Evolution of human influenza A viruses in nature: sequential mutations in the genomes of new H1N1

Virology-The next fifty years

Virology has made enormous advances in the last 50 years but has never faced such scrutiny as it does today. Herein, we outline some of the major advances made in virology during this period, particularly in light of the COVID-19 pandemic, and suggest some areas that may be of research importance in the next 50 years. We focus on several linked themes: cataloging the genomic and phenotypic diversity of the virosphere; understanding disease emergence; future directions in viral disease therapies, vaccines, and interventions; host-virus interactions; the role of viruses in chronic diseases; and viruses as tools for cell biology. We highlight the challenges that virology will face moving forward-not just the scientific and technical but also the social and political. Although there are inherent limitations in trying to outline the virology of the future, we hope this article will help inspire the next generation of virologists.

Cell-Adapted Mutations and Antigenic Diversity of Influenza B Viruses in Missouri, 2019-2020 Season

Influenza B viruses (IBVs) are causing an increasing burden of morbidity and mortality, yet the prevalence of culture-adapted mutations in human seasonal IBVs are unclear. We collected 368 clinical samples from patients with influenza-like illness in Missouri during the 2019–2020 influenza season and recovered 146 influenza isolates including 38 IBV isolates. Of MDCK-CCL34, MDCK-Siat1, and humanized MDCK (hCK), hCK showed the highest virus recovery efficiency. All Missourian IBVs belonged to the Victoria V1A.3 lineage, all of which contained a three-amino acid deletion on the HA protein and were antigenically distant from the Victoria lineage IBV vaccine strain used during that season. By comparing genomic sequences of these IBVs in 31 paired samples, eight cell-adapted nonsynonymous mutations were identified, with the majority in the RNA polymerase. Analyses of IBV clinical sample–isolate pairs from public databases further showed that cell- and egg-adapted mutations occurred more widely in viral proteins, including the receptor and antibody binding sites on HA. Our study suggests that hCK is an effective platform for IBV isolation and that culture-adapted mutations may occur during IBV isolation. As culture-adapted mutations may affect subsequent virus studies and vaccine development, the knowledge from this study may help optimize strategies for influenza surveillance, vaccine strain selection, and vaccine development.

Evolutionary Virology at 40

RNA viruses are diverse, abundant, and rapidly evolving. Genetic data have been generated from virus populations since the late 1970s and used to understand their evolution, emergence, and spread, culminating in the generation and analysis of many thousands of viral genome sequences. Despite this wealth of data, evolutionary genetics has played a surprisingly small role in our understanding of virus evolution. Instead, studies of RNA virus evolution have been dominated by two very different perspectives, the experimental and the comparative, that have largely been conducted independently and sometimes antagonistically. Here, we review the insights that these two approaches have provided over the last 40 years. We show that experimental approaches using in vitro and in vivo laboratory models are largely focused on short-term intrahost evolutionary mechanisms, and may not always be relevant to natural systems. In contrast, the comparative approach relies on the phylogenetic analysis of natural virus populations, usually considering data collected over multiple cycles of virus-host transmission, but is divorced from the causative evolutionary processes. To truly understand RNA virus evolution it is necessary to meld experimental and comparative approaches within a single evolutionary genetic framework, and to link viral evolution at the intrahost scale with that which occurs over both epidemiological and geological timescales. We suggest that the impetus for this new synthesis may come from methodological advances in next-generation sequencing and metagenomics.

Seasonal H3N2 and 2009 Pandemic H1N1 Influenza A Viruses Reassort Efficiently but Produce Attenuated Progeny

