Recombination between temperature-sensitive mutants of the arenavirus Pichinde

The S Genome Segment Is Sufficient to Maintain Pathogenicity in Intra-Clade Lassa Virus Reassortants in a Guinea Pig Model

Genome reassortment in Lassa virus (LASV) has been reported in nature, but phenotypic consequences of this phenomenon are not well described. Here we characterize, both in vitro and in vivo, reassortment between 2 LASV strains: the prototypic 1976 Josiah strain and a more recently isolated 2015 Liberian strain. In vitro analysis showed that although cis- and trans-acting elements of viral RNA synthesis were compatible between strains, reassortants demonstrated different levels of viral replication. These differences were also apparent in vivo, as reassortants varied in pathogenicity in the guinea pig model of LASV infection. The reassortant variant containing the Josiah S segment retained the virulence of the parental Josiah strain, but the reassortant variant containing the S segment of the Liberian isolate was highly attenuated compared to both parental strains. Contrary to observations in reassortants between LASV and other arenavirus species, which suggest that L segment-encoded factors are responsible for virulence, these studies highlight a role for S segment-encoded virulence factors in disease, and also suggest that inefficient interactions between proteins of heterologous strains may limit the prevalence of reassortant LASV variants in nature.

Widespread recombination, reassortment, and transmission of unbalanced compound viral genotypes in natural arenavirus infections

Arenaviruses are one of the largest families of human hemorrhagic fever viruses and are known to infect both mammals and snakes. Arenaviruses package a large (L) and small (S) genome segment in their virions. For segmented RNA viruses like these, novel genotypes can be generated through mutation, recombination, and reassortment. Although it is believed that an ancient recombination event led to the emergence of a new lineage of mammalian arenaviruses, neither recombination nor reassortment has been definitively documented in natural arenavirus infections. Here, we used metagenomic sequencing to survey the viral diversity present in captive arenavirus-infected snakes. From 48 infected animals, we determined the complete or near complete sequence of 210 genome segments that grouped into 23 L and 11 S genotypes. The majority of snakes were multiply infected, with up to 4 distinct S and 11 distinct L segment genotypes in individual animals. This S/L imbalance was typical: in all cases intrahost L segment genotypes outnumbered S genotypes, and a particular S segment genotype dominated in individual animals and at a population level. We corroborated sequencing results by qRT-PCR and virus isolation, and isolates replicated as ensembles in culture. Numerous instances of recombination and reassortment were detected, including recombinant segments with unusual organizations featuring 2 intergenic regions and superfluous content, which were capable of stable replication and transmission despite their atypical structures. Overall, this represents intrahost diversity of an extent and form that goes well beyond what has been observed for arenaviruses or for viruses in general. This diversity can be plausibly attributed to the captive intermingling of sub-clinically infected wild-caught snakes. Thus, beyond providing a unique opportunity to study arenavirus evolution and adaptation, these findings allow the investigation of unintended anthropogenic impacts on viral ecology, diversity, and disease potential.

Reassortant analysis of guinea pig virulence of pichinde virus variants

The new world arenavirus Pichinde (PIC) is the basis of an accepted small animal model for human Lassa fever. PIC (Munchique strain) variant P2 is attenuated in guinea pigs, whereas variant P18 is extremely virulent. Previous sequence analysis of the S segments of these two viruses indicated a small number of possible virulence markers in the glycoprotein precursor (GPC) and nucleoprotein (NP) genes. In order to determine the role of these S segment genes in guinea pig virulence in this system, we have generated reassortant viruses. When tested in outbred guinea pigs, the reassortant containing the S segment from the virulent parent P18 (S18L2) caused significantly higher morbidity than the reciprocal reassortant. This increased morbidity was associated with higher viral titers in serum and spleen. However, the S18L2 reassortant was not as fully virulent in this system as the P18 parent, indicating a role for L segment genes in virulence.

