing a milieu conducive to viral replication and genetic reassortment. Surprisingly, with continued replication, some avian-like swine viruses acquired the ability to recognize human virus receptors, raising the possibility of their direct transmission to human populations. These findings help to explain the emergence of pandemic influenza viruses and support the need for continued surveillance of swine for viruses carrying avian virus genes.

Differences in the biological phenotype of low-yielding (L) and high-yielding (H) variants of swine influenza virus A/NJ/11/76 are associated with their different receptor-binding activity

Low- (L) and high-yielding (H) variants of A/sw/NJ/11/76 influenza virus were compared for their growth properties in embryonated chicken eggs and MDCK cells and for their binding affinity for the membrane fractions prepared from cells of the chicken embryo allantoic membrane. MDCK, and swine tracheal cells, as well as for soluble sialic acid containing macromolecules and monovalent sialosides. We have shown, that during infection in MDCK cells and in eggs, the progeny of the L variant remain predominantly cell associated, in contrast to those of H. As a result, accumulation of the L mutant in allantoic or culture fluid is significantly slowed in comparison with the H variant. Visualization of the infectious foci formed by the viruses in MDCK cell monolayers and on the allantoic membrane revealed that L spreads predominantly from cell to cell, while the spread of H involves release of the virus progeny into solution and its rapid distribution over the cell monolayer via convectional flow of the liquid. In the binding assays, L displayed significantly higher binding affinity than H for cellular membranes, gangliosides, and sialylglycoproteins, however, the affinity of the variants for the monovalent sialic acid compounds was comparable. Unlike H. L bound strongly to dextran sulfate. The data obtained suggest that all distinctions of the L and H biological phenotypes reported previously [Kilbourne, E.D., Taylor, A. H. Whitaker, C.W., Sahai, R., and Caton, A (1988) Hemagglutinin polymorphism as the basis for low-and high-yield phenotypes of swine influenza virus. Proc. Natl. Acad. Sci. USA 85, 7782-7785] could be rationally explained by a more avid binding of the L variant to the surface of target cells, and that this effect is mainly due to enhanced electrostatic interactions.

RNA virus mutations and fitness for survival

RNA viruses exploit all known mechanisms of genetic variation to ensure their survival. Distinctive features of RNA virus replication include high mutation rates, high yields, and short replication times. As a consequence, RNA viruses replicate as complex and dynamic mutant swarms, called viral quasispecies. Mutation rates at defined genomic sites are affected by the nucleotide sequence context on the template molecule as well as by environmental factors. In vitro hypermutation reactions offer a means to explore the functional sequence space of nucleic acids and proteins. The evolution of a viral quasispecies is extremely dependent on the population size of the virus that is involved in the infections. Repeated bottleneck events lead to average fitness losses, with viruses that harbor unusual, deleterious mutations. In contrast, large population passages result in rapid fitness gains, much larger than those so far scored for cellular organisms. Fitness gains in one environment often lead to fitness losses in an alternative environment. An important challenge in RNA virus evolution research is the assignment of phenotypic traits to specific mutations. Different constellations of mutations may be associated with a similar biological behavior. In addition, recent evidence suggests the existence of critical thresholds for the expression of phenotypic traits. Epidemiological as well as functional and structural studies suggest that RNA viruses can tolerate restricted types and numbers of mutations during any specific time point during their evolution. Viruses occupy only a tiny portion of their potential sequence space. Such limited tolerance to mutations may open new avenues for combating viral infections.

Virulence of influenza A virus for mouse lung

The experimental infection of mouse lung with influenza A virus has proven to be an invaluable model for studying the mechanisms of viral adaptation and virulence. These investigations have identified critical roles for the haemagglutinin (HA) and matrix (M) genes of the virus in determining virulence for mouse lung. For the HA gene, the loss of glycosylation sites from the encoded polypeptide or changes which may affect the pH of HA-mediated endosome fusion have been observed following adaptation. These alterations also have the potential to impact on receptor specificity, beta inhibitor sensitivity and activation cleavage which may act in concert to account for the increased virulence of adapted strains. For the M gene, two specific changes in the M1 protein have been identified in strains adapted to, or virulent for, mouse lung. These changes are likely to affect pH-dependent association/dissociation of M1 with the viral ribonucleoprotein, and control virulence as well as growth. The role of other genes in mouse lung virulence remains unknown.

