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Asian Pacific Journal of Tropical Medicine 2023年第1期16卷 33-38页

作者： Hewa Babarandage Chathurika Harshani Ruvini Tharuka Wijewickrama Gayan Wimalarathne Chrishan Jude S Jayamaha janaki i abeynayake Medical Research institute Colombo-08Sri Lanka

Objective:To analyze data on socio-demographic and clinical characteristics of SARS-CoV-2 infected population whose samples were received from Medical Research institute,Sri ***:Laboratory based retrospective study was done on patient samples which were tested positive for SARS-CoV-2 by National Reference Virology Laboratory at the Medical Research institute,Sri Lanka,from November,2020 to November,*** on sociodemographic characteristics and clinical presentation of 13126 patients were ***:The mean age of the study population was(36.0±7.2)years and the majority were men(64.0%).The highest number of positive cases were found in the 21-30 years-of-age *** distinct peaks were noted in the incidence of SARS-CoV-2 positive *** addition,42.5%of the positive samples tested positive(42.5%)were from Medical Officer of Health collection ***,60.6%(7951)of the infected subjects were asymptomatic whereas the remaining were *** highest percentage of symptomatic patients were observed in the 91-100 years-of-age group while the highest asymptomatic subjects were found in the 31-40 years-of-age *** percentage of asymptomatic children(65.3%)was significantly(Pigher than that of adults(43.4%).Conclusions:The findings of this study aid decision makers to focus on the vulnerable groups,and geographic and temporal distribution of patients in the public health strategies that aim at preventing the spread of the disease and reducinig its mortalities.

关键词： COViD-19 SARS-CoV-2 Socio-demographic Clinical

Laboratory response to an infant with suspected measles vaccine associated fever and rash in Sri Lanka

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infectious Medicine 2023年第1期2卷 57-62页

作者： Buddhini Samaraweera Malsha G.Thrimavithana Lakmini Gunathilake Prabath Gankanda Janitha Nanayakkara janaki i.abeynayake The Departement of Virology Teaching Hospital KarapitiyaGalleSri Lanka The Ministry of Heath ColomboSri Lanka The Department of Virology Medical Research InstituteColombo 08Sri Lanka

Background:Measles is a highly contagious *** Lanka(SL)has eliminated the measles in *** coun-try is at risk of importation of measles and there could be vaccine-associated measles like ***,it is important to investigate patients with fever,rash to differentiate the wild-type from vaccine-type exclud-ing other suspected pathogens to direct infection prevention and control *** objective is to describe the laboratory investigation procedure in an immunocompetent child,developed fever,rash following measles containing vaccine in post-measles eliminated period,***:This laboratory based investigation was carried out in National Measles Laboratory,*** and throat swab were received from a patient with fever,rash,cough and coryza developed at tenth day of receiving the measles containing live-attenuated *** were tested for measles,rubella,and other relevant pathogens according to the laboratory testing algorithm for an immunocompetent child with fever,rash and flu like ***:Measles vaccine type A,Edmonston-strain virus was detected after sequencing in throat swab and measles igM and igG were positive at sixth-week of *** addition,influenza A RNA was detected in throat swab at day-three with detectable parvoB19 igM in blood sample received at sixth-week of post-onset ***:Measles like illness of this immunocompetent child who received measles containing vaccine could be due to measles vaccine-type A or influenza *** a measles eliminated,resource-limited setting in SL,there should be a well-defined,testing algorithm to exclude prevalent possible pathogens according to epidemiological and clinical information.

关键词： Measles vaccine Vaccine-type virus Laboratory diagnosis Sequencing Measles elimination

Polio eradication surveillance in Sri Lanka,2019-2023

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Asian Pacific Journal of Tropical Medicine 2024年第6期17卷 268-272页

作者： M.A.Y.Fernando N.S.Madarasinghe C.Rangana N.Weerasinghe D.C.U.D.Weligamage J.i.abeynayake Department of Medical Microbiology and immunology Faculty of MedicineUniversity of ColomboSri Lanka Department of Virology Medical Research InstituteColombo 08Sri Lanka Medical Research institute Colombo 08Sri Lanka

