By Dean L. Winslow, MD, FACP, FIDSA

Professor of Medicine, Division of General Medical Disciplines, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine

Dr. Winslow reports no financial relationships relevant to this field of study.

SYNOPSIS: Metagenomic next-generation sequencing was applied to examine serum from 204 adult patients with acute liver failure (ALF). Researchers identified a potential viral etiology in eight of the 187 patients with ALF of indeterminate etiology. Potential pathogens identified in these included HSV-1, HBV, parvovirus B19, CMV, and HHV-7.

SOURCE: Somasekar S, Lee D, Rule J, et al. Viral surveillance in serum samples from patients with acute liver failure by metagenomic next-generation sequencing. Clin Infect Dis 2017;65:1477-1485.

As part of the ongoing Acute Liver Failure Study Group (ALFSG), 204 sera samples collected between 1998 and 2010 were analyzed using traditional nucleic acid testing and metagenomic next-generation sequencing (mNGS). In this group were 187 patients who had acute liver failure (ALF) of indeterminate etiology and 17 controls (four cases each of hepatitis A and hepatitis B, three cases of acetaminophen toxicity, two cases of autoimmune hepatitis, three cases of drug-induced liver injury, and one case of hepatic ischemia).

A blinded analysis of mNGS data showed positive results for a potential viral pathogen in 27 patients. In the first group, seven of eight of the Hep A- or Hep B-positive controls were detected by mNGS. The one HBV+ control that was missed by mNGS had very low copy number of virus and was confirmed by conventional NAT. A second group of 11 cases tested positive by either serology or PCR or both but were considered indeterminate by the investigator. Eight of 11 of these cases were confirmed by mNGS. One case of HIV, one case of CMV (with co-infection with EBV), and one case of HBV (with HCV and HDV co-infection) were missed, but NAT for these viruses also were negative, suggesting that DNA or RNA in the sample had been degraded. In the last group, previously unrecognized viral infections were found in eight cases: HSV-1 alone in three cases, and one case each of HBV, parvovirus B19, HHV-7, CMV, and HPV-159, a cutaneous betapapillomavirus. (The latter virus is found commonly on the skin and may represent skin contamination of the sample at the time of phlebotomy.)

The parvovirus B19 case also was interesting, occurring in a previously healthy 75-year-old man. The HHV-7 case may have represented reactivation (rather than the cause of acute liver failure) in a very ill patient with a noninfectious cause of ALF, since > 90% of adults have evidence of previous infection with HHV-7.


This study shows that mNGS can be a powerful and useful tool to diagnose disease. Applied to ALF in adults (where up to 20% of cases may be of indeterminate etiology by conventional clinical testing, especially in the developing world),1 mNGS may be particularly useful. In addition to making the diagnosis of mixed viral infection in three cases in this series, the study also showed the importance of HSV-1, either as a single agent or co-infecting agent, as a cause of ALF. Four patients had previously unrecognized HSV-1 (subsequently confirmed by PCR). All four of these patients were immunocompetent, were quite ill, and the two with extremely high transaminase elevations died.

While further study of mNGS in ALF is important, this paper clearly shows the potential clinical utility of this powerful new diagnostic technique. Until mNGS is more readily available, the results of this study do suggest that initial workup of ALF include conventional NAT testing for HSV-1 and parvovirus B19 in addition to testing for hepatitis A-E viruses.


  1. Bernal W, Wendon J. Acute liver failure. N Engl J Med 2013;369:2525-2534.