In pursuit of influenza: Fort Monmouth to Valhalla (and back)

In reviewing 50 years of personal research on influenza, I have journeyed, literally and figuratively, from an army camp epidemic in Fort Monmouth NJ in 1947 to a (literal and figurative) Valhalla, where I now conduct my research. Having entered the field as a physician, I have always sought practical applications of my work, yet in every instance, such applications have led me to seek further answers in basic research as new questions arose. I entered the area of influenza virus genetics by the back door through an interest in the effects of corticosteroid hormones on viral replication, used the genetic approach in analyzing the morphological variation of the virus and, in so doing, exploited the finding of a linkage of high-yield growth to spherical morphology. Today, all influenza vaccine viruses are high-yield genetic reassortants. Subsequent study of reassortant viruses facilitated the identification and isolation of the two major antigens of the virus in antigenic hybrids and showed their differing functions in the induction of immunity. In turn, a new approach to influenza vaccination has been discovered and is presently under clinical investigation.

Genetic variation in swine influenza virus A isolate associated with proliferative and necrotizing pneumonia in pigs

A new antigenic variant of H1N1 swine influenza virus A (Sw/QC/5393/91 [QC/91]) has been found to be associated with porcine proliferative and necrotizing pneumonia. Analysis of its genomic RNA by T1 oligonucleotide mapping revealed that considerable genomic divergence exists between QC/91 and the swine influenza viruses currently circulating in North American swine herds. Analysis of the nucleotide sequence of the HA1 region of the hemagglutinin RNA of QC/91, in comparison with those of most common H1N1 human and swine influenza A viruses, showed the presence of multiple point mutations. Two amino acid substitutions appeared to be located in antigenic sites Sb and Ca. This correlates with antigenic variations demonstrated between A/NJ/8/76, A/Sw/WI/49/76, and Québec isolate A/Sw/QC/5393/91 of swine influenza virus A. Another mutation was responsible for the loss of a glycosylation site, which may have also affected the antigenicity. The other mutations seem to have been accumulated progressively over time. This significant constancy in the fixation of mutations with time suggests that genetic diversity of these viruses may best be interpreted as the result of drifts in the population of circulating swine influenza viruses in Québec.

A H1 hemagglutinin of a human influenza A virus with a carbohydrate-modulated receptor binding site and an unusual cleavage site

Two receptor binding variants of the influenza virus A/Tübingen/12/85 (H1N1) were separated by their different plaque formation in MDCK cells. Hemagglutination of variant I was restricted to red blood cells of guinea pigs, whereas variant II also hemagglutinated chicken cells. The variants differed also in their ability to bind to alpha 2,6-linked sialic acid. Evidence is presented that this difference is determined by a complex carbohydrate side chain at asparagine131 near the receptor binding site which is absent in variant II. With both variants, the arginine found at the cleavage site of all other human isolates analyzed so far was replaced by lysine.

Hemagglutinin mutations related to antigenic variation in H1 swine influenza viruses

The hemagglutinin (HA) of a recent swine influenza virus, A/Sw/IN/1726/88 (H1N1), was shown previously to have four antigenic sites, as determined from analysis of monoclonal antibody (MAb)-selected escape mutants. To define the HA mutations related to these antigenic sites, we cloned and sequenced the HA genes amplified by polymerase chain reaction of parent virus and MAb-selected escape mutants. The genetic data indicated the presence of four amino acid changes. After alignment with the three-dimensional structure of H3 HA, three changes were located on the distal tip of the HA, and the fourth was located within the loop on the HA. We then compared our antigenic sites, as defined by the changed amino acids, with the well-defined sites on the H1 HA of A/PR/8/34. The four amino acid residues corresponded with three antigenic sites on the HA of A/PR/8/34. This finding, in conjunction with our previous antigenic data, indicated that two of the four antigenic sites were overlapping. In addition, our previous studies indicated that one MAb-selected mutant and a recent, naturally occurring swine isolate reacted similarly with the MAb panel. However, their amino acid changes were different and also distant on the primary sequence but close topographically. This finding indicates that changes outside the antigenic site may also affect the site. A comparison of the HA amino acid sequences of early and recent swine isolates showed striking conservation of genetic sequences as well as of the antigenic sites. Thus, swine influenza viruses evolve more slowly than human viruses, possibly because they are not subjected to the same degree of immune selection.

