Complete sequence of the genome of the human isolate
of Andes virus CHI-7913: comparative sequence and
protein structure analysis

NICOLE D. TISCHLER,^1,2 JORGE FERNÁNDEZ,⁶ ILSE MÜLLER,⁵ RODRIGO MARTÍNEZ,^1,2 HÉCTOR GALENO,⁶ ELIECER VILLAGRA,⁶ JUDITH MORA,⁶ EUGENIO RAMÍREZ,⁶ MARIO ROSEMBLATT,^1,2,3 and PABLO D.T. VALENZUELA^1,2,3,4

Fundación Ciencia para la Vida¹, Instituto Milenio MIFAB², Universidad Andrés Bello³, Pontificia Universidad Católica de Chile⁴, Bios Chile IGSA⁵. Av. Marathon 1943, Santiago, Chile, Instituto de Salud Pública de Chile⁶. Av. Marathon 1000, Santiago, Chile

Corresponding author: Pablo D.T. Valenzuela, Fundación Ciencia para la Vida, Av. Marathon 1943, Santiago, Chile.
Telephone: (56-2) 239-8969. E-mail: pvalenzu@bionova.cl

Received: December 19, 2002. Accepted: January 20, 2003

ABSTRACT

We report here the complete genomic sequence of the Chilean human isolate of Andes virus CHI-7913. The S, M, and L genome segment sequences of this isolate are 1,802, 3,641 and 6,466 bases in length, with an overall GC content of 38.7%. These genome segments code for a nucleocapsid protein of 428 amino acids, a glycoprotein precursor protein of 1,138 amino acids and a RNA-dependent RNA polymerase of 2,152 amino acids. In addition, the genome also has other ORFs coding for putative proteins of 34 to 103 amino acids. The encoded proteins have greater than 98% overall similarity with the proteins of Andes virus isolates AH-1 and Chile R123. Among other sequenced Hantavirus, CHI-7913 is more closely related to Sin Nombre virus, with an overall protein similarity of 92%. The characteristics of the encoded proteins of this isolate, such as hydrophobic domains, glycosylation sites, and conserved amino acid motifs shared with other Hantavirus and other members of the Bunyaviridae family, are identified and discussed.

Key terms: Hantavirus, genome sequence, RNA polymerase, human isolate

INTRODUCTION

Hantaviruses are enveloped rodent-borne negative sense RNA viruses that cause either hemorrhagic fever with renal syndrome or Hantavirus pulmonary syndrome (HPS), a severe and often fatal disease in humans (Schmaljohn and Hjelle, 1997).

Like other viruses in the Bunyaviridae family, Hantaviruses posses a tripartite RNA genome. The small or S RNA segment encodes the nucleocapsid protein N, the medium or M RNA segment encodes a glycoprotein precursor that is cleaved into the envelope glycoproteins G1 and G2, and the large or L RNA segment, which encodes a RNA-dependent RNA polymerase.

Andes virus (ANDV) belongs to the genus Hantavirus, which was first reported in 1995 to cause several fatal cases of HPS in Argentina (López et al., 1996) and later recognized to be genetically and serologically different from others in the world and responsible for most of the HPS cases in Argentina and Chile (López et al., 1997). In Chile, 276 cases of HPS have been reported through November 2002 with a 40% mortality rate.

Up to know, knowledge of the genetic organization of ANDV has been limited to the sequence of the isolate Chile R-123 (Meissner et al., 2002) and the partial genomic sequences of isolate AH-1 (López et al., 1997; Padula et al., 2002). We report here the complete genomic sequence of the Chilean ANDV CHI-7913, whose isolation from a 10-year-old HPS patient has been recently described (Galeno, et al., 2002). A preliminary account of this work has been reported (Tischler et al., 2002).

MATERIALS AND METHODS

Virus, cells and media

The Andes virus used in this study was isolated from a 10-year-old patient who died of HPS (ANDV CHI-7913) and has been described previously (Galeno et al., 2002). Vero E6 cells were originally provided by Dr. B. Hjelle, and were grown in Eagles minimal essential medium (MEM). The virus was grown via the conventional method (Lee, H.W., 1999) in Vero E6 cells grown to confluence in T25 flasks with MEM containing 10% fetal calf serum and antibiotics. The presence of viral antigens in infected cells was confirmed by immunofluorescence as described previously (Galeno et al., 2002). All experiments involving infectious virus were performed in a bio-safety level 3 (BLS-3) laboratory.

