Saffold cardioviruses of 3 lineages in children with respiratory tract infections, Beijing, China

Abstract

To clarify the potential for respiratory transmission of Saffold cardiovirus (SAFV) and characterize the pathogen, we analyzed respiratory specimens from 1,558 pediatric patients in Beijing. We detected SAFV in 7 (0.5%) patients and identified lineages 1-3. However, because 3 patients had co-infections, we could not definitively say SAFV caused disease.

Figure 1

Phylogenetic analysis of Saffold cardiovirus (SAFV) strains obtained in Beijing, China, 2007–2009, based on viral protein (VP) 1 (A), P1 capsid proteins (B), and full-length genomes (C). The trees, with 500 bootstrap replicates, were generated by using the neighbor-joining algorithm in MEGA 4.0 (10). Strains identified in this study are indicated by a specific identification code (BCH or BCHU), followed by the patient number and labeled with dark triangles (BCH133, BCH350, BCH895, BCH1031, BCHU79, BCHU115, and BCHU353). GenBank accession nos. of the complete genome sequences are BCH1031 GU943513, BCHU115 GU943514, and BCHU79 GU943518; of the P1 gene, BCH350 GU943515, BCH895 GU943516, and BCHU353 GU943517; and of the VP1 gene of BCH133, GU126461. SAFV-1 (prototype), UC1-UC7, Can112051-06, D/VI2229/2004, BR/118/2006, D/VI2273/2004, D/VI2223/2004, LZ50419, GL317, Pak12, Pak971, Afg1449, Pak1141, Pak2578, Pak5003, Pak5152, Pak6572, and NL2007, TEMV-GDVII, Theiler-like virus NGS910, and Vilyuisk virus were used as reference sequences (GenBank accession nos. NC009448, NC010810, EU604745-EU604750, AM922293, EU681176-EU681179, FJ586240, FJ464767, FJ463600-FJ463602, FJ463604, FJ463605, FJ463615-FJ463617, FM207487, X56019, AB090161, and EU723237). Scale bars indicate nucleotide substitutions per site.

Figure 2

Alignment of Saffold cardiovirus (SAFV) viral protein (VP) 1 CD (A) and VP2 EF (B) loop sequences from strains isolated in Beijing, China, 2007–2009. Columns highlighted in black show absolute amino acid conservation; those highlighted in gray show amino acids with highly similar properties. Strains identified in this study are labeled with dark triangles (BCH133, BCH1031, BCHU115, BCH350, BCH895, BCHU353 and BCHU79) (GenBank accession nos. GU126461, GU943513–GU943518), SAFV-1 (prototype), SAFV-1 GL317, SAFV-2 Can112051-06, SAFV-2 BR/118/2006, SAFV-2 D/VI/2229/2004, SAFV-2 Pak971, SAFV-2 UC1, SAFV-3 Pak2578, SAFV-3 D/VI/2223/2004, SAFV-3 D/VI/2273/2004, SAFV-3 NL2007, SAFV-4 Pak12, SAFV-5 Pak5152, SAFV-6 Pak 6572, SAFV-7 Afg1449, SAFV-8 Pak1141, Theiler-like virus NGS910, TMEV GDVII, and EMCV were used as reference sequences (GenBank accession nos. NC009448, FJ464767, AM922293, EU681177, EU681176, FJ463601, NC010810, FJ463605, EU681179, EU681178, FM207487, FJ463600, FJ463616, FJ463617, FJ463602, FJ463604, AB090161, X56019, X87335).

Figure A1

Recombination analyses of Saffold cardioviuses (SAFVs), isolated in Beijing, China, 2007–2009. The relationships among the aligned cardiovirus genome sequences were analyzed by SimPlot software version 3.5.1 (11). A) Sliding-window SimPlot graph generated by using the sequence of the BCHU79 (SAFV-2) as a query against SAFVs, Theiler-like virus, and Theiler murine encephalomyelitis virus–GDVII. B) Bootscan analysis of the sequence of SAFV BCHU79 in comparison to SAFVs, Theiler-like virus, and Theiler murine encephalomyelitis virus–GDVII. C) Sliding-window SimPlot graph generated by using the sequence of the BCH1031 (SAFV-3) as a query against SAFVs, Theiler-like virus, and Theiler murine encephalomyelitis virus–GDVII. D) Bootscan analysis of the sequence of SAFV BCH1031 in comparison to SAFVs, Theiler-like virus, and Theiler murine encephalomyelitis virus–GDVII. Because the genome sequence identity between BCH1031 and BCH115 is as high as 94%, BCH1031 was used to conduct the SimPlot analysis. The nucleotide position is given on the x-axis, and the percent nucleotide sequence similarity is given on the y-axis. The positions relative to viral genes are shown by genome diagrams above the plots and scans. SAFV-1 (prototype), SAFV-2 UC1, SAFV-2 D/VI/2229/2004, SAFV-2 BR118/2006, SAFV-3 D/VI/2273/2004, SAFV-3 D/VI/2223/2004, SAFV-3 NL2007, SAFV-5 Pak5003, SAFV-5 Pak5152, SAFV-6 Pak 6572, Theiler-like virus NGS910, and Theiler murine encephalomyelitis virus–GDVII were used as reference sequences (GenBank accession nos. NC009448, NC010810, EU681176–EU681179, FM207487, FJ463615–FJ463617, AB090161, and X56019).