Single amino acid substitutions in the hemagglutinin can alter the host range and receptor binding properties of H1 strains of influenza A virus

We have previously characterized an influenza A (H1N1) virus which has host-dependent growth and receptor binding properties and have shown that a mutation which removes an oligosaccharide from the tip of the hemagglutinin (HA) by changing Asn-129 to Asp permits this virus to grow to high titer in MDBK cells, (C. M. Deom, A. J. Caton, and I. T. Schulze, Proc. Natl. Acad. Sci. USA 83:3771-3775, 1986). We have now isolated monoclonal antibodies specific for the mutant HA and have used escape mutants to identify alterations in HA sequence which reduce virus yields from MDBK cells without reducing those from chicken embryo fibroblasts. Two types of escape mutants which grow equally well in chicken embryo fibroblasts were obtained. Those with the parent phenotype contain Asn at residue 129 and are glycosylated at that site. Those with the mutant phenotype are unchanged at residue 129 but have a Gly to Glu substitution at residue 158, which is close to residue 129 on the HA1 subunit. Binding assays with neoglycoproteins containing N-acetylneuraminic acid in either alpha 2,3 or alpha 2,6 linkage to galactose showed that the MDBK-synthesized oligosaccharides at Asn-129 reduce binding to both of these receptors, leaving the HA's preference for alpha 2,6 linkages unchanged. Glu at residue 158 greatly reduces binding to both receptors without reducing virus yields from MDBK cells. We conclude that changes in the receptor binding properties of the HA can result either from direct alteration of the HA protein by host cell glycosylation or from mutations in the HA gene and that these changes generate heterogeneity that can contribute to the survival of influenza A virus populations in nature.

Structural assignment of novel and immunodominant antigenic sites in the neutralizing antibody response of CBA/Ca mice to influenza hemagglutinin

Information on the antigenic structure of influenza hemagglutinin (HA) has been deduced previously from sequence analyses of laboratory mutant viruses selected, in vitro, with neutralizing monoclonal antibody (mAb) established exclusively from BALB/c (H-2d) mice; and there has been no attempt to investigate the influence of host genetic background, or natural route of infection, on the protective antibody repertoire. CBA/Ca mice are extremely sensitive to X31 virus infection, and in the present study a structural analysis was made of the antibody repertoire, by direct sequencing of the HA genes of laboratory mutant viruses selected, in ovo with mAb from CBA/Ca mice primed by natural infection with X31 virus at two different infectious doses. Single nucleotide substitutions in the HA genes of mutant viruses identified both novel and immunodominant antigenic sites on the HA1 subunit: a majority of mAbs, from different donors, were of the IgG2a isotype and were specific for HA1 158 Gly. In addition, novel laboratory mutants were obtained containing substitutions in the HA1 subunit that had not been reported previously for H3 subtype viruses, either natural variants or laboratory mutants, at residues: HA1 62 Ile----Arg; HA1 165 Asn----Ser (resulting in the loss of a N-glycosylation site); and HA1 273 Pro----Leu. Our findings suggest that host genetic background and/or a natural route of infection may be significant factors in the selection of different and distinct neutralizing antibody responses to influenza HA and therefore be of some relevance in our further understanding of the immune pressure for antigenic drift, and the immunogenic features of a protective antigen.