Viral RNA preparation

Confluent mono-layers of Vero E6 cells were grown in MEM with 10% FCS and infected with ANDV isolate CHI-7913 and incubated at 37ºC in the presence of 5% CO₂. Cells were usually harvested two weeks after infection, lysed with a solution of guanidinium isothiocyanate (Cathala et al., 1983) and the contents transferred to tubes. For RNA extraction, chloroform was added to the tubes, mixed and centrifuged at 12,000 xg for 15 min at 4º C. The RNA present in the aqueous phase was precipitated by the addition of 0.5 volumes of isopropanol. The pellet was washed twice with 70% ethanol, air dried, and dissolved in diethyl pyrocarbonate-treated water.

Genome segment amplification and sequencing

Approximately 1-4 µg of viral RNA was used in each reverse transcriptase reaction. The oligonucleotide primers for reverse transcriptation, as well as for the initial PCR reactions, were based on previously published well-conserved hantaviral sequences (Chizhikov et al., 1995). Subsequently ANDV CHI-7913-specific primers were designed as sequence information became available. Primers were selected as required to cover the entire genome segments by overlaps. The amplified PCR products were purified with a purification kit (Wizard PCR Preps, Promega, Madison, WI, USA), ligated to the vector pGEM-T (Promega, Madison, USA), and used to transform E. coli DH5a cells. Clones with inserts of appropriate size were selected for sequencing using an ABI 310 instrument. To increase the accuracy of the sequence obtained, more than two clones from different PCR products were sequenced.

Nucleotide and amino acid sequence comparisons and analysis

The sequences of the fragments were assembled and edited into contigs using the Sequencher 4.1 and Vector NTI 6.1 programs. Nucleotide sequence analysis and comparisons were carried out using the alignment program BLASTN (NCBI). Protein alignments were realized with BLASTP (NCBI) and ClustalW, based on the Blosum62 substitution matrix. The hydrophobic domains were predicted by TmPred (EMBNet), while the N-glycosylation and O-glycosylation predictions were realized with NetNGlyc 1.0 and NetOGlyc 2.0 (CBS) respectively.

RESULTS AND DISCUSSION

Viral nucleotide sequences were determined by direct sequence analysis of RT-PCR products amplified from RNA preparations of Vero E6 cells infected with ANDV CHI-7913 (Galeno et al., 2002). The nucleotide sequence has been deposited in the Gene Bank under the accession numbers AY228237, AY228238, and AY228239. The features of the nucleotide and amino acid sequence of the S, M and L viral RNA segments are described below.

S segment sequence properties and comparisons

The S RNA segment of the human Andes virus isolate CHI-7913 consists of 1,802 bases encoding a nucleocapsid protein of 428 amino acids. Additionally, the sequence analysis indicates the presence of 10 ORFs; the largest of them encoding a putative protein of 81 amino acids. The ORF in the + 1 frame encodes a putative protein of 63 amino acids, which could be a non-structural protein (NS) (Plyusnin, 2002), similar to the NS-S proteins of Bunyavirus, Phlebovirus and Tospovirus of the Bunyaviridae family (Elliott, 1990).

Comparisons of the nucleotide sequences of the S segment of the isolate ANDV CHI-7913 with ANDV Chile R123 and ANDV AH-1 reveals a sequence identity of 92% and 97% respectively, while only 83% similarity was found in comparison with the North American Sin Nombre virus (SNV), isolate NM H10. Alignment of the 504-base-long 3' non-coding region of CHI-7913 with the same region of ANDV AH-1 and ANDV Chile R123 reveals 97% and 89% identity respectively, while no significant similarity was found with the 3' non-coding region of SNV isolates. For Hantavirus it is known that their 3' non-coding region varies widely, both in nucleotide sequence and length (from 229 nucleotides in Prospect Hill virus to 728 nucleotides in SNV), except for the terminal nucleotides forming the panhandle structures. Assuming that the 3' non-coding region participates in steps of viral replication and packaging, there could be two possible explanations for the difference in their primary structures: (1) molecular mechanisms of replication differ from one host to another; or (2) the secondary rather than the primary structure of the 3' non-coding region is crucial for its proper activity (Plyusnin et al., 1996).