Reassortment of gene segments between coinfecting influenza A viruses (IAVs) facilitates viral diversification and has a significant epidemiological impact on seasonal and pandemic influenza. Since 1977, human IAVs of H1N1 and H3N2 subtypes have cocirculated with relatively few documented cases of reassortment. We evaluated the potential for viruses of the 2009 pandemic H1N1 (pH1N1) and seasonal H3N2 lineages to reassort under experimental conditions. Results of heterologous coinfections with pH1N1 and H3N2 viruses were compared to those obtained following coinfection with homologous, genetically tagged, pH1N1 viruses as a control. High genotype diversity was observed among progeny of both coinfections; however, diversity was more limited following heterologous coinfection. Pairwise analysis of genotype patterns revealed that homologous reassortment was random while heterologous reassortment was characterized by specific biases. pH1N1/H3N2 reassortant genotypes produced under single-cycle coinfection conditions showed a strong preference for homologous PB2-PA combinations and general preferences for the H3N2 NA, pH1N1 M, and H3N2 PB2 except when paired with the pH1N1 PA or NP. Multicycle coinfection results corroborated these findings and revealed an additional preference for the H3N2 HA. Segment compatibility was further investigated by measuring chimeric polymerase activity and growth of selected reassortants in human tracheobronchial epithelial cells. In guinea pigs inoculated with a mixture of viruses, parental H3N2 viruses dominated but reassortants also infected and transmitted to cage mates. Taken together, our results indicate that strong intrinsic barriers to reassortment between seasonal H3N2 and pH1N1 viruses are few but that the reassortants formed are attenuated relative to parental strains.IMPORTANCE The genome of IAV is relatively simple, comprising eight RNA segments, each of which typically encodes one or two proteins. Each viral protein carries out multiple functions in coordination with other viral components and the machinery of the cell. When two IAVs coinfect a cell, they can exchange genes through reassortment. The resultant progeny viruses often suffer fitness defects due to suboptimal interactions among divergent viral components. The genetic diversity generated through reassortment can facilitate the emergence of novel outbreak strains. Thus, it is important to understand the efficiency of reassortment and the factors that limit its potential. The research described here offers new tools for studying reassortment between two strains of interest and applies those tools to viruses of the 2009 pandemic H1N1 and seasonal H3N2 lineages, which currently cocirculate in humans and therefore have the potential to give rise to novel epidemic strains.

Fetal calf serum inhibits virus genome expression in Madin-Darby canine kidney cells persistently infected with influenza A virus

A cell line of Madin-Darby canine kidney (MDCK) cells persistently infected with human influenza A virus has been established and designated as MDCK-IVpi cells. Production of progeny virus in MDCK-IVpi cells was suppressed when the cells were incubated in the presence of 10% fetal calf serum (FCS). FCS impaired virus mRNA synthesis in MDCK-IVpi cells, which resulted in a scarcity of virus proteins for virion formation. However, MDCK-IVpi cells well supported the growth of superinfecting heterologous influenza viruses, even in the presence of FCS. A certain fetuin-like substance in FCS might be responsible for the observed inhibition of virus replication.

Methods for subtyping and molecular comparison of human viral genomes

The development over the past two decades of molecular methods for manipulation of RNA and DNA has afforded molecular virologists the ability to study viral genomes in detail that has heretofore not been possible. There are many molecular techniques now available for typing and subtyping of viruses. The available methods include restriction fragment length polymorphism analysis, Southern blot analysis, oligonucleotide fingerprint analysis, reverse hybridization, DNA enzyme immunoassay, RNase protection analysis, single-strand conformation polymorphism analysis, heteroduplex mobility assay, nucleotide sequencing, and genome segment length polymorphism analysis. The methods have certain advantages and disadvantages which should be considered in their application to specific viruses or for specific purposes. These techniques are likely to become more widely used in the future for epidemiologic studies and for investigations into the pathophysiology of virus infections.

Genetic and antigenic analyses of influenza A (H1N1) viruses, 1986-1991

Eighteen strains of human influenza A (H1N1) viruses isolated between August 1986 and January 1991 were analyzed in this study. Examination of the total viral genome of 12 strains by T1 mapping revealed that considerable genetic heterogeneity exists among these viruses. Partial sequencing of each of the non-HA RNA segments of 4 viruses having divergent T1 oligonucleotide maps indicated that only one was a reassortant virus that had genes from both the influenza A (H1N1) and (H3N2) subtypes. This reassortant obtained its PB2 gene from a virus of the H3N2 subtype and the other 7 RNA segments from an H1N1 parent. Sequencing studies of the HA1 domains of the hemagglutinin (HA) genes of these 18 strains revealed that although these viruses are antigenically similar to the reference strains A/Taiwan/1/86 and A/Singapore/6/86, 7 conserved amino acid substitutions that are shared by recently isolated H1N1 viruses have occurred in the main stream of evolution of the H1N1 subtype. Our data indicate that: (1) Genetic reassortment continues to contribute to genetic variability of H1N1 viruses. (2) Genetic variants of non-reassortant H1N1 viruses are co-circulating in the world. (3) The HA's of recent H1N1 viruses are related to those of the 1986 reference strains. (4) Although there has been little detectable antigenic variability, the HA genes of human epidemic influenza A (H1N1) viruses have continued to evolve at an evolutionary rate similar to that for the H1N1 and H3N2 viruses analyzed previously.

