Detection of novel sequences related to african Swine Fever virus in human serum and sewage

Abstract

The family Asfarviridae contains only a single virus species, African swine fever virus (ASFV). ASFV is a viral agent with significant economic impact due to its devastating effects on populations of domesticated pigs during outbreaks but has not been reported to infect humans. We report here the discovery of novel viral sequences in human serum and sewage which are clearly related to the asfarvirus family but highly divergent from ASFV. Detection of these sequences suggests that greater genetic diversity may exist among asfarviruses than previously thought and raises the possibility that human infection by asfarviruses may occur.

FIG. 1.

Novel viral sequences with similarity to ASFV genes. Novel viral sequences were positionally mapped to the complete genome of the ASFV BA71V strain (29) based on the similarity of the associated amino acid sequences to ASFV proteins. Each novel viral sequence is represented by a black bar, and the ASFV genomic nucleotide position to which it is similar is indicated below the bar.

FIG. 2.

Novel viral sequences are divergent from ASFV. (A) The translated sequence from the novel DNA polymerase consensus sequence was aligned to corresponding sequences from various ASFV isolates using AlignX (VectorNTI suite; Invitrogen). Residues which are highly conserved are shaded in gray, and those which are divergent are in black. (B) Phylogenetic analysis of the translated SF-8.3 sequence and corresponding sequences from the EP364R genes of various ASFV isolates was performed using the neighbor-joining method with 1,000 bootstrap replicates. Bootstrap values over 65% are shown. Sequences were aligned using ClustalX (2.0), and phylogenetic trees were visualized using TreeView (16). GenBank accession numbers for ASFV sequences are provided in the supplemental material. Abbreviations: Benin, Benin 97/1 (5); Kenya, Kenya 1950; Malawi, Malawi Lil-20/1 1983; Mkuzi, Mkuzi 1979; OURT, OURT 88/3 (5); Pretorisuskop, Pretorisuskop/96/4; Tengani, Tengani 62.

FIG. 3.

Phylogenetic analysis of novel viral sequences. Translated novel viral sequences similar to ASFV (A) DNA polymerase, (B) RNA polymerase, and (C) topoisomerase II were compared to corresponding sequences from dsDNA viruses and high-scoring nonviral BLAST matches as described in the legend to Fig. 2. Sequences are shown in color as follows: asfarviruses, red; mimivirus, brown; poxviruses, purple; herpesviruses, gray; phycodnaviruses, green; ascoviruses, orange; iridoviruses, blue; nonviral BLAST matches, black. Bootstrap values over 65% are shown. In panel A, virus intrafamily subclassifications are also shown where applicable. For panels B and C, virus families for which the corresponding RNA polymerase and topoisomerase II sequences could not be identified by BLAST were omitted from the analyses. GenBank accession numbers for the sequences analyzed are provided in the “Supplemental methods” section of the supplemental material. Abbreviations: AmEPV, Amsacta moorei entomopoxvirus; APMV, Acanthamoeba polyphaga mimivirus; ATCV1, Acanthocystis turfacea chlorella virus 1; CIV, Chilo iridescent virus; CVM1, chlorella virus Marburg 1; D. autotrophicum, Desulfobacterium autotrophicum; DpAV4, Diadromus pulchellus ascovirus 4; EBV, Epstein-Barr virus; EhV86, Emiliania huxleyi virus isolate 86; ESV, Ectocarpus siliculosus virus; FsV158, Feldmannia species virus isolate 158; G. anomala, Glugea anomala; H. andersenii, Hemiselmis andersenii; H. butylicus, Hyperthermus butylicus; HCMV, human cytomegalovirus; HHV6, human herpesvirus 6; HSV1, herpes simplex virus type 1; HSV2, herpes simplex virus type 2; HvAV3, Heliothis virescens ascovirus 3; I. scapularis, Ixodes scapularis; ISKNV, infectious spleen and kidney necrosis virus; K. JI2008, Kabatana sp. strain JI2008; KSHV, Kaposi's sarcoma-associated herpesvirus; L. acerinae, Loma acerinae; LDV, lymphocystis disease virus; LSDV, lumpy skin disease virus; M. labreanum, Methanocorpusculum labreanum; M. marisnigri, Methanoculleus marisnigri; MIV, mosquito (Aedes taeniorhynchus) iridescent virus; MsEPV, Melanoplus sanguinipes entomopoxvirus; OSGIV, orange-spotted grouper iridovirus; OsV5, Ostreococcus virus 5; PBCV1, Paramecium bursaria chlorella virus 1; S. islandicus, “Sulfolobus islandicus”; SfAV1, Spodoptera frugiperda ascovirus 1; SGIV, Singapore grouper iridovirus; TFV, tiger frog virus; TnAV2c, Trichoplusia ni ascovirus 2c; VZV, varicella-zoster virus; YMTV, Yaba monkey tumor virus. Other abbreviations are as defined for Fig. 2.