The 428-amino-acid nucleoprotein encoded by the S segment belongs to the most conserved proteins of Hantavirus and has been proven to be highly immunogenic in humans (Jenison et al., 1994, Bharadwaj et al., 2000), thus making it the protein of choice for immunodiagnostic tests to detect virus infections. Despite its high similarity to ANDV (99% with isolates AH-1 and Chile R123) and SNV (93% with isolate NM H10) or other Hantavirus (e.g. 85% with Puumala isolate Hallnas B1 and 77% with Hantaan isolate 76_118), no conserved amino acid sequence motifs could be identified in comparisons done with nucleoproteins from Bunyavirus, Phlebovirus, Nairovirus and Tospovirus. The absence of a common motif supports the theory, that determined secondary, tertiary or even quaternary structures but not sequence specific interactions are responsible for RNA binding.

M segment sequence properties and comparisons

The largest ORF of the 3,641-base-long M segment RNA of isolate CHI-7913 encodes a glycoprotein precursor from nucleotide 34 to 3,450. Another 12 ORFs are present in the M segment, encoding putative proteins between 34 and 103 amino acids. The entire M segment shows 94% identity with the ANDV isolate Chile R123, 96% with AH-1, but only 77% with the SNV isolate NM H10. The 5' non-coding region proved to be with 100% identity highly conserved with the same region of ANDV isolates Chile R123 and AH-1, while the 3' non-coding region showed 91% and 92% identity respectively. In comparison with the 5' and 3' non-coding regions of SNV isolate NM H10, no significant similarities were found.

The 1,138-amino-acid-glycoprotein precursor encoded by the M segment RNA is the most variant protein of ANDV CHI-7913, presenting only an 87% similarity to the glycoprotein precursor of SNV isolate NM H10. When the amino acid sequence of the human isolate ANDV CHI-7913 was compared with the ANDV isolates Chile R123 and AH-1, nine non-conserved amino acid differences were found (see Table I).

Remarkable for Hantavirus glycoproteins is the high content of highly conserved cysteine residues (5.2%) and the virtually identical hydrophobic profiles (Antic, et al., 1992), indicating a highly conserved tertiary protein structure of the hantaviral envelope proteins.

When Hantavirus glycoproteins are aligned with glycoproteins of Phlebovirus, Bunyavirus, Nairovirus and Tospovirus, only two of these cysteine residues (positions 768 and 773 in the CHI-7913 sequence) are maintained invariant. The cysteine residue at amino acid position 12 is only found in Hantavirus causing HPS, with the exception of Laguna Negra virus. The cysteine residues at positions 637 and 642 are associated only with South American Hantavirus (AND, Laguna Negra, Hu39694, Lechiguanas and Oran virus), while the cysteine at position 511 was found exclusively in ANDV (isolates CHI-7913, Chile R123 and AH-1). We have also found that these conserved cysteine residues are located in a highly conserved amino acid motif among members of the Bunyaviridae family (Table II). This motif (from amino acids 766 to 781) is located in the N-terminal part of the mature G2 protein and contains in addition to the conserved cysteines, partially conserved tryptophan and glycine residues.

It has been reported that vitronectin, which binds to ß3-integrins in an arginine-glycine-aspartic acid dependent manner, inhibits the entry of SNV and New York virus (NYV) into Vero E6 cells (Gavrilovskaya et al., 1998). We have found that ANDV, SNV and NYV share six conserved amino acid sequences with human and mouse vitronectin (Table III). Of these motifs, the motif 1 (amino acids 422 to 431) contains a highly conserved arginine and aspartic acid, while the motif 6 (amino acids 872 to 888) contains two highly conserved glycines.