The herald waves of influenza virus infections detected in Sendai and Yamagata cities in 1985-1990

The community surveillance of respiratory virus infections performed during 1985-1987 in Sendai and 1988-1990 in Yamagata has identified a total of five herald waves of influenza virus infections: A/H3N2 virus infections in 1985 and 1989, A/H1N1 virus infections in 1986 and 1988, and type B virus infections in 1989. To investigate the antigenic and genetic relationships between the herald wave and epidemic strains, influenza A/H1N1 viruses isolated during the 1986 and 1988 herald waves were compared with those isolated during the 1986-1987 and 1988-1989 epidemic seasons, respectively, utilizing hemagglutination inhibition tests with anti-hemagglutinin monoclonal antibodies and oligonucleotide mapping of total viral RNAs. The results showed that multiple variants differing in antigenic and genetic properties were cocirculating during the 1986 herald wave as well as during each of the two epidemics (only one strain was isolated in the 1988 herald wave). It was also observed that viruses which had the antigenic and/or genetic characteristics closely similar to those of the viruses circulating in the 1986 and 1988 herald waves, were isolated during the winters of 1986-1987 and 1988-1989, respectively.

Increased virulence of a mouse-adapted variant of influenza A/FM/1/47 virus is controlled by mutations in genome segments 4, 5, 7, and 8

To cause disease, influenza virus must possess several genetically determined abilities that mediate stages in pathogenesis. The virulent mouse-adapted variant A/FM/1/47-MA (FM-MA), derived from the avirulent A/FM/1/47 (FM) strain, had acquired mutations in genes that control virulence. The purpose of this study was to identify those genes that had mutated to result in increased virulence and to obtain viruses that differed in virulence because of differences in individual genome segments. The genes that had mutated to increase virulence were initially identified by genetic analysis of reassortants obtained by crossing FM-MA with the avirulent strain A/HK/1/68 (HK). FM-MA genome segments 4, 5, 7, and 8 were significantly associated with virulence, as determined by using the Wilcoxon ranked sum analysis. The role of FM-MA segments 4, 7, and 8 was confirmed by reintroduction of these genes into the parental strain, which also provided virus strains that differed in virulence because of mutations in individual genome segments. Segments 4, 7, and 8 were responsible for a 10(3.6)-fold increase in virulence that was proportioned 10(2.2)-, 10(0.7)-, and 10(0.8)-fold, respectively. The role of segment 5 could not be confirmed on transfer back into the parental strain because of reversion during preparation of such reassortants. The incidence of reversion was shown to be significantly associated with culturing of FM-MA in chicken embryo cells but was not associated with growth in MDCK cells. The genetic analysis of FM-MA suggests that adaptation to increased virulence is an incremental process that involves the acquisition of mutations in multiple genes, each of which plays an individual role in pathogenesis. The structural and functional properties of segments 4, 7, and 8 that control the virulence of FM-MA can now be determined by using viruses that differ in virulence because of mutations in these individual genome segments.

Genetic drift of equine 2 influenza A virus (H3N8), 1963-1988: analysis by oligonucleotide mapping

Comparative analysis by RNA oligonucleotide fingerprints of total genomic RNA as well as the individual RNA segments of equine 2 influenza A virus strains from 1963, 1968, 1979, 1984, 1987 and 1988 revealed genetic diversity. Strains from the epizootic outbreak during 1978-1979 showed minor differences among their genomes. The Swedish isolates from 1979 up to 1988 showed increasing genomic heterogeneity indicating genetic drift.

Genetic variation and microevolution of dengue 2 virus in Southeast Asia

Dengue 2 (DEN 2) virus strains collected from dengue hemorrhagic fever (DHF) patients and Aedes aegypti mosquitoes in Thailand, Burma, and Vietnam over a 25-year period have been analyzed by computer assisted T1-RNase-resistant oligonucleotide fingerprinting. Fifty-seven DEN 2 virus strains of the Thailand topotype were separated into four major clusters by phylogenetic analysis of 97 unique oligonucleotides identified in a common well-resolved region of the fingerprints. Similarities in the 57 fingerprints indicated that DEN 2 virus of a single, continually evolving genetic population has been involved in endemic transmission of the disease. Virus isolates from DHF cases and mosquitoes are genetically very similar, indicating that different genetic topotypes are not selectively the cause of severe DEN disease in Thailand. Microevolution of the DEN 2 virus genome from 1962-1986 was gradual with detectable changes in the pattern of oligonucleotides through time. Segregation of the DEN 2 virus fingerprints into the three decades (1960s, 1970s, and 1980s) revealed the rate of genetic change to be one consensus oligonucleotide per year. Based on average association coefficient (Sab) values between the consensus fingerprints for each decade, the similarity between the consensus fingerprints decreased by 1.4% per year. Genetic variation during each of the three decades was found to be essentially the same (0.866 +/- 0.053). Constancy in the microevolutionary rate and genetic variability suggests that a balance of genetic drift and natural selection acting on the viral population did not significantly change throughout the 25-year period.