Molecular evolution of hemagglutinin genes of H1N1 swine and human influenza A viruses

The hemagglutinin (HA) genes of influenza type A (H1N1) viruses isolated from swine were cloned into plasmid vectors and their nucleotide sequences were determined. A phylogenetic tree for the HA genes of swine and human influenza viruses was constructed by the neighbor-joining method. It showed that the divergence between swine and human HA genes might have occurred around 1905. The estimated rates of synonymous (silent) substitutions for swine and human influenza viruses were almost the same. For both viruses, the rate of synonymous substitution was much higher than that of nonsynonymous (amino acid altering) substitution. It is the case even for only the antigenic sites of the HA. This feature is consistent with the neutral theory of molecular evolution. The rate of nonsynonymous substitution for human influenza viruses was three times the rate for swine influenza viruses. In particular, nonsynonymous substitutions at antigenic sites occurred less frequently in swine than in humans. The difference in the rate of nonsynonymous substitution between swine and human influenza viruses can be explained by the different degrees of functional constraint operating on the amino acid sequence of the HA in both hosts.

Sequence of an influenza virus hemagglutinin determined directly from a clinical sample

The sequence of the HA1 region of the hemagglutinin gene of an influenza virus has been determined without growing the virus in eggs or in cultured cells. The virus used was an H1 strain of influenza A from a clinical specimen taken from a patient in 1987. RNA was extracted directly from virus that had been sedimented out of the transport medium in which the sample had been stored. DNA copies of the hemagglutinin gene, obtained by reverse transcription, were then amplified by the polymerase chain reaction and were sequenced by the dideoxy termination method. The deduced amino acid sequence is highly similar to that of other H1 viruses that had been isolated at about the same time and cultured for a limited number of passages in eggs. Furthermore, the HA1 sequence of progeny virus from this isolate obtained after one passage in chicken embryos is identical to that of the virus obtained directly from the nasopharynx. The results suggest that H1 isolates that have been grown for a limited number of passages in embryonated eggs have HA1 subunits that faithfully represent the virus population in the clinical samples from which they were derived.

Antigenic stability of H3 influenza viruses in the domestic duck population of southern China

An antigenic analysis was carried out on 145 duck influenza virus isolates of the H3 haemagglutinin subtype obtained over five years continuous surveillance from the region of southern China, a hypothetical influenza epicentre. This was done using a panel of twelve monoclonal antibodies raised to an early human strain of the H3 subtype. We demonstrate the existence of an extensive range of antigenic profiles, broadly similar but not identical to the human H3 strain, which persisted over the five year period. This variability was as great during discrete twelve month periods as over the whole five years. Hierarchic progression (observed with human strains) was not evident and no correlation of antigenic drift, in either positive or negative direction, was observed with the domestic duck isolates over time. Changing dominant antigenic profiles were, however, observed in faecal isolates with time within a single farm. The much broader range of profiles detected in pond water samples from the same farm suggested the existence of a heterogeneous antigenic reservoir. Local switching of dominant profiles may occur due to changes of cohorts as birds are taken to market. In vitro and in vivo passage experiments revealed a high degree of heterogeneity in antigenic profiles in progeny of uncloned isolates, whereas the profiles of cloned isolates were largely conserved. These results suggested that particular antigenic profiles in primary isolates may result from mixtures of subpopulations of the wild type virus in natural duck infections. Switching between reactivity profiles of different progeny is likely to be largely a result of regrouping of these subpopulations with lesser effects due to mutation. Hypervariability in some of the cloned isolates was observed with a few monoclonal antibodies recognising a region of HA reported to be hypervariable in swine influenza virus. Reactivity with one particular antibody was correlated with passage in chicken eggs. The ability of this enormously varied pool of duck influenza H3 strains to cross the species barrier to man and give rise to viruses with hierarchic capabilities was considered.

