Deep sequencing reveals persistence of cell-associated mumps vaccine virus in chronic encephalitis

Abstract

Routine childhood vaccination against measles, mumps and rubella has virtually abolished virus-related morbidity and mortality. Notwithstanding this, we describe here devastating neurological complications associated with the detection of live-attenuated mumps virus Jeryl Lynn (MuVJL5) in the brain of a child who had undergone successful allogeneic transplantation for severe combined immunodeficiency (SCID). This is the first confirmed report of MuVJL5 associated with chronic encephalitis and highlights the need to exclude immunodeficient individuals from immunisation with live-attenuated vaccines. The diagnosis was only possible by deep sequencing of the brain biopsy. Sequence comparison of the vaccine batch to the MuVJL5 isolated from brain identified biased hypermutation, particularly in the matrix gene, similar to those found in measles from cases of SSPE. The findings provide unique insights into the pathogenesis of paramyxovirus brain infections.Electronic supplementary materialThe online version of this article (doi:10.1007/s00401-016-1629-y) contains supplementary material, which is available to authorized users.

Encephalitis diagnosis using metagenomics: application of next generation sequencing for undiagnosed cases

“…45 The use of brain tissue rather than CSF may increase diagnostic yield. In three cases a pathogen was detected in brain biopsy but not in CSF 32,35,48 while the opposite was not observed, although in one instance the proportion of pathogen reads was greater in CSF than brain biopsy. 33 In our hands, the diagnostic yield for metagenomics in encephalitis is, to date, 50% (8/16) all of which were brain biopsies.…”

“…This included two cases of human parvovirus 4 (PARV4), 28 first described in 2005 when it was associated with a viraemic patient in whom an acute viral infection was suspected 49 ; one case of human coronavirus OC-43, 43 typically a human respiratory pathogen never previously described in a human case of encephalitis but known to cause encephalitis in mice 50 ; one case of human astrovirus MLB1, 46 of mumps vaccine virus in a child who was vaccinated prior to a primary immunodeficiency diagnosis. 48 The five cases in which rare causes of encephalitis were identified were Brucella melitensis, Candida tropicalis, Leptospira santarosai and two cases of Balamuthia mandrillaris.…”

“…33 In our hands, the diagnostic yield for metagenomics in encephalitis is, to date, 50% (8/16) all of which were brain biopsies. The eight identified pathogens were coronavirus OC-43, 43 two cases of vaccine derived mumps virus, 48,54 Toxoplasma gondii (unpublished) and four cases of astrovirus VA1/HMO-C 31,42 (two cases unpublished). All of our positive results were in immunocompromised patients and in the majority of cases there was a high index of suspicion of infection, suggesting metagenomics may be best applied to a targeted population in whom it will be most rewarding.…”

“…In this context brain biopsies are a more useful specimen than cerebrospinal fluid (CSF) since it allows immunostaining of the affected tissue. Moreover, in encephalitis caused by mutated pathogens such as in subacute sclerosing panencephalitis (SSPE) caused by chronic measles infection 52 or cases of mumps vaccine encephalitis 48 the pathogen may not be detected in CSF but only in brain parenchyma.…”

“…This approach overcomes the common problem of reagent contamination with microbial nucleic acids; of 33 cases in which the presence or absence of contaminating reads was reported, 22 cases reported the presence of environmental bacteria, plant viruses, bacteriophages and/or avian retroviruses. 24,29,31,33,35,36,[38][39][40][41]43,45,47,48 Turn-around times Only 5 cases reported the time from specimen collection to pathogen identification; for these the turn-around time was 2-6 days, with a median time of 6 days. Due to limitations of currently available sequence library preparation methods and sequencing chemistries a sample-to-answer turn-around time as short as 48 hours 24 is only achievable with a fast downstream analysis pipeline; in the reported case analysis took only 97 minutes compared to up to two days in other, computationally intensive, pipelines.…”