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.

Analysis of some swine influenza H1N1 viruses by oligonucleotide fingerprinting

The genome of the swine influenza H1N1 virus Sweden/83 was compared to other H1N1 viruses by oligonucleotide fingerprinting. This analysis revealed that Sweden/83 is identical to the Danish strain Sjaelland/82 and is thus to be placed in the group of "US viruses". On the other hand, the Danish strain Als/82 was found to be different, i.e., related to the Belgium/79 strain which is a representative of the "European viruses". The results of the present genomic analysis confirm the previous findings of relationships between the above strains.

RNA genome stability of Toscana virus during serial transovarial transmission in the sandfly Phlebotomus perniciosus

We have carried out a T1 ribonuclease fingerprinting analysis of the RNA genomes of Toscana virus isolates from successive generations of an experimentally virus-infected laboratory colony of Phlebotomus perniciosus sandflies. This analysis detected no virus RNA genome changes during transovarial transmission of the virus over 12 sandfly generations (a period of almost 2 years). These results demonstrate that although RNA viruses can exhibit high rates of mutational change under a variety of conditions, Toscana virus RNA genomes can be maintained in a stable manner during repeated transovarial virus transmission in the natural insect host. The implications of these results for insect RNA virus evolution are discussed.

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.

A new concept of the epidemic process of influenza A virus

Influenza A virus was discovered in 1933, and since then four major variants have caused all the epidemics of human influenza A. Each had an era of solo world prevalence until 1977 as follows: H0N1 (old style) strains until 1946, H1N1 (old style) strains until 1957, H2N2 strains until 1968, then H3N2 strains, which were joined in 1977 by a renewed prevalence of H1N1 (old style) strains. Serological studies show that H2N2 strains probably had had a previous era of world prevalence during the last quarter of the nineteenth century, and had then been replaced by H3N2 strains from about 1900 to 1918. From about 1907 the H3N2 strains had been joined, as now, by H1N1 (old style) strains until both had been replaced in 1918 by a fifth major variant closely related to swine influenza virus A/Hswine1N1 (old style), which had then had an era of solo world prevalence in mankind until about 1929, when it had been replaced by the H0N1 strains that were first isolated in 1933. Eras of prevalence of a major variant have usually been initiated by a severe pandemic followed at intervals of a year or two by successive epidemics in each of which the nature of the virus is usually a little changed (antigenic drift), but not enough to permit frequent recurrent infections during the same era. Changes of major variant (antigenic shift) are large enough to permit reinfection. At both major and minor changes the strains of the previous variant tend to disappear and to be replaced within a single season, worldwide in the case of a major variant, or in the area of prevalence of a previous minor variant. Pandemics, epidemics and antigenic variations all occur seasonally, and influenza and its viruses virtually disappear from the population of any locality between epidemics, an interval of many consecutive months. A global view, however, shows influenza continually present in the world population, progressing each year south and then north, thus crossing the equator twice yearly around the equinoxes, the tropical monsoon periods. Influenza arrives in the temperate latitudes in the colder months, about 6 months separating its arrival in the two hemispheres. None of this behaviour is explained by the current concept that the virus is surviving like measles virus by direct spread from the sick providing endless chains of human influenza A.(ABSTRACT TRUNCATED AT 400 WORDS)

Genome analysis of human rotaviruses by oligonucleotide mapping of isolated RNA segments

The genomes of adult diarrhoea rotaviruses isolated in different parts of China during winter outbreaks in 1983 and 1984 were compared by segmental oligonucleotide (ON) mapping. The RNA profiles of most of the isolates were indistinguishable but it was found that some corresponding RNA segments had identical or very closely related ON maps whereas others differed considerably. This finding can be taken to suggest that the strains compared may be genetically related by a natural reassortment event. The genomes of cocirculating group A rotaviruses isolated in Scotland during winter outbreaks in 1981/82 were also compared. The ON maps of corresponding RNA segment differed extensively irrespective of whether or not the segments comigrated on gels.