Abnormal processing of multiple proteins in Alzheimer disease

Cerebrovascular amyloid is the main constituent of the perivascular and neuritic plaques typical of Alzheimer disease, whereas neurofilaments and microtubule-associated tau protein have been considered primary contributors to the formation of the characteristic Alzheimer tangles. Plaques and tangles and their constituents have at times been ascribed a role in pathogenesis of the disease. Normally, neurofilaments become phosphorylated only upon axonal entry. In many neurologic disorders, neurofilament phosphorylation, as detected by any of the available monoclonal antibodies (mAbs) to neurofilament phosphorylated epitopes is shifted from an axonal to a cell-body location. An exception is provided by Alzheimer disease, where tangles (which are neuronal cell-body-derived structures) exhibit only one phosphorylated epitope. However, the very presence of neurofilaments in tangles and plaques has been questioned because of a reported cross-reaction of mAbs to phosphorylated neurofilaments with tau protein. On reinvestigating this cross-reactivity we found that four of five mAbs to phosphorylated neurofilaments and four of five mAbs to nonphosphorylated neurofilaments failed to react with tau protein. A fifth mAb (07-5) to phosphorylated neurofilament cross-reacted with partially denatured tau protein at an affinity 1/1700th of that for denatured neurofilaments; nondenatured tau protein in tissue sections did not cross-react. A fifth mAb (02-40) to nonphosphorylated neurofilament also cross-reacted weakly. In Alzheimer disease normal-appearing axons were revealed with all the mAbs to phosphorylated neurofilaments, but tangles were revealed with only one of them (mAb 07-5). mAb to tau protein did not stain or did so indistinctly. Four of five mAbs to nonphosphorylated neurofilaments failed to reveal axons. Upon dephosphorylation of tissue, staining by mAbs to phosphorylated neurofilaments disappeared, and axons were revealed with the mAb to tau protein and all mAbs to the nonphosphorylated neurofilaments. Tangles became stained with tau mAb and one mAb to the nonphosphorylated neurofilaments (mAb 10-1). Quantitative evaluation of immunocytochemical staining intensities and immunoblot cross-reactivity showed that neurofilaments are, indeed, constituents of tangles--apparently exceeding the concentration of tau protein 17-fold. Contribution of both conformation and primary structure to IgG specificity may explain the lack of any cross-reaction of mAbs to neurofilaments with tau protein in intact tissue and the appearance of cross-reaction in immunoblots where conformation specificity may be largely lost. The present data extend earlier findings of abnormal processing of neurofilaments and tau protein in Alzheimer disease and, together with reported abnormal processing of cerebrovascular amyloid beta-protein, suggest that inhibition of the processing of multiple proteins is basic to the pathogenesis of Alzheimer disease, whereas formation of plaques and tangles could be merely the most striking histologic result.

Laboratory characterization of a swine influenza virus isolated from a fatal case of human influenza

A swine influenza virus-like type A (H1N1) virus, designated A/Wisconsin/3523/88, was isolated in September 1988 from a Wisconsin woman who had died with primary viral pneumonia. Antigenic analyses with hemagglutinin-specific monoclonal antibodies and postinfection ferret serum indicated that the hemagglutinin of A/Wisconsin/3523/88 was antigenically closely related to viruses currently circulating in swine. Genetic analysis of the A/Wisconsin/3523/88 virus by RNA fingerprinting and partial RNA sequence analysis of seven of the eight segments indicated that the genome of the human isolate was similar to that of enzootic swine viruses. These laboratory data supported the epidemiologic findings that this human infection occurred by transmission of an enzootic swine influenza virus and that the virus showed no major genetic changes potentially related to increased pathogenesis.

Evolution to predominance of swine influenza virus hemagglutinin mutants of predictable phenotype during single infections of the natural host

L and H2 mutants of the A/NJ/11/76 H1N1 strain of swine influenza virus differ by having either a lysine or a glutamic acid at position 153 of the hemagglutinin glycoprotein of the virus. In two separate experiments, experimental infection of swine with various doses of the H2 mutant resulted in the emergence in 11 of 20 animals of virus with the L phenotype. All evidence indicates that the H2----L mutation, selection, and evolution to predominance occurred within the 7-day span of individual infections. L and H2 mutations appear to act as alleles in the adaptation of virus, respectively, to natural and laboratory hosts. Although the gradual evolution of mutants during sequential infections is commonplace, the present recognition of rapid and predictable evolution of mutants of increased replication efficiency and specific phenotype in the natural host, to our knowledge, is unprecedented.

