Journal Pre-proof The laboratory investigation of a measles outbreak in the eve of its elimination in Sri Lanka Buddhini Samaraweera (Formal analysis) (Methodology) (Validation) (Writing - original draft) (Writing - review and editing), Adhyana Mahanama (Formal analysis) (Software) (Validation)
Writing – original draft) (Writing review and editing), Almarz Z Ahamad (Data curation) (Validation), Gayan I Wimalaratne (Investigation), Janaki Abeynayake (Conceptualization) (Supervision) (Methodology) (Project administration) (Validation) (Writing - review and editing)
PII:
S1386-6532(19)30260-4
DOI:
https://doi.org/10.1016/j.jcv.2019.104230
Reference:
JCV 104230
To appear in:
Journal of Clinical Virology
Received Date:
24 July 2019
Revised Date:
11 November 2019
Accepted Date:
25 November 2019
Please cite this article as: Samaraweera B, Mahanama A, Ahamad AZ, Wimalaratne GI, Abeynayake J, The laboratory investigation of a measles outbreak in the eve of its elimination in Sri Lanka, Journal of Clinical Virology (2019), doi: https://doi.org/10.1016/j.jcv.2019.104230
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The laboratory investigation of a measles outbreak in the eve of its elimination in SriLanka Buddhini Samaraweera1, Adhyana Mahanama1,Almarz Z Ahamad1, Gayan I Wimalaratne1, Janaki Abeynayake1,* [email protected] 1
Medical Research Institute, Colombo 08, Sri Lanka
*
Corresponding author: Janaki Abeynayake
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Word count in the abstract – 252
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Highlights
The study revealed that, 19% of the suspected patients were positive for measles with
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73% having re-infections.
A majority who contracted measles was at or over 22 years, and had received only one
Measles genotype D8 was detected in two separate provinces suggesting the spread of
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dose of MCV in NEIP during the childhood.
virus within the country.
Laboratory confirmation by additional testing such as measles RNA real time PCR, anti-
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measles IgG avidity and sequencing/genetic analysis is critical in the verge of measles elimination to facilitate the early detection of outbreak and to implement effective control measures.
Abstract 1
Background Measles is highly contagious and cause significant morbidity and mortality. Sri-Lanka has the goal to eliminate endogenous measles by 2020 in par with WHO. Objective To describe laboratory confirmation and genotype distribution of measles cases during the
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outbreak occurred from mid-March to May 2019, Sri-Lanka Study design
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This retrospective study was conducted at National Measles Reference Laboratory (NMRL), SriLanka. All samples received were tested according to the testing flow chart at NMRL with WHO
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recommended kits. Blood samples were tested for anti-measles IgM and IgG with IgG avidity for
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IgG positives. Samples within 5days post-onset rash were tested with measles real-time RT-PCR. Products of genotyping PCR were sent to Regional Reference Laboratory, Thailand for
descriptive statistics.
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Results
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sequencing. Subsequent phylogenetic analysis was done at NMRL. Data were analyzed by
A total of 182 blood and 46 throat/nasopharyngeal swabs were received from 195 suspected cases and 37(19%) were positive for measles by anti-measles IgM, rRT-PCR or both. Majority was females, with mean age of 20 years. Cases represented three main geographical areas;
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Western-35%, Central-32% and Southern-27%. High avidity IgG was detected in 27/37(73%). Sequencing data of six cases (4 from Western and 2 from Central province) revealed genotype D8.
Conclusion
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Nineteen percent of the suspected patients were measles positive with 73% having re-infections. Majority were 22 years or over. Measles genotype was D8 in two provinces, suggesting the spread of virus within the country. Laboratory confirmation with measles PCR; IgG avidity and sequencing/genetic analysis is critical in the verge of measles elimination.
Key words
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Measles
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Elimination Outbreak
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Real time PCR and Genotyping
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Measles IgG avidity
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Background
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Measles is a highly contagious viral disease which results in a range of clinical manifestations spanning from asymptomatic infection, moderate illness to life threatening complications [1].It is a vaccine preventable disease and effective, safe and cost effective measles vaccine is one of the major arms in measles elimination [2].