Genetic variation among human strains of influenza C virus isolated in Japan

The RNA genomes of sixteen human strains of influenza C virus isolated in Japan between 1964 and 1983 were compared by SDS-polyacrylamide gel electrophoresis and oligonucleotide fingerprinting. A high degree of genetic variation was observed among the strains analysed. However, there were some strains with the genomes closely related to one another, and they could be divided into two groups. The first group consists of C/Shizuoka/79, C/Kanagawa/1/81 and four strains of C/Yamagata/81. The 1981 strains of this group were all isolated in March of the year. The second one consists of C/Kyoto/41/82, C/Nara/82 and C/Hyogo/1/83 that were isolated between February 1982 and December 1983. Little or no difference was observed in the genomes of the same group, while the difference was evident between two groups. The Aichi/1/81 strain isolated in November 1981 had a genome distantly related to either of these two groups. Thus three different types of influenza C virus were isolated during the period of 12 mth from March 1981 to February 1982, suggesting that multiple influenza C viruses with distant genetic relationship were circulating at the same time in Japan.

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

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

Evolution of enterovirus 70 in nature: all isolates were recently derived from a common ancestor

The data of large RNase T1-resistant oligonucleotide mapping of enterovirus 70 (EV 70) previously reported (Takeda et al., Virology 134, 375-388, 1984) were subjected to further genetical analysis to estimate the evolutionary rate of genome RNA of EV 70 and to clarify the phylogenetic relationship among isolates. A proportion of common spots between strains decreased as the year elapsed and eventually, only seven spots were common to all the 16 isolates tested, indicating that the substitution is scattered throughout the genome. On the other hand, some specific sets of spots were conserved among geographically or epidemiologically related strains. Base sequence variation of the isolates was deduced according to Aaronson et al. (Nucleic Acids Res. 10, 237-246, 1982) from pariwise comparison of the common spots and used as a genetic distance between them. The base substitution rate of virus genome was estimated by regression analysis of the genetic distance of the isolates against the sampling time. A fairly constant and rapid rate was obtained; it was 1.83 X 10(-3)/base/year. Based on the substitution rate, genetic distance and sampling time of the strains, the phylogenetic tree of EV 70 was constructed using Unweighted Pair Group Method Using Arithmetic Averages (UPGMA) (Nei, Molecular Population Genetics and Evolution, North Holland, Amsterdam, 1975). The tree supports the previous hypothesis that evolution of EV 70 started from a single common ancestor. The time of its emergence was estimated to be 1967 +/- 15 months. The virus branched into many strains early during the first pandemic and has evolved in a divergent fashion, yielding genetically polymorphic viruses in the world.

The antigenicity and evolution of influenza H1 haemagglutinin, from 1950-1957 and 1977-1983: two pathways from one gene

Nucleotide sequence analysis of the region of the haemagglutinin gene coding for the HA1 domain of the protein was performed on 19 human influenza A strains of H1 subtype representative of the two epidemic periods from 1977-1983 and from 1950-1957. The amino acid changes relative to A/USSR/90/77 are summarised and are consistent with the view that variation in these field strains involves changes largely at the Sb and Ca antigenic sites previously characterised in laboratory mutants of the haemagglutinin of influenza A/PR/8/34. The Sa and Cb sites are less variant and are probably masked by carbohydrate side chains. We discuss the significance of other amino acid changes which do not correspond to previously defined antigenic sites. We also define the "mainstream" amino acid changes characteristic of the divergent evolutionary pathways of the 1950-1957 and 1977-1983 periods and note that the rate of evolution is faster in the earlier period.

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

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

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

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

Evolution of the A/Chicken/Pennsylvania/83 (H5N2) influenza virus

The epidemiological features of the H5N2 outbreak of influenza in poultry were studied by sequencing the HA genes of several viruses isolated during the epidemic. Comparison of the nucleotide sequences of the HA genes indicated there was a single introduction of virulent virus. The variation rate (silent mutations) in the HA gene of the virulent Ck/Penn virus was 9.0 or 14.4% per 10 years depending on the viruses compared and was similar to that in H3 HA gene of human influenza A virus. The virulent and avirulent viruses isolated after October 1983 were derived from a common ancestoral virus and the virulent virus did not supersede the avirulent virus, instead, the virulent and avirulent viruses coexisted and evolved separately during the course of the epidemic. The evolutionary changes in the HA of H5N2 viruses that occurred during the epidemic permitted us to establish that a virus (A/Chick/Washington/84) that was isolated 8 months after the last H5N2 virus had been isolated from poultry in Pennsylvania belonged to the family of potentially dangerous H5N2 viruses and was a direct descendent of the virus that spread to Maryland and Virginia. All of the virulent Ck/Penn viruses retained the amino acid changes at residues 13 and 69 in the HA.