Objective:To evaluate the polio laboratory surveillance carried out from January,2019 to May,2023 by the Polio Regional Reference Laboratory,Sri ***:This retrospective study analyzed all stool samples received under the acute flaccid paralysis(AFP)and immunodeficient vaccine-derived poliovirus(VDPV)surveillance at Polio Regional Reference Laboratory,Sri Lanka from January,2019 to May,*** results of the testing methodologies were extracted from the laboratory data system,i.e.,poliovirus virus isolation,intra-typic differentiation/VDPV real time reverse transcriptase polymerase chain reaction(iTD/VDPV rRTPCR)and sequencing,along with the data on timing of reporting results,stool adequacy and *** was analyzed using descriptive ***:A total of 2141 stool samples from 1644 cases were received for AFP surveillance from Sri Lanka(93.61%),Maldives(1.52%),and immunodeficient VDPV(4.86%)*** polioviruses(19/1644,1.15%)and non-polio enteroviruses(73/1644,4.44%)were isolated,while Sabin-like 3 virus was detected in majority(12/19,63.15%)among the poliovirus *** polioviruses or circulating VDPVs were not detected among the *** all years of the study,the non-polio AFP detection rate was>1/100000 in children aged less than 15 years,whereas stool adequacy rate was>80%.All results were reported within 14 days of receipt,ensuring timely reporting as per global ***:The Polio Regional Reference Laboratory,Sri Lanka plays a vital role in maintaining the polio-free status in the country through its robust laboratory surveillance,while adhering to the surveillance ***-detection of wild polioviruses and circulating VDPV during the study period reinforces the polio-free status in the country.

关键词： Poliovirus Polio laboratory surveillance Regional reference laboratory Polio eradication

Surveillance of emerging SARS-CoV-2 variants by nanopore technology-based genome sequencing

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Asian Pacific Journal of Tropical Medicine 2023年第7期16卷 313-320页

作者： J.i.abeynayake G.P.Chathuranga M.A.Y.Fernando M.K.Sahoo Department of Virology Medical Research InstituteP.O.Box:527Baseline RoadColombo 08Sri Lanka Department of Pathology Stanford University School of MedicinePalo AltoCaliforniaUnited States of America

Objective:To surveill emerging variants by nanopore technology-based genome sequencing in different COViD-19 waves in Sri Lanka and to examine the association with the sample characteristics,and vaccination ***:The study analyzed 207 RNA positive swab samples received to sequence laboratory during different *** N gene cut-off threshold of less than 30 was considered as the major inclusion *** RNA was extracted,and elutes were subjected to nanopore *** the sequencing data were uploaded in the publicly accessible database,***:The Omicron,Delta and Alpha variants accounted for 58%,22%and 4%of the variants throughout the *** than 1%were Kappa variant and 16%of the study samples remained *** variant was circulated among all age groups and in all the *** value and variants assigned percentage was 100%in Ct values of 10-15 while only 45%assigned Ct value over ***:The present study examined the emergence,prevalence,and distribution of SARS-CoV-2 variants locally and has shown that nanopore technology-based genome sequencing enables whole genome sequencing in a low resource setting country.

关键词： Emerging SARS-CoV-2 variants Laboratory surveillance Nanopore technology Genome sequencing Bioinformatics analysis and phylogeny Sociodemographic and sample cutoff(Ct)threshold Global sharing of genomic data/GiSAiD

Evaluation of the diagnostic performance of a commercial molecular assay for the screening of suspected monkeypox cases in Sri Lanka

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infectious Medicine 2023年第2期2卷 136-142页

作者： H.B.C.Harshani G.A.Liyanage D.V.R.G.Ruwan U.K.i.U.Samaraweera J.i.abeynayake Medical Research institute Colombo 08Sri Lanka

Background:The main objective of the present study was to compare the diagnostic performance of the commercial LightMix Modular Monkeypox Virus(MPXV)qPCR(TiB Molbiol,Germany)assay with the in-house non-variola orthopox/monkeypox generic real-time PCR assay(iCMR-NiV,Pune)for the screening of(MPXV)cases at Medical Research institute(MRi)in Sri ***,clinical and sociodemographic data of suspected/confirmed cases received at MRi for the MPXV screening were also ***:The diagnostic performance of the commercial LightMix Modular MPXV qPCR assay with the in-house nonvariola orthopox/monkeypox generic real-time PCR assay for the screening of suspected MXPV cases was evaluated using standard methods with minor ***-demographic and clinical profiles of suspected and confirmed MPXV cases were also ***:The commercial LightMix Modular MPXV assay was able to detect MPXV with 100%sensitivity and specificity with non-variola orthopox/monkeypox generic rtPCR *** the period of study,from the total of 25 samples tested,only 2 were MPXV-positive(males).The most common symptoms of suspected MPXV cases were lesions or rashes(92%).Conclusions:With the continually increasing number of cases,access to MPXV testing should be made more widely *** commercial LightMix Modular MPXV(TiB Molbiol)qPCR assay offers comparable performance to the non-variola orthopox/monkeypox generic real time PCR assay for MPXV detection during the present outbreak.

关键词： Orthopoxvirus Monkeypox virus Real-time PCR assays Patient screening