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In 2012, the Global Vaccine Action Plan, set the objective of eliminating measles in five World Health Organization (WHO) regions by 2020 through the combined effect of effective immunization program and a strong surveillance system [3]. As the laboratory plays a major role in measles surveillance system, Global Measles and Rubella Laboratory Network has introduced quality assurance programs to maintain standards of its member laboratories. This would ensure timely and accurate laboratory diagnosis of measles infection for effective monitoring of 3
progress towards elimination and for early detection of outbreaks to implement preventive measures [4,5].
Sri Lanka’s measles elimination strategic plan was initiated with the introduction of a measles containing vaccine (MCV) to the National Extended Immunization Program (NEIP) in 1984, as a single dose at the age of 9 months [6]. Following this, the annual incidence of measles in the
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country reduced steadily from 12-49/100,000 population (in 1971 to 1980) to reach the
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elimination target of less than 5 per million populations in 2011[7]. During the period, several local outbreaks of measles hit the country (two major outbreaks in 1999 and 2013) leading to the
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introduction of several changes to the measles vaccination program which included initiation of a
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second dose of MCV vaccine in 2001[8]. The country had since then been able to maintain more than 95% vaccination coverage for both doses of the vaccine paving the way for successful
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elimination.
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Measles outbreaks can occur due to imported cases or endogenous transmission in populations with low immunity. Successful immunization with two doses of measles containing vaccine conveys sero-conversion of 97% [5].But it is evident, vaccine induced immunity wanes off with time compared to natural immunity [9,10]. On the verge of elimination, a country faces the
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problem of low level of natural immunity and less chance of boosting the existing vaccine induced immunity in the population. This may carry a high risk for measles infection, which can lead to outbreak situations even in the background of high coverage of measles vaccination in the country [11].
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Objective
To describe the laboratory confirmation of measles suspected cases and genotype distribution of the confirmed cases during the outbreak in early 2019, Sri Lanka
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Study design
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This study retrospectively analyzed182 blood and 46 throat and nasopharyngeal swab samples of suspected patients and their contacts received to National Measles Reference Laboratory
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(NMRL), Medical Research Institute(MRI), Sri Lanka for the laboratory confirmation of measles
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viral infection, during the period of 10 weeks starting from mid March to end of May 2019.All samples were tested according to the following laboratory testing flow chart (figure 1).
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Suspected all blood samples were tested for anti-measles IgM irrespective of the date of sample collection. The anti-measles IgM was performed by WHO recommended Euroimmun Anti-
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Measles Virus Indirect IgM ELISA Nucleoprotein kit (Luebeck, Germany).The test runs were validated and results were analyzed according to the manufacturer’s instructions. The antimeasles IgM positive samples were considered as measles positive cases and the anti-measles
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IgM ELISA test negative samples were considered as negative for anti-measles IgM in that particular sample. However, clinical histories received along with anti-measles IgM negative samples were carefully evaluated to identify the date of sample collection in relation to onset of rash. The negative blood samples received from day one to five of illness were tested with real time reverse transcriptase polymerase chain reaction (PCR).
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Measles IgG was performed on all blood samples irrespective of sample collection date with Euroimmun Anti-Measles Virus Indirect IgG ELISA kit (Luebeck, Germany).Further, measles IgG avidity was measured in all IgG positive samples with Euroimmun Anti-Measles Virus IgG avidity ELISA kit (Luebeck, Germany) that uses urea as denaturing agent. Relative avidity index (RAI) was calculated for each sample according to the manufacturer instructions. Samples with
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RAI < 40%were labeled as low avidity IgG and samples with RAI >60% were considered as
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high avidity IgG according to the manufacturer’s instructions. If the RAI was in between 40%60%, those samples were reported as equivocal [12]. Low avidity IgG can be detected in patients
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with recent measles viral infection or vaccination within four months of sample collection and
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high avidity IgG is positive in patients who had past measles viral infection or vaccination before
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four months of sample collection [13, 14, 15,16].