Protein and nucleic acid analyses of influenza C viruses isolated from pigs and man

The virus-coded proteins and the genomes of influenza C virus isolates obtained from Chinese pigs in 1981-1982 and of human influenza C virus strains isolated between 1947 and 1981 were compared. Using SDS polyacrylamide gel electrophoresis and one-dimensional peptide mapping we found the virus-coded proteins of the pig influenza C viruses to be similar to those of human influenza C virus strains. The sizes of the genomes of human and pig influenza C viruses were indistinguishable. Genome analysis by oligonucleotide (ON) mapping revealed that the genomes of the pig influenza C viruses were very similar to but not identical with those of human influenza C virus strains. ON changes were found scattered over the whole genome. ON mapping of isolated segments of several influenza C virus strains suggested that two pig strains (C/P/B/10/81 and C/P/B/32/81) are related by a reassortment event which is likely to have occurred in nature. The rate of genome variation in influenza C viruses seemed to be similar to that seen in influenza B, and slower than that recorded for influenza A viruses.

Heterogeneity among influenza H3N2 isolates recovered during an outbreak. Brief report

Isolates of the H3N2 subtype recovered during an outbreak have been analyzed at the genomic and protein level. No reassortant genomes were detected. By T1-oligonucleotide fingerprinting of RNA segments coding for hemagglutinin (HA), nucleoprotein (NP), and neuraminidase (NA) two genotypes were found.

Analysis of Ross River virus genomic RNA using HaeIII digests of single-stranded cDNA to infected-cell RNA and virion RNA

To study genetic relationships between isolates of Ross River virus (RRV), an alphavirus with a chromosome of approximately 12,000 nucleotides, total high-molecular-weight RNA from RRV-infected baby hamster kidney (BHK) cells was transcribed into 32P-labeled, complementary DNA using reverse transcriptase and random calf-thymus DNA primers. The cDNA was digested with HaeIII or TaqI (restriction nucleases which cleave single-stranded DNA), and the restriction fragments separated on a standard DNA sequencing gel. The resulting HaeIII or TaqI restriction digest profiles mainly comprised virus-specific bands; cell RNAs were transcribed poorly. In reconstruction experiments, purified 49 S RRV genomic RNA and a 10-fold mass excess of mock-infected-cell RNA were reverse transcribed in the same reaction mix. Under these conditions there was no interference with the transcription of viral RNA sequences. When the level of viral RNA was lowered to one-hundredth that of cell RNA in the reaction mix, there was no qualitative change in restriction digest profiles. The procedure is rapid, simple, uses small amounts of 32P, does not require purification of virus or viral RNA, and permits cross-comparison between several virus strains on a single one-dimensional gel. The method should be applicable to other single-stranded RNA viruses of moderate genome complexity.

Antigenic heterogeneity among influenza A(H3N2) field isolates during an outbreak in 1982/83, estimated by methods of numerical taxonomy

Fourteen influenza A(H3N2) field isolates, mainly obtained during the first weeks of the 1982/83 influenza epidemic in The Netherlands, and nine influenza A(H3N2) reference strains were examined by means of haemagglutination inhibition (HI) tests with 23 polyclonal ferret sera. The resulting HI patterns were subjected to various methods of numerical taxonomy using, among others, taxonomic distance and correlation between strains for resemblance coefficients. Marked differences between distance and correlation coefficients were found in strains which differed in avidity only. The field isolates could be divided into four groups in respect of their taxonomic resemblance to the reference strains. The same grouping was found for five of the field isolates by testing these against 200 human sera.

