SCC<i>mec</i> IVa of ST72 HL1.

<p>The HL1 SCC<i>mec</i> IVa element and the adjacent unique downstream region are compared to the SCC<i>mec</i> IVa elements of USA300 and USA400. SCC<i>mec</i> regions are shaded in grey boxes. Colored internal boxes in the case of HL1 show differing regions. Regions present in USA300 and USA400, but absent from HL1 are in dark grey, internal boxes. Solid grey bar, class B <i>mec</i> region; dotted grey bar, left extremity (L–C) region. Rep, replication protein; Mob, plasmid mobilization protein; Bleo-Resis, bleomycin resistance protein; Kan Nucl-T, kanamycin nucleotidyltransferase; (R), (R)-specific enoyl-CoA-hydratase; HMGCoA, hydroxymethylglutaryl CoA reductase; ACME, arginine catabolic mobile element (downstream of SCC<i>mec</i> in USA300).</p

ΦSa3 prophage in ST72 HL1 compared to USA300 and USA400.

<p>Broken lines, missing ORFs; red, virulence determinants; blue, phage gene or phage-related gene; grey, ORF not identical to other strains.</p

Plasmids in ST72 HL1.

<p>Plasmids in ST72 HL1.</p

Genomic islands in ST72 HL1 compared to USA300 and USA400.

<p>A, vSaα genomic island. B, vSaβ genomic island. C, vSaγ genomic island. Broken lines, missing ORFs; red, virulence determinants; green, type I restriction-modification system specificity subunit; yellow, lipoproteins; blue, bacteriocin-related genes; yellow, determinants; grey= ORF not identical to other strains.</p

Phylogenetic tree of orthopoxviruses including ERPV.

<p>Concatenated sequences of 96 ORFs conserved in each viral genome were used to perform the analysis. ERPV branches from the same node as ECTV.</p

Unassigned ORFs with homology to CPXV proteins.

a<p>Similar in ECTV-Mos.</p>b<p>Similar in ECTV-Nav.</p>c<p>Missing from ECTV-Mos. Others are identical in the three genomes.</p><p>Abbreviation: aa, amino acids.</p

Comparison of genomes of ERPV and ECTV-Nav and ECTV-Mos.

a<p>Genome sizes are from the first nt of the left CRS to the nt before the right CRS.</p>b<p>The ORF number includes the homolog of O3, which was not originally annotated in ECTV-Nav or ECTV-Mos.</p

Molecular Characterization of Human Pathogenic Bunyaviruses of the Nyando and Bwamba/Pongola Virus Groups Leads to the Genetic Identification of Mojuí dos Campos and Kaeng Khoi Virus

<div><p>Background</p><p>Human infection with Bwamba virus (BWAV) and the closely related Pongola virus (PGAV), as well as Nyando virus (NDV), are important causes of febrile illness in Africa. However, despite seroprevalence studies that indicate high rates of infection in many countries, these viruses remain relatively unknown and unstudied. In addition, a number of unclassified bunyaviruses have been isolated over the years often with uncertain relationships to human disease.</p><p>Methodology/Principal Findings</p><p>In order to better understand the genetic and evolutionary relationships among orthobunyaviruses associated with human disease, we have sequenced the complete genomes for all 3 segments of multiple strains of BWAV (n = 2), PGAV (n = 2) and NDV (n = 4), as well as the previously unclassified Mojuí dos Campos (MDCV) and Kaeng Khoi viruses (KKV). Based on phylogenetic analysis, we show that these viruses populate 2 distinct branches, one made up of BWAV and PGAV and the other composed of NDV, MDCV and KKV. Interestingly, the NDV strains analyzed form two distinct clades which differed by >10% on the amino acid level across all protein products. In addition, the assignment of two bat-associated bunyaviruses into the NDV group, which is clearly associated with mosquito-borne infection, led us to analyze the ability of these different viruses to grow in bat (RE05 and Tb 1 Lu) and mosquito (C6/36) cell lines, and indeed all the viruses tested were capable of efficient growth in these cell types.</p><p>Conclusions/Significance</p><p>On the basis of our analyses, it is proposed to reclassify the NDV strains ERET147 and YM176-66 as a new virus species. Further, our analysis definitively identifies the previously unclassified bunyaviruses MDCV and KKV as distinct species within the NDV group and suggests that these viruses may have a broader host range than is currently appreciated.</p></div

Genome map of ERPV and comparison to ECTV-Naval.

<p>Left (LITR) and right (RITR) inverted terminal repeats are indicated by deep blue arrows. ORFs are in yellow and numbered from left to right with the direction of transcription indicated by the arrow. Direct repeats (DRs) are indicated in light blue. Single nucleotide polymorphisms (SNPs) are gold; insertions and deletions are indicated in red and purple, respectively, with single nt and larger changes by a thin oval and a diamond, respectively. Asterisks signify mutations that affect the predicted amino acid sequence.</p

Assembly of contigs and gap closure.

<p>(A) Five contigs were assembled de novo using 159,077 sequence reads generated by pyrosequencing, providing an estimated coverage of 60X with 5 gaps. (B) The gaps were filled by PCR and Sanger sequencing. Blue arrows indicate positions of primers used for PCR. Gaps 2 and 5 contained direct repeats (DRs) necessitating synthesis and sequencing of additional internal PCR fragments. DRI contains a 69 bp sequence repeated 2.3X; DRII contained an 85 bp sequence repeated 10.4X; and DRIII contained a 25 bp sequence repeated 7.0X. The non-repetitive I (NRI) and NRII sequences flank DRI. ORFs are indicated by numbered yellow arrows.</p