Intrapatient Variation of the Respiratory Syncytial Virus Attachment Protein Gene

Intrapatient variability of the attachment (G) protein gene of respiratory syncytial virus (RSV) was examined using both population and single-genome sequencing. Samples from three patients infected with a group B virus variant which has a 60-nucleotide duplication in the G protein gene were examined. These samples were chosen because occasional mixed sequence bases were observed. In a minority of RSV genomes from these patients considerable variability was found, including point mutations, insertions, and deletions. Of particular note, the deletion of the exact portion of the gene which had been duplicated in some isolates was observed in viral RNAs from two patients.Human respiratory syncytial virus (RSV) is a major cause of lower respiratory tract infection in infants and vulnerable adults (3, 9) and is unusual in that it can repeatedly reinfect individuals (5, 6). RSV isolates are classified into two groups, A and B, and the attachment (G) protein, a target for neutralizing antibodies, is the most variable of the viral proteins, showing considerable genetic and antigenic variability both within and between the groups (7, 8). The G protein is able to accommodate drastic changes, which have been observed both in culture during the selection of monoclonal antibody escape mutants (4, 12, 13) and in vivo with the emergence of new variants, including a group B strain with a duplication of 60 nucleotides (17). This strain with a 60-nucleotide duplication was first reported from Buenos Aires in 1999 (17) and then was subsequently detected in samples from 1998 in Madrid (16). The strain then became the dominant group B strain worldwide, indicating a selective advantage for this variant (16, 18). Thus, major genetic changes can be introduced into the G gene sequence while the virus replicates in its natural host, which can then be selected under favorable epidemiological conditions.Previous investigations of the genetic diversity of RSV exploited direct sequencing of PCR-amplified products (2), which represent the population average of the in vivo variants. Such sequences are derived from multiple copies of cDNA and represent the dominant sequence, and they thus do not allow detection of minority populations below about 20% prevalence (11). Information on intrapatient viral diversity during infections may therefore be missed, knowledge of which could be important in the overall understanding of the genetic diversity of this virus. We report here the analysis of individual RSV RNA molecules derived by single-genome amplification (SGA) and sequencing from clinical samples using a methodology developed for the analysis of HIV genomes (11, 14).RSV-positive samples were collected from infants admitted to Kilifi District Hospital, Kenya (10). Viral RNA extraction and cDNA synthesis were carried out as previously described (15). For population sequencing, a nested PCR was carried out on the cDNA using primers that amplified the ectodomain-coding part of the G protein gene, with the PCR product being directly sequenced. In the 2007-2008 RSV epidemic in Kilifi, group B viruses were predominant. By population sequencing of ∼100 group B samples, all were found to have the 60-nucleotide duplication observed in the Buenos Aires variant (data not shown). However, in some specimens there were some mixed bases at some positions, so the variability at the level of the single cDNA molecule was further investigated.Three samples that gave occasional mixed signals in the sequence chromatograms were further analyzed by SGA and sequencing. For SGA the cDNAs were serially diluted 3-fold up to 1:6,361. Ten nested PCRs were carried out on each dilution using Platinum high-fidelity PCR Supermix (Invitrogen) (containing Taq polymerase together with the proofreading enzyme Pyrococcus species GB-D polymerase). Based on the Poisson distribution, it has been shown that for a sample dilution yielding approximately 30% positive PCRs there is an 80% likelihood that each PCR is derived from a single cDNA molecule (11). For each of the identified endpoint dilutions, the cDNA was amplified in 80 separate nested PCRs using the high-fidelity enzyme and the positive reaction products sequenced. The nomenclature for the sequences reported in this paper is place of isolation (Kenya [Ken])/year of isolation/strain number. For SGA sequences an additional Roman number is given.The predicted length derived by population sequencing of the G proteins of the three samples examined by SGA was 310 amino acids, showing a 6-nucleotide deletion and a changed stop codon relative to the Buenos Aires strain (Fig. ​(Fig.1).1). The dominant sequences represented 60 to 88% of the sequences derived by SGA. The differences were due to point mutations, duplications, and deletions, as summarized in Table ​Table1;1; the consequences of these changes for the predicted length of the G protein are shown in Table ​Table22.Open in a separate windowFIG. 1.Nucleotide sequence alignment of part of the G protein gene (from nucleotide 400) of the sample 2 population sequence (Ken/08/80900) and a minority sequence (Ken/08/80900/ii), with the sequences of prototype group B strain CH18537 (accession number {"type":"entrez-nucleotide","attrs":{"text":"M17213","term_id":"333942","term_text":"M17213"}}M17213) and Buenos Aires strain BA/3833/99B (accession number {"type":"entrez-nucleotide","attrs":{"text":"AY333362","term_id":"33355616","term_text":"AY333362"}}AY333362). This shows the duplication of 60 nucleotides in the Kenyan and Buenos Aires viruses relative to CH18537 and the loss of the same 60 nucleotides in the Kenyan minority sequence. Termination codons are underlined.

TABLE 1.

