Detection of Novel Sequences Related to African Swine Fever Virus in Human Serum and Sewage▿

[Gert van der Hoek]

J. Virol. December 2009 vol. 83no. 24 13019-13025


[FONT=&quot]ABSTRACT[/FONT]

[FONT=&quot]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.[/FONT]​

[FONT=&quot] [/FONT]
[FONT=&quot]The family Asfarviridae contains a single double-stranded DNA (dsDNA) virus called African swine fever virus (ASFV), which is thought to have evolved from an ancestral virus common to the nucleocytoplasmic large DNA viruses including poxviruses, iridoviruses, and phycodnaviruses (10, 11). ASFV infects ticks and swine but has not been reported to infect humans. ASFV infection of wild swine typically causes persistent infection with few symptoms (9, 17, 24, 25), but domesticated pigs can develop severe disease including acute hemorrhagic fever with nearly 100% mortality. As there is no vaccine and disease is contained by animal quarantine and slaughter, ASFV outbreaks can decimate pig populations and have significant economic impact. A 2007 outbreak in the former Soviet republic of Georgia resulted in the death and slaughter of over 80,000 pigs (20).[/FONT]

[FONT=&quot]ASFV is endemic in sub-Saharan Africa but has also been introduced to countries in Europe, South America, and the Caribbean (26). Characterization of various ASFV isolates has led to the identification of 22 genotypes based on sequence variation in the portion of the B646L gene encoding the C terminus of the major capsid protein (2, 4, 14). Within this segment of B646L, approximately 14% of the nucleotide sites are variable among the ASFV isolates studied (2, 4). The ASFV genome has been completely sequenced for the Vero cell-adapted BA71V strain (29) and several wild isolates (5). Like many other large dsDNA viruses, ASFV contains open reading frames with homology to cellular genes involved in DNA replication, transcription, repair, and protein modification (29). ASFV also has an array of open reading frames with potential function in modulating host cell function or immune response (7).[/FONT]

[FONT=&quot]We report here the discovery of novel viral sequences in human serum from the Middle East and in sewage from Spain that have clear similarity to ASFV genes. Of the 36 sequences identified, 29 did not have significant overlap or nucleotide identity with any of the other sequences. These 29 sequences are similar to 18 different ASFV genes, with some sequences matching to different regions within the same ASFV genes. Sequence and phylogenetic analyses indicate that the novel viral sequences are most closely related to the asfarvirus family but are highly divergent from known ASFV strains. We therefore hypothesize that these viral sequences are derived from at least one novel virus in the Asfarviridae family, which we refer to herein as ASFV-like virus (ASFLV).[/FONT]


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[bertrand789]

merci,


une publication de 2009 indiquant

d'une part 22 serotypes, nous en sommes ? 23 ,

d'autre part, abordant :[FONT=&quot]dans le [/FONT][FONT=&quot]s?rum humain du Moyen -[/FONT][FONT=&quot]Orient et dans les [/FONT][FONT=&quot]eaux us?es de l' [/FONT][FONT=&quot]Espagne[/FONT]

vu les cartes produites, en ce lieu, on n'a rien fait d'autre: nous sommes en 2018

 

[Gert van der Hoek]

[h=1]Virus Identification in Unknown Tropical Febrile Illness Cases Using Deep Sequencing[/h]
PLoS Negl Trop Dis. 2012 Feb; 6(2): e1485.

[h=2]Abstract[/h] [FONT=&quot] Dengue virus is an emerging infectious agent that infects an estimated 50?100 million people annually worldwide, yet current diagnostic practices cannot detect an etiologic pathogen in ∼40% of dengue-like illnesses. Metagenomic approaches to pathogen detection, such as viral microarrays and deep sequencing, are promising tools to address emerging and non-diagnosable disease challenges.

In this study, we used the Virochip microarray and deep sequencing to characterize the spectrum of viruses present in human sera from 123 Nicaraguan patients presenting with dengue-like symptoms but testing negative for dengue virus. We utilized a barcoding strategy to simultaneously deep sequence multiple serum specimens, generating on average over 1 million reads per sample. We then implemented a stepwise bioinformatic filtering pipeline to remove the majority of human and low-quality sequences to improve the speed and accuracy of subsequent unbiased database searches.

By deep sequencing, we were able to detect virus sequence in 37% (45/123) of previously negative cases. These included 13 cases with Human Herpesvirus 6 sequences. Other samples contained sequences with similarity to sequences from viruses in the Herpesviridae, Flaviviridae, Circoviridae, Anelloviridae, Asfarviridae, and Parvoviridae families. In some cases, the putative viral sequences were virtually identical to known viruses, and in others they diverged, suggesting that they may derive from novel viruses. These results demonstrate the utility of unbiased metagenomic approaches in the detection of known and divergent viruses in the study of tropical febrile illness.
[/FONT]

[FONT=&quot]Asfarviridae = African Swine Fever Virus[/FONT]

 

[Gert van der Hoek]

[h=2]Febrile Children in Nicaragua?What Can Metagenomic Analysis Tell Us?[/h] Clinical Infectious Diseases[FONT=&quot], Volume 55, Issue 7, 1 October 2012, Pages iii?iv,[/FONT]
https://doi.org/10.1093/cid/cis643

Viral sequences were detected in 45 of 123 serum samples (37%) by deep sequencing and in 10 (8%) by Virochip analysis. Hepatitis A virus sequences were detected in 2 subjects. Two additional samples contained viral RNA sequences, both representing GB virus (GBV-C; ?hepatitis G virus?). Human herpesvirus (HHV) type 6 sequences were found in 13 of the 123 samples (10.6%), with all aligning best with HHV-6B. All the subjects from whom these sequences were recovered were 7?12 months of age, ages at which primary HHV-6 infection commonly occurs. Epstein-Barr virus and African swine fever virus sequences were each identified in a single sample.