Towards reliable whole genome sequencing for outbreak preparedness and response.

BACKGROUND: To understand the dynamics of infectious diseases, genomic epidemiology is increasingly advocated, with a need for rapid generation of genetic sequences during outbreaks for public health decision making. Here, we explore the use of metagenomic sequencing compared to specific amplicon- and capture-based sequencing, both on the Nanopore and the Illumina platform for generation of whole genomes of Usutu virus, Zika virus, West Nile virus, and Yellow Fever virus. RESULTS: We show that amplicon-based Nanopore sequencing can be used to rapidly obtain whole genome sequences in samples with a viral load up to Ct 33 and capture-based Illumina is the most sensitive method for initial virus determination. CONCLUSIONS: The choice of sequencing approach and platform is important for laboratories wishing to start whole genome sequencing. Depending on the purpose of genome sequencing the best choice can differ. The insights presented in this work and the shown differences in data characteristics can guide labs to make a well informed choice.

An efficient molecular approach to distinguish chains of measles virus transmission in the elimination phase.

Measles viruses continue to spread globally, despite the availability of a safe and effective vaccine. Molecular surveillance of measles virus has become an essential tool to demonstrate whether cascades of infections in a certain region or country are the result of endemic spread or the repeatedly introduction of the virus in contained outbreaks. Currently, molecular surveillance of measles viruses worldwide is mainly based on 450 nucleotides of the C-terminal region of the nucleoprotein (N450). However, as a result of the disappearance of particular measles virus clades over the past decades, this gene segment does not provide sufficient resolution anymore to answer these questions. To increase the molecular resolution, sequence data were collected from three regions of the measles virus genome, the partial non-coding region between the M and F gene (M-F NCR4465-4754), partial H gene (H8022-8621) and the partial L gene (L10724-11438) for measles viruses detected in 2018 and 2019 in the Netherlands. Analysis of obtained sequence data indicated that sequencing of these three regions resulted in an increase in molecular resolution for measles virus genotype B3 and D8 viruses, two of the four global genotypes currently predominant in the European region. Furthermore, this improved resolution was sufficient to support an epidemiology characterized by repeat introduction of measles virus rather than endemic virus spread. In conclusion, sequencing of the M-F NCR4465-4754, H8022-8621 and L10724-11438 regions of the measles virus is an efficient and useful approach for molecular surveillance of measles viruses.

Co-detection of the measles vaccine and wild-type virus by real-time PCR: public health laboratory protocol.

In rare cases vaccination with the measles virus vaccine genotype A (MeVA) may cause a vaccine reaction with clinical signs similar to infection with wild-type measles virus (MeVwt). Rapid differentiation between MeVA and MeVwt infection is important for taking adequate public health measures. Recently, a few MeVA real-time reverse-transcription quantitative PCR methods (RT-qPCRs) were described that can distinguish between MeVA and MeVwt. However, detection of MeVA does in theory not exclude infection with MeVwt. In the present study, we established a protocol for determination of co-infections with MeVA and MeVwt. To this end, MeVA RT-qPCRs were used in combination with the routine measles virus (MeV) RT-qPCR, and the results suggested that the differences between the RT-qPCR Ct values (delta Ct, ∆Ct) could be used as criteria. Subsequently, we tested samples from vaccine-associated measles cases that were confirmed by genotyping. In addition, experimental mixtures of MeVA and MeVwt were tested in different concentrations. All tested MeVA clinical samples had ∆Ct ≤3.6. The results of experimental mixtures showed a mean ∆Ct ≤2.8 for genotype A alone and >3.2 when combined with either genotype B3 or D8. The results of a receiver operator characteristic analysis indicated that the optimum ∆Ct for use as a cut-off value was 3.5, while with ∆Ct values of 2.9 and 3.7 sensitivity and specificity were respectively 1.00. Thus, ∆Ct could be used to exclude the presence of MeVwt if MeVA is detected and ∆Ct is <2.9, while ∆Ct >3.7 were highly suggestive of co-infection and ≥2.9 ∆Ct <3.7 warranted additional confirmation, such as next-generation sequencing. This RT-qPCR-based protocol could be used for the exclusion of infection with MeVwt in cases with vaccine-associated measles reaction, crucial for the timely implementation of public health prevention and control measures.

Mumps outbreak in a highly vaccinated student population, The Netherlands, 2004.

In September 2004 a mumps outbreak occurred at an international hotel school in The Netherlands. We investigated this outbreak to identify risk factors for mumps. There were 105 mumps cases (overall mumps attack rate (AR) 12% (95% CI: 10-15%)). The AR for Dutch vaccinated and unvaccinated participants was 12% (95% CI: 10-15%) and 15% (95% CI: 3-42%), respectively. Independent risk factor was mumps contact. Explanations for the relatively high AR among vaccinated participants include primary vaccine failure, waning immunity and incomplete vaccine-induced immunity in the context of high mumps virus exposure in a school party and a crowded boarding school.

Air travel as a risk factor for introduction of measles in a highly vaccinated population.

Epidemiological and molecular investigation of two small measles clusters in The Netherlands in July/August 2007 revealed an association with travel by air of the index cases and nosocomial spread in the first cluster. Although these importations did not result in an outbreak among unvaccinated subjects, the observations illustrate the challenges for measles control in a country with high measles vaccination coverage (> 95%) but with pockets of low coverage.

Evaluation of serological and virological tests in the diagnosis of clinical and subclinical measles virus infections during an outbreak of measles in The Netherlands.

We evaluated different approaches for diagnosing measles virus (MV) infection in unvaccinated children and in healthy contact persons (n=194) during a measles epidemic in The Netherlands. MV RNA was detected by reverse-transcriptase polymerase chain reaction in throat-swab specimens from 93% of the patients with clinical symptoms. MV RNA was detected from 5 days before until 12 days after the onset of symptoms. Most patients (88%) also secreted MV RNA in their urine until 5 weeks after the onset of symptoms. Oral fluid proved to be the most practical specimen for the simultaneous detection of MV-specific IgM antibody and viral RNA, which, together, confirmed 93% of measles cases. Viral RNA was also detected in oropharyngeal specimens from 3 healthy contact persons with serological proof of MV infection. The results of this study emphasize the feasibility of combined detection of viral RNA and MV-specific IgM antibodies in oropharyngeal specimens for the diagnosis of clinical and subclinical MV infection.