Measles qualitative real-time reverse transcriptase PCR was performed for blood, throat and
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nasopharyngeal swabs, which were collected within first five days of post onset rash, using WHO recommended, Center for Disease Control (CDC Atlanta, USA) evaluated primers and probes with the superscript enzyme (Invitrogen SuperScript111 Platinum, USA).Reverse transcription, amplification and real time detection was done using ABI 7500 Standard PCR
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platform with all the recommended controls including human RNaseP gene. Assay validation and qualitative analysis of samples were done according to the guideline provided by WHO and samples were labeled as measles RNA detected or not detected. Subsequently, measles real time reverse transcriptase PCR positive samples were tested with WHO recommended; CDC evaluated measles genotyping conventional reverse transcriptase PCR with forward and reverse
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primers of MeV216 and MeV214 respectively [17]. The amplified products of the genotyping conventional reverse transcriptase PCR, which gave a good band in the gel electrophoresis, was sent to the Regional Reference Laboratory (RRL), Thailand for sequencing. Following the sequencing procedures at RRL, the sequences of PCR products were piled up in ABI files and send to NMRL at Sri Lanka, where those ABI files analyzedusing‘MEGA7’ software program to
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detect the measles genotype and to create the phylogenetic tree.
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Measles virus sequences were genotyped using the 450 bp fragment of the N gene recommended for genotyping by WHO by the member state sequence database, the Measles Nucleotide
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Surveillance (MeaNS) tool. Phylogenetic analyses were performed by alignment and epi-link
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tree was generated using ClustalW. Sequences shorter than the recommended 450 bp were
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excluded from the phylogenetic analysis [18,19].
The socio-demographic data such as age, geography, and occupation gathered from the test
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request forms accompanied the samples were scrutinized with the test results. Statistical analysis was done using descriptive statistics by the Statistical Package for Social Sciences (SPSS) version 24.
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Results
During the 10-week study period, 195 measles suspected patients were tested (182 blood and 46 throat and nasopharyngeal swab samples) and 37 (19%) were confirmed to have the infection by positive anti-measles IgM and/or measles virus RNA detection (Table 2). The mean age of
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positive patients was 20 years, mode 22 years (30% of total) and age ranged from nine months to 27 years with majority being females (68%).
Measles infected cases in the present outbreak were mainly from three provinces of the country namely Western (35%), Central (32%) and Southern (27%). Eighty four percent of them had a
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Moreover, none of the patients had a travel history out of the country.
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contact history to a measles positive case within the country and 6/37 (16%) were sporadic cases.
Among the measles positive group, 10 medical students (27%), 19 nursing students (51%) and 2
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priests were included. Measles vaccination details were only available in 4 (11%) patients and all
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of them had been given only one dose of Measles Containing Vaccine (MCV). The sociodemographic, vaccination and epidemiological details of the measles patients are presented in
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Table 1.
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Of the total positives, 28 serum samples were anti- measles IgM positive and 17 samples (07 nasopharyngeal/throat swabs, 08 serum samples and 02 swab and serum samples) were measles real-time reverse transcriptase PCR positive. Both anti-measles IgM and measles real time reverse transcriptase PCR were positive in eight patients. Measles real time reverse transcriptase
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PCR (rRT-PCR) was positive in nine patients with negative anti-measles IgM (Table 2).
High avidity IgG antibodies were identified in 27 patients (73%), out of the 37 positive patients and low avidity IgG, in only 5% (2/37). High IgG avidity index was observed in seven patients with negative anti-measles IgM and positive real time RT-PCR. Further, it was also observed
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high avidity IgG antibodies in 20 patients with positive anti-measles IgM with positive or negative real time RT-PCR(Table 2).
Following sequencing and phylogenetic analysis measles genotype D8 was detected in six measles positive patients. Four of them were from the Western province while the other two were from the Central province. Figure 2 illustrates the phylogenetic analysis of the genotypes
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detected in Sri Lanka from 2017 to May 2019 and Table 3 presents the circulating measles
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genotypes in the county during the same period.
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Discussion
Sri Lanka with the elimination target of zero endogenous cases of measles in 2020 has a strong
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measles surveillance program with an accredited measles diagnostic laboratory which supports to confirm the reported suspected measles cases in the phase of elimination. Moreover, the
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laboratory confirmation of all suspected cases of measles is a critical arm of surveillance and control activities during outbreak [1].
The only confirmed case in 2018, which was reported from the Western Province (Colombo),
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was identified as measles positive with measles genotype H1. The phylogeny (figure 2) showed the epidemiological link clearly, and revealed non-endogenous origin. Furthermore, this link was supported by the history taken from the patient. This highlighted the successful progress of Sri Lanka towards Measles elimination goals in par with WHO.