Mispair formation in DNA can involve rare tautomeric forms in the template

The formation of pyridine-pyrimidine- and pyrimidine-pyrimidine base pairs after in vitro DNA replication with the large fragment of Escherichia coli DNA polymerase I indicates that Watson-Crick-like base pairing between pyrimidine bases can occur in the enzyme due to the presence of the rare tautomers of deoxycytidylate and thymidylate in the template strand. The implications to mispair formation in DNA, such as the difference between the structures of the mispairs during and after replication, are discussed and the possible action of mutagenic DNA protonating and deprotonating agents in vivo is considered.

Hemagglutinin polymorphism as the basis for low- and high-yield phenotypes of swine influenza virus

Single amino acid substitutions at the rim of the receptor binding site of the hemagglutinin molecule of swine influenza virus markedly influence the replicative capacity of the virus in chicken embryos, Madin-Darby canine kidney cells (MDCK), and swine as well as its antigenic phenotype. Mutants of low-yield (L) phenotype replicate poorly in chicken embryos and produce small plaques in MDCK cells but are highly infective for swine. Such mutants have lysine at position 153 and glycine at position 155 of the hemagglutinin (residues 156 and 158 in the H3 model). High-yield (H) mutants have the converse replicative characteristics and can be antigenically distinguished from L mutants (and from each other) based on their differential reactivity with two monoclonal antibodies, 9C8 and Sa-13. H mutants differ from L mutants in that the H mutants express glutamic acid at either position 153 or 155. L and H mutants act in an allelic fashion in effecting predictable one-step adaptation to different hosts. Selection for replication (e.g., high-yielding) phenotype results in concordant pleiotropic change in antigenic phenotype and in genotype. Conversely, immunoselection leads to change in replicative phenotype. Although the mechanism by which these mutations affect viral replication has not yet been defined, they may reflect differences in the affinity of each mutant for different host receptors.

Nucleotide sequence and genomic organization of Aleutian mink disease parvovirus (ADV): sequence comparisons between a nonpathogenic and a pathogenic strain of ADV

A DNA sequence of 4,592 nucleotides (nt) was derived for the nonpathogenic ADV-G strain of Aleutian mink disease parvovirus (ADV). The 3'(left) end of the virion strand contained a 117-nt palindrome that could assume a Y-shaped configuration similar to, but less stable than, that of other parvoviruses. The sequence obtained for the 5' end was incomplete and did not contain the 5' (right) hairpin structure but ended just after a 25-nt A + T-rich direct repeat. Features of ADV genomic organization are (i) major left (622 amino acids) and right (702 amino acids) open reading frames (ORFs) in different translational frames of the plus-sense strand, (ii) two short mid-ORFs, (iii) eight potential promoter motifs (TATA boxes), including ones at 3 and 36 map units, and (iv) six potential polyadenylation sites, including three clustered near the termination of the right ORF. Although the overall homology to other parvoviruses is less than 50%, there are short conserved amino acid regions in both major ORFs. However, two regions in the right ORF allegedly conserved among the parvoviruses were not present in ADV. At the DNA level, ADV-G is 97.5% related to the pathogenic ADV-Utah 1. A total of 22 amino acid changes were found in the right ORF; changes were found in both hydrophilic and hydrophobic regions and generally did not affect the theoretical hydropathy. However, there is a short heterogeneous region at 64 to 65 map units in which 8 out of 11 residues have diverged; this hypervariable segment may be analogous to short amino acid regions in other parvoviruses that determine host range and pathogenicity. These findings suggested that this region may harbor some of the determinants responsible for the differences in pathogenicity of ADV-G and ADV-Utah 1.