Diversity in the SGA-derived sequences

Effect of Complement and Viral Filtration on the Neutralization of Respiratory Syncytial Virus

The addition of 10 hemolytic units of guinea pig complement has been shown to enhance the neutralizing capacity of respiratory syncytial (RS) immune sera produced in guinea pigs and ferrets. This same immune sera, when tested without complement, had little or no neutralizing capacity. The addition of complement to RS immune horse serum did not significantly increase its neutralizing capacity. Immune horse serum effectively neutralized RS virus without complement. Other studies indicated that a 50% tissue culture infective dose of between 30 and 100 should be used in RS serum neutralization tests and that incubation should be for 90 to 105 min at room temperature. The neutralizing capacity of guinea pig immune serum was not increased by the use of filtered virus. The rate of virus neutralization, however, was increased with the addition of 10 hemolytic units of complement. The neutralizing capacity of RS immune horse serum was much greater for filtered than for unfiltered RS virus. The addition of complement increased the rate of virus neutralization but did not increase the neutralizing capacity of the horse immune serum.     

Requirement of Cysteines and Length of the Human Respiratory Syncytial Virus M2-1 Protein for Protein Function and Virus Viability

The M2-1 protein of human respiratory syncytial virus (hRSV) promotes processive RNA synthesis and readthrough at RSV gene junctions. It contains four highly conserved cysteines, three of which are located in the Cys(3)-His(1) motif at the N terminus of M2-1. Each of the four cysteines, at positions 7, 15, 21, and 96, in the M2-1 protein of hRSV A2 strain was individually replaced by glycines. When tested in an RSV minigenome replicon system using beta-galactosidase as a reporter gene, C7G, C15G, and C21G located in the Cys(3)-His(1) motif showed a significant reduction in processive RNA synthesis compared to wild-type (wt) M2-1. C96G, which lies outside the Cys(3)-His(1) motif, was fully functional in supporting processive RNA synthesis in vitro. Each of these cysteine substitutions was introduced into an infectious antigenomic cDNA clone derived from hRSV A2 strain. Except for C96G, which resulted in a viable virus, no viruses were recovered with mutations in the Cys(3)-His(1) motif. This indicates that the Cys(3)-His(1) motif is critical for M2-1 function and for RSV replication. The functional requirement of the C terminus of the M2-1 protein was examined by engineering premature stop codons that caused truncations of 17, 46, or 67 amino acids from the C terminus. A deletion of 46 or 67 amino acids abolished the synthesis of full-length beta-galactosidase mRNA and did not result in the recovery of viable viruses. However, a deletion of 17 amino acids from the C terminus of M2-1 reduced processive RNA synthesis in vitro and was well tolerated by RSV. Relocation of the M2-1 termination codon upstream of the M2-2 initiation codons did not significantly affect the expression of the M2-2 protein. Both rA2-Tr17 and rA2-C96G did not replicate as efficiently as wt rA2 in HEp-2 cells and was restricted in replication in the respiratory tracts of cotton rats.     

Respiratory Syncytial Virus Infection of the Newborn

In an outbreak of respiratory syncytial (R.S.) virus infection in a maternity hospital the respiratory illness was of a mild nature and the virus was not found in infants without respiratory symptoms. This confirms the suggestion that R.S. virus can infect infants at a very early age. Rapid diagnosis was achieved by applying the direct fluorescent antibody technique to cells in nasal secretions. This proved to be more sensitive than culture techniques where there was delay between the onset of respiratory symptoms and submission of specimens to the laboratory.     

Structure of the Human Respiratory Syncytial Virus M2-1 Protein in Complex with a Short Positive-Sense Gene-End RNA

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猪2型圆环病毒ORF1与ORF2基因和伪狂犬病毒基因的重组与表达的研究

根据GenBank发布的猪2型圆环病毒(PCV2 )序列(AY0 35 82 0 ) ,设计两对特异性引物,采用PCR方法,分别扩增了猪2型圆环病毒ORF1和ORF2基因。将ORF1和ORF2基因的PCR产物回收并酶切后,依次插入到伪狂犬病毒gE gI双缺失通用转移载体pIECMV中,构建了猪2型圆环病毒_伪狂犬病毒重组中间转移质粒pIEORF1-ORF2。采用脂质体介导法,将重组中间转移质粒pIEORF1_ORF2与伪狂犬病毒TK^- gE^- LacZ⁺ 基因组共转染IBRS_2细胞,待发生细胞病变后收集病毒液进行空斑纯化,利用检测PCV2ORF1基因和ORF2基因的PCR方法筛选重组病毒TK^- gE^- gI^- ORF1-ORF2⁺ ,用Southernblotting鉴定重组病毒,并用Westernblotting检测ORF1_ORF2融合蛋白的表达情况,在此基础上也测定了重组病毒在不同细胞上的增殖滴度。结果表明,外源基因ORF1和ORF2已成功插入到TK^- gE^- LacZ⁺ 亲本株的基因组中,并获得了表达,表达的蛋白可与PCV2阳性血清发生反应。同时发现ORF1和ORF2基因的插入不影响重组病毒的增殖特性,其毒力与亲本株相当。     

截短的猪繁殖与呼吸综合征ORF5基因及重组蛋白的原核表达

通过PCR方法从重组质粒pGEM-ORF5扩增得到缺失N端疏水序列的基因片段dORF5(deleting ORF5)。将dORF5克隆至原核高效表达载体pGEX-4T-1,在E.coliRosetta细胞中成功表达了重组蛋白GST-dORF5。用Western blotting鉴定表达蛋白,证明dORF5基因得到表达。本试验得到的重组蛋白,为进一步研究PRRS病毒结构蛋白的结构和功能奠定了基础。