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However, in contrast to the situation in 2018, National Measles Reference Laboratory received a comparatively high sample volume in March 2019, which continued through May 2019.Total sample volume was 143 during the year 2018, where as in 2019, it rose up to a 293 which included 246 blood samples and 47 throat swabs, until the end of May. During this period, 37 patients with confirmed measles viral infection was identified.
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Detection of virus RNA by reverse transcriptase PCR is a widely available case confirmation
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method and samples such as nasopharyngeal/throat swabs and serum collected within the first five days of onset of rash are the most frequently used[20,21]. Urine samples can also be used
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for the purpose and has the added advantage of detecting the virus for a longer period [21].
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Timing of collection of the sample is crucial and failure to collect the appropriate specimen at the correct time, reduces its’ utility. During the study period, the sample type collected mostly was
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serum, and they had been collected at day 3 or after the onset of the rash, in par with the surveillance case definition (for serological testing), thus limiting their utility in the real-time
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RT-PCR. Hence, other investigations were also used depending on the timing of sample collection for case confirmation.
Accordingly, anti-measles IgM assay, anti-measles IgG assay, and anti-measles IgG avidity
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assay were used to test the samples and collective interpretation was done to identify the measles infected cases. Anti-measles IgM positive cases were defined as recent measles infection. However, only 02/37 showed low IgG avidity where as majority (27/37) demonstrated high avidity IgG antibody indicating those patients have had past immunologic experience with measles either through natural infection or vaccination. Timing of the infection can be
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demarcated with anti-measles IgG avidity assay by demonstrating the IgG avidity index; which differentiates the infection occurred four months before if the index is high or within the recent four months if the index is low. Moreover, those who showed up with anti-measles IgM positive and low IgG avidity were described as having primary measles infection. Yet, the presence of high avidity measles IgG antibody excluded the possibility of primary infection with measles
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[13,14, 15, 16].
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The first case or the Index case detected in the outbreak was a medical student from the Western province (Colombo), who presented directly to the laboratory with fever, Koplik spots and rash.
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He was confirmed to have measles viral infection with genotype D8 with the epi-link to
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AF280803 Mancheter.UNK/30.94-D8 WHO reference strain (figure 2). Subsequently, contacts (medical students and patients) of the index case, who reported with similar symptoms and signs
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were also tested for measles and 11 cases (9 medical students and 2 priests) were identified. Out
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of them genotyping was done in 5 cases and all were of genotype D8 (Figure 2).
During the same period another two clusters of measles like illness were reported from the Central province and the Southern province involving nursing students and 12 and 10 cases from each cluster were positive for measles respectively. One case was genotyped from the cluster in
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the Central province and it was identified as genotype D8 (figure 2). Genotyping data from the cluster from the Southern province was not available at the time of writing of the article. At the same time the authors also wish to highlight that only a few cases were genotyped during the investigation of the outbreak due to the inadequacy of the sample at the final stages of the
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investigations, lack of a good band in the Measles conventional genotyping PCR and financial restrictions. Moreover, genotyped samples comprised of the initial cases reported in each cluster.
In the current study, a higher percentage of positive patients were 22 years or above and presented within a short time period through different geographical areas around the country (table 1). Moreover, a majority of measles positive medical students and nursing students were in
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the same age group with a high risk of significant exposure to measles infected patients at the
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health care settings [22, 23, 24, 25].Furthermore, retrospective analysis revealed this age cohort received only one vaccine through NEIP, which implies waning of immunity due to single dose
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of measles vaccine.
Of the total positives in this study population, majority of the patients had high avidity measles
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IgG, where seven of them were negative for anti-measles IgM but positive for measles RNA rRT-PCR, which met the criteria to be categorized as a re-infection following primary exposure
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to natural infection or vaccination [13].Re-infections may also give rise to low and delayed antimeasles IgM with rapid anti-measles IgG response with high avidity due to the boosting of immunological memory [2,13,26,27]. Therefore, negative anti-measles IgM may not necessarily exclude measles infection in suspected patients especially if there is a strong epidemiological
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link. Finally, this study also emphasizes the importance of availability and testing with additional tests such as measles RNA real time PCR/ measles genotyping PCR and anti-measles IgG avidity in a reference laboratory to confirm measles outbreaks in situations like near elimination with high vaccine coverage.