Production of subtype-specific antipeptide antibodies to human interferon-alpha 1 and -alpha 4

Antibodies that are specific to the human interferon (IFN)-alpha 1 and -alpha 4 subtypes have been produced by immunizing rabbits with two short synthetic peptides, corresponding to residues 99-111 of IFN-alpha 1 and residues 37-50 of IFN-alpha 4, respectively. The IFN-alpha 1 peptide has at least three closely clustered residues that are different from those in the other IFN-alpha subtypes, while the IFN-alpha 4 peptide has only two unique amino acid residues, separated by five common residues. The antibodies raised against the IFN-alpha 1 peptide react with recombinant human IFN-alpha 1 but do not cross-react with recombinant human IFN-alpha 4 or IFN-alpha 2. The antibodies raised against the IFN-alpha 4 peptide react with IFN-alpha 4, cross-react with IFN-alpha 1 but not with IFN-alpha 2; the affinity of the antibodies to IFN-alpha 1, however, is at least 10 times lower than their affinity to IFN-alpha 4.

Antigenic relationships between avian paramyxoviruses. III. A mathematical model of antigenic drift and a computer-assisted approach for construction of a phylogenetic tree

The suggested model of antigenic kinship between related paramyxoviruses is based on another concept of antigenic determinant, as compared to the previously suggested combinatorial mathematical model by the authors. According to it, antigenic changes of any determinant do not proceed by "leaps" but can be changed gradually. Such changed determinant can induce a correspondingly changed type of antibodies which still preserve a certain kinship to the original type of the determinant (before its changing) revealed by cross reaction serological tests. Accordingly, there can be "families" of the determinants differing by degree of relatedness to (or, reversely, by antigenic distance from) the "original" ("ancestor") determinant. In addition to another interpretation of the antigenic kinship, the new mathematical model was used as an approach for revealing phylogenetic relationships between antigenically related viruses.

The molecular biology of influenza virus pathogenicity

It is an accepted concept that the pathogenicity of a virus is of polygenic nature. Because of their segmented genome, influenza viruses provide a suitable system to prove this concept. The studies employing virus mutants and reassortants have indicated that the pathogenicity depends on the functional integrity of each gene and on a gene constellation optimal for the infection of a given host. As a consequence, virtually every gene product of influenza virus has been reported to contribute to pathogenicity, but evidence is steadily growing that a key role has to be assigned to hemagglutinin. As the initiator of infection, hemagglutinin has a double function: (1) promotion of adsorption of the virus to the cell surface, and (2) penetration of the viral genome through a fusion process among viral and cellular membranes. Adsorption is based on the binding to neuraminic acid-containing receptors, and different virus strains display a distinct preference for specific oligosaccharides. Fusion capacity depends on proteolytic cleavage by host proteases, and variations in amino acid sequence at the cleavage site determine whether hemagglutinin is activated in a given cell. Differences in cleavability and presumably also in receptor specificity are important determinants for host tropism, spread of infection, and pathogenicity. The concept that proteolytic activation is a determinant for pathogenicity was originally derived from studies on avian influenza viruses, but there is now evidence that it may also be relevant for the disease in humans because bacterial proteases have been found to promote the development of influenza pneumonia in mammals.

Nucleotide sequence and genome organization of canine parvovirus

The genome of a canine parvovirus isolate strain (CPV-N) was cloned, and the DNA sequence was determined. The entire genome, including ends, was 5,323 nucleotides in length. The terminal repeat at the 3' end of the genome shared similar structural characteristics but limited homology with the rodent parvoviruses. The 5' terminal repeat was not detected in any of the clones. Instead, a region of DNA starting near the capsid gene stop codon and extending 248 base pairs into the coding region had been duplicated and inserted 75 base pairs downstream from the poly(A) addition site. Consensus sequences for the 5' donor and 3' acceptor sites as well as promotors and poly(A) addition sites were identified and compared with the available information on related parvoviruses. The genomic organization of CPV-N is similar to that of feline parvovirus (FPV) in that there are two major open reading frames (668 and 722 amino acids) in the plus strand (mRNA polarity). Both coding domains are in the same frame, and no significant open reading frames were apparent in any of the other frames of both minus and plus DNA strands. The nucleotide and amino acid homologies of the capsid genes between CPV-N and FPV were 98 and 99%, respectively. In contrast, the nucleotide and amino acid homologies of the capsid genes for CPV-N and CPV-b (S. Rhode III, J. Virol. 54:630-633, 1985) were 95 and 98%, respectively. These results indicate that very few nucleotide or amino acid changes differentiate the antigenic and host range specificity of FPV and CPV.