Evolution of enterovirus type 70: oligonucleotide mapping analysis of RNA genome

Different isolates of enterovirus type 70 (EV70) taken between 1971 and 1981 were studied by molecular biological methods to elucidate their evolutional change. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed that only a few isolates had a slight alteration in mobility in some viral proteins. On the contrary, oligonucleotide mapping of virion RNA could clearly delineate the molecular changes among isolates. The number of base changes of isolates became greater as the years elapsed. In addition, the number of base changes among recent isolates from different areas of the world was much greater than those among early isolates. Thus, when the isolates were arranged three-dimensionally according to the number of base changes between each other, the constellation of the strains gave rise to a conical shape. The central axis of the figure was the time of isolation of the strains. The early isolates clustered near the top of the conical figure and the recent isolates tended to disperse divergently at the bottom. The figure indicated that all EV70 strains were derived from a common ancestor, and its top would be the time of emergence of the original strain. It was estimated to be around 1966, 3 years prior to the first epidemic in Accra, Ghana. From the results, it was presumed that EV70 would have emerged at a single focus in Africa as a novel human virus. After having circulated there for a few years, the virus spread to the other parts of the world. Based on the difference in the oligonucleotide spots between the recent isolates and early isolates, the base changes of EV70 that occurred during 10 years was estimated to be 320, about 4% (0.4% a year on the average) of the bases of the total RNA genome.

Molecular epidemiology of human rotaviruses. Analysis of outbreaks of acute gastroenteritis in Glasgow and the west of Scotland 1981/82 and 1982/83

The molecular epidemiology of rotavirus infections in Glasgow and the west of Scotland during 1981/82 and 1982/83 was investigated by electron microscopy, ELISA testing and RNA migration pattern analysis. In 1981/82, rotaviruses of both the 'long' and the 'short' electropherotype (in different variants) co-circulated from the onset throughout the winter peak of the outbreak. Approximately 80% of the children were infected during the first year of life. No differences in incidence were found between sexes. In 1982/83 the isolated rotaviruses were almost exclusively of the 'long' electropherotype (in different variants) and 36% of the children were infected beyond the first year of life. Rotaviruses of the 'long' electropherotype serologically were of subgroup II and serotype 1 and those of the 'short' electropherotype of subgroup I and serotype 2.

Comparison of nine strains of influenza C virus in growth characteristics and viral polypeptides. Brief report

Nine strains of influenza C virus were compared in their growth characteristics and viral polypeptides using LLCMK2 cells. The results suggested that influenza C virus undergoes genetic changes like influenza A or B virus.

Applications of Oligonucleotide Fingerprinting to the Identification of Viruses

This chapter focuses on applications of oligonucleotide fingerprinting to the identification of viruses. Fingerprinting is a technique by which oligonucleotides, produced by cleavage of RNA molecules with specific ribonucleases, are separated in two dimensions. It is a definitive method of identifying RNA viruses according to their genotypes. It is not subject to the problems of antigenic drift or antigenic convergence that complicate serological identification. Furthermore, it provides a semiquantitative means of following the evolution of viral genomes in nature. Because all regions of the genome are represented by the large diagnostic oligonucleotides, a survey of the total genomic changes can be monitored. Fingerprinting has two limitations as a diagnostic tool. First, although highly definitive, fingerprinting is not as rapid or inexpensive as serological techniques and cannot be as easily scaled up for routine identification of a large number of samples. Second, the evolutionary range of fingerprinting is short and relationships may not be evident for isolates of rapidly evolving viruses obtained over long intervals. However, these limitations are not large, compared to the full benefits offered to the virologist by the fingerprinting method.

Antigenic analysis of H1N1 viruses isolated in the Houston metropolitan area during four successive seasons

We evaluated the antigenic stability of viruses within the H1N1 subtype, using 307 isolates spanning four winter seasons. The isolates from each seasonal period appeared relatively homogenous in hemagglutination inhibition tests employing ferret antisera. However, a panel of seven monoclonal antibodies to A/USSR/90/77 detected extensive micro-heterogeneity. Antigenic variation occurred in the hemagglutinin antigen within a few weeks after the initial appearance of A/USSR/90/77-like strains in 1977-78 season as evidenced by low reactivity to one or several of the monoclonal antibodies. By the end of the season, few of the isolates reacted with the complete panel. Antigenic heterogeneity of the hemagglutinin was detected among H1N1 viruses throughout each epidemic interval. Some of the antigenic changes detected by monoclonal antibodies appeared on isolates in succeeding years, but others were restricted to a few strains isolated during a given year. The cumulative nature of some of these antigenic changes was indicated by the observation that 20 (19%) of 107 isolates examined in the fourth season failed to react with five of the monoclonal antibodies. Strains similar to most reference variants from around the world circulated in the Houston community.