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Conclusion The study revealed that, 19% of the suspected patients were positive for measles with 73% having re-infections. A majority who contracted measles was at or over 22 years, and had received only one dose of MCV in NEIP during the childhood. Measles genotype D8 was detected in two separate provinces suggesting the spread of virus within the country. Laboratory confirmation by additional testing such as measles RNA real time PCR, anti-measles IgG avidity
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early detection of outbreak and to implement effective control measures.
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and sequencing/genetic analysis is critical in the verge of measles elimination to facilitate the
Conflict of Interest
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A conflicting interest exists when professional judgement concerning a primary interest (such as patient’s welfare or the validity of research) may be influenced by a secondary interest (such as financial gain or
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personal rivalry). It may arise for the authors when they have financial interest that may influence their interpretation of their results or those of others. Examples of potential conflicts of interest include employment, consultancies, stock ownership, honoraria, paid expert testimony, patent
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applications/registrations, and grants or other funding.
Credit Author Statement
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Buddhini Samaraweera - Formal analysis, Methodology, Validation. Writing-original draft, review and editing Adhyana Mahanama – Formal analysis, Software, Validation, Writing – original draft, review and editing Almarz Z Ahamad – Data curation, Validation Gayan I Wimalaratne - Investigation Janaki Abeynayake – Conceptualization, Supervision, Methodology, Project administration, Validation, Reviewing and editing the original article
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Acknowledgements Authors would like to acknowledge all the staff members at the Department of Virology at Medical Research Institute for their immense support
Disclosure statement
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Authors would like to declare that there are no potential conflicts of interests
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4. World Health Organization (2012) Global measles and rubella strategic plan: 2012-
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2020. https://apps.who.int/iris/rest/bitstreams/53400/retrieve. Accessed on 30 May
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5. World Health Organization (2019) Measles. https://www.who.int/news-room/factsheets/detail/measles . Accessed on 02 June 2019 6. Niroshana Jathun Dahanayaka, Sithumini Pahalagamage, Ranjan Madushanka Ganegama, Prasanna Weerawansa and Suneth Buddhika Agampodi (2015) The 2013
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measles outbreak in Sri Lanka:experience from a rural district and implications for measles elimination goals. Infectious Diseases of Poverty 4:51
7. Epidemiology Unit (2018) Measles Elimination Strategic Plan. Weekly Epidemiology Report 45;33,1-2
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8. Epidemiology Unit (2012) Immunization Hand book. http://www.epid.gov.lk/web/images/stories/Immunization_Guide_2012.pdf Accessed on 26th May 2019 9. Plotkin SA, Orenstein WA (2008) Vaccine. Amsterdam, Saunders Elsevier 10. Mossong J, Muller CP (2003) Modelling measles re-emergence as a result of waning of immunity in vaccinated populations. Vaccine 21:4597–4603
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neutralizing antibodies and high-avidity measles IgG accurately identify measles reinfection cases. Clinical and Vaccine Immunology 23: 707–716
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12. EUROIMMN Avidity determination of antibodies against Measles Viruses (IgG) test
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instruction,EI2610-9601-1G.