TABLE III

Conserved amino acid motifs shared by glycoprotein precursors (GP) of HPS
causing virus (ANDV, SNV, NYV) and the ß3-integrin ligand vitronectin in
comparison with nonpathogenic Hantavirus (PHV). Bold letters indicate identical
amino acids, underlined letters conserved amino acids.

The predicted glycoprotein precursor of the ANDV CHI-7913 contains four hydrophobic domains. The first domain extends from the N-terminal amino acids 1 to 19 and is most likely a hydrophobic signal peptide, which exists typically in secretory and type I trans-membrane proteins for their translocation into the lumen of the ER (Rapoport et al., 1996). A signal peptidase complex usually removes the signal sequence (Perlman and Halvorson, 1983). This seems to be also valid for Hantavirus glycoproteins, as the exact N-terminus of the mature G1 protein of Hantaan virus as been determined to start at the position threonine 18 (Schmaljohn et al., 1987). Studies of B cell epitopes confirm this results also for ANDV, as sera of patients infected with ANDV revealed a strong reactivity with a peptide carrying amino acids 14-26, but not with a peptide carrying amino acids 1-13 (N. Tischler, unpublished data). The second and fourth hydrophobic domains (aa 490 to aa 509 and aa 1,109 to aa 1,129) are potential trans-membrane regions for each mature glycoprotein. The third hydrophobic region extends from amino acids 630 to 648 and is probably a second signal peptide for the cleavage of the glycoprotein precursor into the mature G1 and G2 proteins. The cleavage probably occurs at the highly conserved pentapeptide WAASA (Loeber et al., 2001), also present in the ANDV CHI-7913 sequence.

Oligosaccharide chains are essential components for the correct folding of the glycoproteins and participate in many molecular recognition reactions of receptors and ligands. They can also determine whether viral envelope proteins are recognized by components of the host immune defense system. Hence, glycosylation differences could be related to pathogenic differences of virus strains.

Previous studies showed that only ANDV produce HPS synthomes in Syrian Hamsters while SNV does not (Hooper et al., 2001). To investigate if those differences in pathogenesis could be realted with a different glycosylation pattern, the glycosylation prediction of amino acid sequences of 8 North American Hantavirus and 7 South American Hantavirus were compared. Five putative asparagine glycosylation sites with the characteristic sequence NXS/T (where X is any amino acid different to proline) are predicted for the ANDV CHI-7913 glycoprotein precursor. Of these, only four are conserved in HPS-associated Hantavirus (aa 138-141, aa 350-353, aa 402-405, aa 930-933). The fifth putative N-glycosylation site, which comprises the aa 524 527, was found in all of the South American Hantavirus studied, except in Laguna Negra virus. Within the North American Hantavirus this site is present only in the Limestone Canyon and Prospect Hill virus (Table IV), of which no human infection has been determined (Schmaljohn et al., 1997). Based on mucin-type O-glycosylation prediction, three main O-glycosylation clusters could be defined (Table IV). Among HPS associated Hantavirus, threonine 93 was found to be the only conserved putative O-glycosylation site, while threonine 92, threonine 583 and serine 307 are conserved in all of the South American Hantavirus. Interestingly, the glycosylation of serine 97 was predicted only for all South American Hantavirus, excluding Oran and Lechiguanas virus, which instead have an alanine residue. Additionally, the putative glycosylation cluster of serine 307, threonine 308 and serine 309 present in site 2 is found in all South American Hantavirus, with the exception of Laguna Negra virus, which presents an amino acid change of threonine 308 into serine. In contrast, the glycosylation of threonine 89 present in site 1 is predicted only for all North American Hantavirus, while threonine 90 is found to be glycosylated in all North American Hantavirus except Limestone Canyon and Bayou virus.

TABLE V

Different codon usage of AND and SN virus L segments. Alignments between L segments and encoded proteins of ANDV isolates CHI-7913, Chile R123 and SN virus NM H10. The sign (-) indicates no significant similarity (E value > 10).