Characterization of temperature-sensitive mutants of Pichinde virus

The synthesis of viral proteins and S RNAs in cells infected with 12 temperature-sensitive (ts) mutants of Pichinde virus was characterized. The mutants could be divided into five groups on the basis of the patterns of radiolabeled proteins immunoprecipitated from infected-cell lysates. Markedly reduced nucleoprotein levels and undetectable amounts of glycoprotein precursor and L protein were synthesized at the nonpermissive temperature in cells infected with five of the mutants. Reduced but detectable amounts of the viral proteins were synthesized at the nonpermissive temperature in cells infected with a single mutant. Two mutants were associated with the intracellular accumulation of glycoprotein precursor, which was apparently not transported across the cell membrane in cells incubated at the nonpermissive temperature. The synthesis of viral proteins in cells infected with two mutants was indistinguishable from those produced by wild-type virus. Two additional mutants were associated with markedly reduced amounts of immunoprecipitable proteins in infected cells incubated at both the permissive and nonpermissive temperatures. Analysis of viral RNA with radiolabeled single-stranded cDNA probes representing complementary and genomic-sense sequences corresponding to the 3' region of S RNA revealed two basic patterns of viral RNA synthesis. At the nonpermissive temperature, the synthesis of complementary- and genomic-sense sequences and mRNA of the S RNA segment was markedly reduced in cells infected with representative members of these mutant groups, suggesting the presence of mutations altering transcriptase activity. Viral-complementary- and genomic-sense sequence and RNA synthesis, as well as nucleoprotein mRNA in cells, was detected in reduced amounts for mutants associated with reduced levels of proteins at both temperatures. Interestingly, RNA species larger than the S RNA segment were detected in cells infected with some of the mutants, especially those with putative transcriptase lesions. These molecules suggest a possible oligomeric intermediate in the synthesis of S RNA of Pichinde virus.

Ambisense RNA genomes of arenaviruses and phleboviruses

This chapter reviews the evidence that shows that arenaviruses and members of one genus of the Bunyaviridae (phleboviruses) have some proteins coded in subgenomic, viral-sense mRNA species and other proteins coded in subgenomic, viral-complementary mRNA sequences. This unique feature is discussed in relation to the implications it has on the intracellular infection process and how such a coding arrangement may have evolved. The chapter presents a list of the known members of the arenaviridae, their origins, and the vertebrate hosts from which isolates have been reported. It discusses the structural components, the infection cycle, and genetic attributes of arenaviruses. In order to determine how arenaviruses code for gene products, the S RNA species of Pichinde virus and that of a viscerotropic strain of LCM virus (LCM-WE) have been cloned into DNA and sequenced. The arenavirus S RNA is described as having an ambisense strategy, to denote the fact that both viral and viral-complementary sequences are used to make gene products. The chapter discusses the infection cycle, the structural and genetic properties of bunyaviridae member.

Conserved sequences and coding of two strains of lymphocytic choriomeningitis virus (WE and ARM) and Pichinde arenavirus

Analyses of the 3' end sequences of the small, S, and large, L, RNA species of lymphocytic choriomeningitis (LCM) virus isolates ARM and WE, and DNA clones of LCM-WE, have shown that there are extensive RNA sequence homologies between the 3' ends of the two RNA species of both LCM strains. Limited sequence data of DNA clones representing the LCM-WE L RNA species indicate that a gene product (presumably the minor 200 kdalton virion protein) is coded in a viral-complementary mRNA species. Sequence analyses of LCM-WE S DNA clones indicate that approximately 50% of the 2040 nucleotides representing the 3' half of the viral RNA species (and its encoded 558 amino acid gene product) are identical in type and position to those of Pichinde arenavirus (Auperin, D., et al. (1984a), Virology 134, 208-219). For Pichinde virus, it has been shown that the 3' proximal gene product (the nucleoprotein, N) is translated from a subgenomic, viral-complementary mRNA (Auperin et al., 1984a). Data have recently been obtained (Auperin, D., et al. (1984b) J. Virol., in press) that indicate that the Pichinde glycoprotein precursor, GPC, is coded in a viral-sense subgenomic mRNA species corresponding to the 5' half of the S RNA. The nucleotide sequence that immediately follows the N coding region of both LCM-WE and Pichinde viruses can be arranged in a hairpin configuration. In view of this, and if, like Pichinde virus, LCM has an ambisense S RNA coding strategy, then it is probable that the intergenic hairpins function as transcription terminators for the N and GPC mRNA species of both viruses.

Sequencing studies of pichinde arenavirus S RNA indicate a novel coding strategy, an ambisense viral S RNA

Analyses of the complete sequence of the 1.1 X 10(6)-dalton, small (S) RNA of the arenavirus Pichinde and virus-induced cellular RNA species have revealed that the viral nucleoprotein, N, is coded in a subgenomic, non-polyadenylated, virus-complementary mRNA corresponding to the 3' half of the viral RNA (Auperin et al., Virology 134:208-219, 1984). By contrast, a second S-coded product, presumably the viral glycoprotein precursor (GPC), is coded in a subgenomic, virus-sense mRNA corresponding to the 5' half of the RNA. Between the two genes is a unique RNA sequence that can be arranged in a hairpin configuration and may function as a transcription terminator for both genes. The term ambisense RNA is coined to describe this novel coding strategy of a viral RNA. The unique feature of the strategy is that the presumptive GPC mRNA and its translation product cannot be made until viral RNA replication has commenced. In addition, it allows the two subgenomic mRNA species to be regulated independently from each other or from other viral mRNA species. The implications of this strategy on possible mechanisms for the induction and maintenance of viral persistence, an important attribute of arenavirus infections, are discussed.