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serologie/weitereparameter/english/measle accessed on 29th May 2019 13. Mercader S, Garcia P, Bellini WJ (2012) Measles virus IgG avidity assay for use in
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classification of measles vaccine failure in measles elimination settings. Clinical and Vaccine Immunology 19:1810–1817 14. Rosen JB, Rota JS, Hickman CJ et al (2014) Outbreak of measles among persons with prior evidence of immunity, New York City, 2011.Clinical Infectious Diseases58:1205–
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15. Hamkar R, Mahmoodi M, Nategh R et al (2006) Distinguishing between primary measles infection and vaccine failure reinfection by IgG avidity assay. Eastern Mediterranean Health Journal12:775–782
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16. Mosquera MM, de Ory F, Gallardo V et al (2005) Evaluation of diagnostic markers for measles virus infection in the context of an outbreak in Spain. Journal of Clinical Microbiology 43:5117–5121 17. Bankamp B, Byrd-Leotis LA, Lopareva ENet al (2013) Improving Molecular Tools for Global Surveillance of Measles Virus. Journal of Clinical Virology 58:176-182 18. Sequence analysis for Measles genotyping - Thai-NIH modified from Instruction of SNL-
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19. CDC protocols for the molecular epidemiology of measles virus and rubella virus;03/06/2012
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Antibodies and High-Avidity Measles IgG Accurately Identify Measles Re-infection Cases. Clinical and Vaccine Immunology 8:707-716
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21. Hübschen J.M, Bork S.M,. Brown K.E, Mankertz A, Santibanez S, Ben Mamou M, Mulders M.N, Muller C.P (2017) Challenges of measles and rubella laboratory diagnostic
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in the era of elimination. Clinical Microbiology And Infection 23:8, 511-515 22. Rota JS et al (2011) Two case studies of modified measles in vaccinated physicians exposed to primary measles cases: high risk of infection but low risk of transmission. Journal of Infectious Disease 204: 559-563
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23. Hahné SJM et al (2016) Measles outbreak among previously immunized health care workers, the Netherlands 2014. Journal of Infectious Diseases214:1980-1986
24. Durrheim DN et al (2014) Measles - The epidemiology of elimination. Vaccine 32: 68806883
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25. Ammari LK et al (1993) Secondary measles vaccine failure in healthcare workers exposed to infected patients. Infection Control and Hospital Epidemiology 14:81-86 26. Oliviera SA et al (2001) Atypical measles in a patient twice vaccinated against measles: transmission from as unvaccinated household contact. Vaccine 19:1093-1096 27. Oliveira SA et al (2003) Use of RT-PCR on oral fluid samples to assist the identification
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of ro -p re lP ur na Jo Figure 1: Measles laboratory testing flow chart at NMRL, MRI
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Genotype H1 – 2018 Sri Lanka
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Genotype D8 – 2017 & 2019 Sri Lanka
Figure 2: Phylogenetic analysis of genotype distribution in Sri Lanka 2017-2019
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Table 1: Socio-demographic, vaccination and epidemiological details of confirmed cases Variable
Frequency (percentage) 9 months – 27 years,
Age range, Mean, Mode (n=36)
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20 years, 22 years 03 (8%)
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< 1 year 1 – 4 years
02 (6%)
5 – 9 years
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00 (0)
10 – 14 years
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00 (0)
15 – 19 years
25 – 29 years
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Gender (n=37)
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20 – 24 years
01 (3%) 26 (72%) 04 (11%)
Female
25 (68%)
Male
12 (32%)
Distribution based on occupation (n=37) 10 (27%)
Nursing Students
19 (51%)
Priests
02 (6%)
Not known
06 (16%)
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Medical Students
Geographical distribution of cases (n=37)
22
Western
13 (35%)
Central
12 (32%)
Southern
10 (27%)
Other*
02 (6%)
Vaccination history (n=37) 04 (11%)
MCV not given
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Data not available
33 (89%)
No link to a positive case
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Link to a positive case out of country
31 (84%)
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Epidemiological history (n=37) Link to a positive case within country
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At least one dose of MCV given
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06 (16%)
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(*Sabaragamuwa Province– 01/37, North Western Province – 01/37)
Table 2: Laboratory parameters of Measles positive cases Parameter
Frequency (%)
Measles IgM &rRT-PCR(n=195) 20 (10.3% )
Measles rRT-PCR only positive
09 (4.6%)
Anti-measles IgM &rRT-PCR positive
08 (4.1%)
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Anti-measles IgM only positive
Sample breakdown - rRT-PCR positive patients (n=17) Nasopharyngeal/throat swab only
07 (41%)
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Serum only
08 (47%)
Nasopharyngeal/throat swab and serum both
02 (12%)
Measles IgG&IgG avidity 32 (86%)
High avidity (HA)IgG positive (n=37)
27 (73%)
Low avidity (LA) IgG positive (n=37)
02 (5%)
Equivocal results (n=37)
03 (8%)
HA IgG with positive IgM (n=37)
20 (54%)
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Anti-measles IgG positive (n=37)
07 (19%)
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HA IgG with positive rRT-PCR (n=37)
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Table 3: Geographical distribution of Measles genotypes in the present outbreak Frequency
Province
D8
04
Western
D8
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Genotype
02
Central*
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(*Includes a medical student from the cluster in the Western province as she was residing in the Central Province)
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Table 4: Measles genotypes circulating in the county during 2017-2019 Year
Genotype
2017
D8
2018
H1
2019
D8
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