L segment sequence properties and comparisons

The 6,466-base-long L segment RNA of CHI-7913 contains a 6,453 base long ORF (nucleotide 9-6,464), which encodes a protein of 2,152 amino acids possessing at least the activity of a RNA dependent RNA polymerase. Additionally, another 21 ORFs, which encode putative proteins of 34 to 100 amino acids, are present. Nucleotide sequence comparison analysis with the L segment of another complete genome of ANDV (Chile R123) revealed 93% of identity, while the identity with the L segment of SNV virus isolate NM H10 amounted to 72%. Notably, in six regions of the SNV L segment no significant similarity was found (see Table V). However, when translating those regions into the corresponding amino acid sequence, similarities between 76% and 96% could be determined. This result emphasizes the difference of codon usage in these regions by the ANDV and SNV. However, the conservation of the predicted primary structure of the protein, despite extreme mutations in the nucleotide sequence, could be a result of evolutionally adaptation of the virus to the host codon usage.

The protein of 2,152 amino acids encoded by the L segment of CHI-7913 shows an overall identity of 98% with ANDV R123, while the similarity with SNV NM H10 amounts to 94%. When the derived amino acid sequence of the human isolate CHI-7913 was compared with isolates Chile R123 (complete sequence) and AH-1 (sequence from aa 933 to 1134), twelve non-conserved amino acid changes were found (see Table I).

The deduced amino acid sequence of ANDV CHI-7913 RNA polymerase contains the six motifs previously identified as common to all RNA-dependent RNA polymerases (Poch et al., 1989; Müller et al., 1994), which have been suggested to be related to polymerase function (Müller et al., 1994). All of these motifs are located in the most highly conserved middle region of the protein (from amino acids 860 to 1180). A sequence alignment with other members of the Bunyaviridae family is shown in Table VI. Motif preA characterized by the presence of three strictly conserved basic residues is present between lysine 885 and glutamic acid 910 of ANDV CHI-7913. The first two conserved basic residues of this motif, lysine 885 and arginine 893, are probably part of the "finger sub-domain" of a proposed "right hand" structural model of polymerases (Ollis et al., 1985; Kohlstaedt et al., 1992) and discussed in more detail by Hansen et al., (1997) and O'Really and Kao, (1998). These two residues may participate in positioning and binding. It has been suggested that the third positively charged residue, arginine 903 in ANDV CHI-7913 is located in the vicinity of the active site, close to the binding site of the template strand (Müller et al., 1994).

Motif A, located between residues lysine 964 and aspargine 982 in ANDV CHI-7913 and motif C, located between phenylalanine 1103 and aspargine 1116 in ANDV CHI-7913 (Table VI), are characterized by the presence of strictly conserved aspartic acid residues which have been suggested to be part of the active site (Delarue et al., 1990) and to participate in the binding of metal ions involved in catalysis by the Klenow fragment (Beeze and Steitz, 1991). Motif B, located between residues alanine 1053 and alanine 1074 of ANDV CHI-7913 (Table VI), is characterized by the presence of a strictly conserved glycine residue and may also participate in template binding (Müller et al., 1994). Motifs D and E, located between glycine 1154 and phenylalanine 1176 in ANDV CHI-7913 (Table VI), are characterized by the presence of strictly conserved glycine, glutamic acid and serine residues. Motifs preA, A, B, C, D and E have been associated to the "right hand" structural model of RNA polymerases of which motifs A, B, C and D are present in all polymerases, while motif preA is only found in RNA dependent RNA polymerases and motif E only in polymerases of segmented, negative-stranded RNA virus (Hansen et al., 1997; O'Really and Kao, 1998).

TABLE VI

Conserved amino acid motifs among polymerases of different genus
members of the Bunyaviridae family. Bold letters indicate identical,
underlined letters conserved amino acids.

The complete sequence of the genome and the comparative analysis of the predicted translated proteins of the human isolate ANDV CHI-7913 reported here represents additional information to those reported in the past (López et al., 1997, Padula et al. 2002, Meissner et al, 2002). This will allow further sequence comparisons useful in future studies of ANDV pathogenicity and the development of immunodiagnostics, vaccines and potential immunotherapeutic agents.

ACKNOWLEDGMENTS

We are grateful to Dr. Luis Burzio for helpful discussions during the course of this research and for critical reading of this manuscript. We also want to express our special thanks to Danilo González of the University of Santiago de Chile for his valuable support in bioinformatics.

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