Laboratory testing and phylogenetic analysis during a mumps outbreak in Ontario, Canada

Abstract

BackgroundIn September 2009, a mumps outbreak originated in New York and spread to Northeastern USA and Canada. This study compares the performance of different diagnostic testing methods used in Ontario and describes molecular characteristics of the outbreak strain.MethodsBetween September 2009 and February 2010, specimens from suspect cases were submitted to Public Health Ontario Laboratory for mumps serology, culture and/or real-time reverse-transcriptase PCR (rRT-PCR) testing. rRT-PCR-positive specimens underwent genotyping at Canada’s National Microbiology Laboratory. Whole genome sequencing was performed on four outbreak and three sporadic viral culture isolates.ResultsSix hundred ninety-eight patients had IgM serology testing, of which 255 (37%) had culture and rRT-PCR. Among those, 35/698 (5%) were IgM positive, 39/255 (15%) culture positive and 47/255 (18%) rRT-PCR-positive. Buccal swabs had the highest rRT-PCR positivity (21%). The outbreak isolates were identical to that in the New York outbreak occurring at the same time. Nucleotide and amino acid identity with the Jeryl Lynn vaccine strain ranged from 85.0-94.5% and 82.4-99.4%, depending on the gene and coding sequences. Homology of the HN protein, the main immunogenic mumps virus protein, was found to be 94.5 and 95.3%, when compared to Jeryl Lynn vaccine major and minor components, respectively.ConclusionsDespite higher sensitivity than serology, rRT-PCR testing is underutilized. Further work is needed to better understand the suboptimal match of the HN gene between the outbreak strain and the Jeryl Lynn vaccine strain.

Evaluating the use of whole genome sequencing for the investigation of a large mumps outbreak in Ontario, Canada

“…Traditional SH genotyping differentiated S11, which is genotype C, from the main outbreak, but did not identify that case S1 was distinct from the other Genotype G strains and was therefore likely the result of an independent introduction of mumps virus. From the WGS phylogenetic tree it is apparent that S1 is more closely related to a sample we previously sequenced from a 2010 Ontario outbreak than it is to the other outbreak strains 13 .…”

“…We refined our previously published method for amplifying mumps virus DNA from virus culture samples 13 . At PHO, virus culture is routinely performed on all specimens that are reactive by RT-PCR, to assist with SH genotyping, and we have previously found the sensitivity of culture and RT-PCR to be broadly equivalent.…”

“…Nucleic acid extraction and sequencing was carried out using a modified version of a tiling amplicon-based method to enrich the culture supernatant for viral RNA, which we previously used to sequence mumps virus from a 2010 Ontario outbreak 13 . We extracted RNA using either the QIAamp Viral RNA Mini Kit (Qiagen, Mississauga, ON) or the NucliSENS easyMAG instrument.…”

Mumps: Achievements, Problems and Ways of Solution

“…Использование молекулярно-генетических методов (ПЦР) среди заболевших, ранее привитых против ЭП, при исследовании неинвазивного биологического материала -содержимого буккального мазка и назофарингеального секрета является наиболее информативным для верификации ЭП [2,24,37]. Вирус ЭП обнаруживается в течение 9 дней с момента появления клинических симптомов [2,38,39].…”

“…Информативность используемых диагностических методов, молекулярно-генетического и серологического, в повседневной клинико-эпидемиологической практике напрямую зависит от сроков заболевания. Наибольшую диагностическую значимость в подтверждении диагноза в первые дни заболевания имеет метод обратно-транскриптазной ПЦР (ОТ-ПЦР) с детекцией в режиме реального времени, позволяющий выявлять генетический материал вируса ЭП в содержимом назофаренгиального секрета и буккальных мазках от пациентов с ЭП [24,29,37]. [29].…”