Interpreting the behavior of enzymes: purpose or pedigree?

To interpret the growing body of data describing the structural, physical, and chemical behaviors of biological macromolecules, some understanding must be developed to relate these behaviors to the evolutionary processes that created them. Behaviors that are the products of natural selection reflect biological function and offer clues to the underlying chemical principles. Nonselected behaviors reflect historical accident and random drift. This review considers experimental data relevant to distinguishing between nonfunctional and functional behaviors in biological macromolecules. In the first segment, tools are developed for building functional and historical models to explain macromolecular behavior. These tools are then used with recent experimental data to develop a general outline of the relationship between structure, behavior, and natural selection in proteins and nucleic acids. In segments published elsewhere, specific functional and historical models for three properties of enzymes--kinetics, stereospecificity, and specificity for cofactor structures--are examined. Functional models appear most suitable for explaining the kinetic behavior of proteins. A mixture of functional and historical models appears necessary to understand the stereospecificity of enzyme reactions. Specificity for cofactor structures appears best understood in light of purely historical models based on a hypothesis of an early form of life exclusively using RNA catalysis.

Perspectives on antigenicity and idiotypy

The recent crystal determination of a lysozyme-antilysozyme complex provides a three-dimensional prototype of the manner in which contacts in idiotype-anti-idiotype interactions may be realized. Such interactions can be approximated by two complementary "flat" surfaces. Each IDR (autoantigenic locus) location might provide a particular recognition feature between two interacting partners. The combinatorial manner in which IDR domains are recognized by anti-idiotypic antibodies describe the repertoire of private and public (crossreactive) idiotopes of an antibody. Several interesting features emerge from consideration of the Ab contact residues in the crystal structure. First, framework residues are implicated in contacting the antigen: Thr 30 (FR1) of the heavy chain and Tyr 49 (FR2) of the kappa light chain. Both of these residues lie within predicted IDRs. Framework regions have recently been suggested to be involved in several anti-idiotypic systems, although such regions have, in the past, been disregarded based solely upon sequence analysis. The surface variability analysis, which identifies the repertoire of complementary interacting surfaces, depicts the immunoglobulin as having more variability than generally thought. This variability may also extend to T cell receptors since T cell chains express an extensive surface variable repertoire similar to that of the immunoglobulin light chains (Kieber-Emmons and Köhler, unpublished). Second, the D region plays a critical role in the generation of the antilysozyme combining sites. Similarly, the D segment makes up the largest component of an IDR. Third, while the CDR3 of the heavy chain contributes most to the antibody-lysozyme complex it is not the most surface-exposed (see Novotny, this issue). Nevertheless, surface variability analysis indicates that this region is generally immunodominant which is also observed experimentally. Together, these results indicate that perhaps certain IDR regions are intrinsically more antigenic. Idiotypic structures must be accessible for antibody recognition and binding. From a structural viewpoint, a single antibody molecule has a continuum or several different combining sites. Subsequently, a single residue can be contained in several overlapping idiotypic determinants. Surface variability analysis suggests that the hypervariable regions of Igs provide a diverse idiotope repertoire that can be utilized for binding. Monoclonal antibodies have been shown to have multiple specificities and this capacity for multiple binding is also intrinsic to the definitions that have emerged for anti-idiotypic antibodies.(ABSTRACT TRUNCATED AT 400 WORDS)

Receptor-binding characteristics of monoclonal antibody-selected antigenic variants of influenza virus

Erythrocytes modified to different extents with periodate were used in hemagglutination assays to investigate the binding properties of antihemagglutinin monoclonal antibody-selected antigenic variants of X-31 influenza virus. The results allowed differentiation of groups of variants and are discussed in relation to the nature of the amino acid substitutions in the variant hemagglutinins and their molecular locations relative to the receptor-binding site.