Antigenicity and evolution amongst recent influenza viruses of H1N1 subtype

The sequence of the HA1 subunit region of the haemagglutinin gene of influenza A/USSR/90/77, and A/Brazil/11/78, A/Lackland/3/78, A/England/333/80 and A/India/6263/80 was determined by dideoxy-sequencing methods using total virion RNA and specific oligonucleotide primers for reverse transcriptase. These 1977-1980 strains share a minimum of 85% amino acid sequence homology with influenza A/PR/8/34. Most of the surface amino acid substitutions which occurred during the evolution of A/PR/8/34 to A/USSR/90/77 and subsequently in the 1978-1980 strains are located in the 4 antigenic sites previously defined by an analysis of laboratory-selected mutants of A/PR/8/34. We deduce an evolutionary pathway for the 1977-80 strains and suggest their different epidemic properties may be a consequence of only a few amino acid changes.

Immune response to human influenza virus hemagglutinin expressed in Escherichia coli

Cloned DNA fragments coding for parts of strain WSN (H1N1) influenza virus hemagglutinin (HA) were fused to a bacterial leader DNA derived from the Escherichia coli trp operon. Fusion proteins produced consisted of 190 amino acids of trpLE' protein at the amino terminus, and HA amino acids, either 1-308, 1-396, or 1-548 (complete HA), at the carboxyl terminus. These proteins were expressed at high levels (10-20% of total protein) in E. coli starved for tryptophan. A CNBr fragment (HA1-211) was derived from HA-308. Each of the proteins was purified and used for immunizing mice and rabbits. The antibody produced was shown to bind to (i) the HA fusion proteins, (ii) detergent-treated viral HA, (iii) HA, on intact virions, and (iv) the HA on the surface of cells infected with influenza virus. This shows that the HA fusion proteins expressed in bacteria can elicit antibodies that recognize at least some determinants of the native viral HA, and probably could lead to development of an anti-influenza vaccine.

Sequential mutations in the NS genes of influenza virus field strains

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

[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)

Rapid evolution of RNA genomes

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

Variation of influenza A, B, and C viruses

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

Sequence relationships among the hemagglutinin genes of 12 subtypes of influenza A virus

Nucleotide sequences of the 3' 20% of the hemagglutinin gene of 32 influenza A virus strains from the 12 known hemagglutinin subtypes have been determined. Although the sequences of hemagglutinin genes and proteins of different subtypes differ greatly, cysteine and some other amino acid residues are totally conserved, presumably reflecting evolution of the 12 different hemagglutinins from a single gene. When viruses of one subtype, isolated over a period of time, are compared, the hemagglutinin gene and protein sequences show a slow accumulation of nucleotide changes and some amino acid changes. Since sequence data from the genes coding for the matrix and nonstructural proteins also show an accumulation of changes with time, it seems that antigenic selection (of the surface antigens) does not contribute significantly to the rate of change on influenza gene sequences. Although the rate of nucleotide change during drift is more than sufficient to account for the amino acid sequence differences observed in the 12 subtypes, there is a clear distinction, by antigenic as well as sequence analyses, between viruses of one subtype (0-9% amino acid variation) and viruses of other subtypes (20-74% amino acid variation). No virus has yet been found that is intermediate between subtypes.

Nucleotide-sequence heterogeneity and sequence rearrangements in influenza virus cDNA

Double-stranded cDNA has been synthesized from influenza virus RNA and cloned into derivatives of the bacteriophage M13 for sequence analysis. The characterization of over 200 clones has permitted an analysis both of nucleotide sequence heterogeneity and of clones containing unusual rearrangements of sequence. Heterogeneity, due to genetic variability in the RNA population and to in vitro synthetic errors, was detected at the low level of one nucleotide difference per 3 700 nucleotides. By contrast, gross sequence rearrangements were identified in eight clones. Inversions of sequence within the same cDNA molecule were the predominant type of rearrangement, and three mechanisms for producing such inversions are discussed. In addition, we observed rarer clones containing sequence from one RNA molecule joined to that from another molecule.

Genome analysis of H1N1 influenza virus strains isolated in the U.S.S.R. during an epidemic in 1961-1962

Genome composition and polypeptides of H1N1 influenza virus strains isolated in the U.S.S.R. during an epidemic in 1961-1962 have been studied as well as H2N2 influenza virus strains that dominated at that time. The H1N1 isolates did not contain genes of the simultaneously circulating H2N2 viruses. H1N1 influenza viruses have proved to be genetically similar to A/FM/1/47 (H1N1) influenza virus strain differing in only two genes, rather than to H1N1 influenza viruses isolated in 1977 differing in six genes.

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.