African Swine Fever Virus (Asfarviridae) sequences and HHV-6 found in people with febrile illnesses
Abstract
Virus Identification in Unknown Tropical Febrile Illness Cases Using Deep Sequencing
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.
 
 
 
 
 
 
 
 
 
 