The sequences of the N protein gene and intergenic region of the S RNA of pichinde arenavirus

Two overlapping DNA clones representing more than half of the Pichinde arenavirus S RNA segment were cloned into pBR322 and their nucleotide sequences were determined. The analyses predict that the viral nucleocapsid protein (N) is encoded in a reading frame in the viral complementary RNA sequence starting at viral S RNA nucleotide residue 84 from the 3' end and terminating with an opal codon at residues 1767-1769. The position of the termination codon has been confirmed by primer directed dideoxynucleotide sequencing. The N protein has a calculated size of 62,911 Da and a net positive charge of +9. Viral complementary 15 S mRNA that directs the synthesis of N protein and hybridizes to the predicted N gene DNA has been identified in infected cell extracts. A second nonoverlapping reading frame in the viral complementary sequence originates at nucleotide position 1827 and remains open for at least 71 amino acids (i.e., the extent of the second clone). A long stretch of hydrophobic amino acids is near the amino terminus of this predicted gene product. Between the two reading frames is a 60-nucleotide-long noncoding intergenic region. This nucleotide sequence can be arranged in hairpin configuration involving 14 G-C and 4 A-U base pairs. The possible function of this intergenic region in the regulation of transcription and/or translation is discussed.

The formation of arenaviruses that are genetically diploid

Analyses of RNA extracted from preparations of arenaviruses indicate that the relative molar proportions of the genomic L and S RNA species are frequently far from equal. In order to investigate the genetic significance of this observation temperature-sensitive (ts) mutants of two lymphocytic choriomeningitis (LCM) virus strains (ARM and WE) have been recovered and categorized into recombination groups (Groups I and II). Fingerprint analyses of wild-type progeny viruses obtained from dual infections with ARM Group II and WE Group I ts viruses indicate that they have L/S RNA genotypes of WE/ARM. It is concluded that the ARM Group II ts viruses have mutations in their L RNA species and that the WE Group I ts viruses have mutations in their S RNA species. Correspondingly it is deduced that the ARM Group I ts viruses have S RNA mutations and the WE Group II ts viruses mutations in their L RNA species. Cells coinfected with certain WE Group I mutants, or an ARM Group I and certain WE Group I ts mutants, have also yielded wild-type viruses. Fingerprint analyses have shown that the wild-type viruses obtained from the latter crosses are diploid with respect to their S RNA species. On subsequent passage these wild-type viruses shed high proportions of ts mutants. We interpret the data to indicate that the original Group I ts mutants that yielded the diploid viruses have mutations in different S RNA gene products so that the progeny produce plaques at the nonpermissive temperature by gene product complementation. No wild-type recombinant viruses have been obtained from crosses involving Pichinde and LCM ts mutants.

Pichinde virus L and S RNAs contain unique sequences

Using oligodeoxyribonucleotides produced by limited DNase I digestion of calf thymus DNA as a primer, we synthesized complementary DNA (cDNA) from the L and the S RNAs of Pichinde virus. The reaction conditions for in vitro cDNA synthesis were optimized to allow transcription of about 90% of either L or S RNA. No significant hybridization was observed when the L cDNA was hybridized to the S RNA, or when the S cDNA was hybridized to the L RNA. The results indicate that the L and S RNAs of Pichinde virus contain unique nucleotide sequences.

Virion RNA species of the arenaviruses Pichinde, Tacaribe, and Tamiami

The principal RNA species isolated from labeled preparations of the arenavirus Pichinde usually include a large viral RNA species L (apparent molecular weight = 3.2 X 10(6)), and a smaller viral RNA species S (apparent molecular weight = 1.6 X 10(6)). In addition, either little or considerable quantities of 28S rRNA as well as 18S rRNA can also be obtained in virus extracts, depending on the virus stock and growth conditions used to generate virus preparations. Similar RNA species have been identified in RNA extracted from Tacaribe and Tamiami arenavirus preparations. Oligonucleotide fingerprint analyses have confirmed the host ribosomal origin of the 28S and 18S species. Such analyses have also indicated that the Pichinde viral L and S RNA species each contain unique nucleotide sequences. Viral RNA preparations isolated by conventional phenol-sodium dodecyl sulfate extraction often have much of their L and S RNA species in the form of aggregates as visualized by either electron microscopy or oligonucleotide fingerprinting of material recovered from the top of gels (run by using undenatured RNA preparations). Circular and linear RNA forms have also been seen in electron micrographs of undenatured RNA preparations, although denatured viral RNA preparations have yielded mostly linear RNA species with few RNA aggregates or circular forms.