A Binomial Model Approach: Comparing the R0 Values of SARS-CoV-2 rRT-PCR Data from Laboratories across Northern Cyprus

Northern Cyprus has implemented relatively strict measures in the battle against the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The measures were introduced at the beginning of the COVID-19pandemic, in order to prevent the spread of the disease. One of these measures was the use of two separate realtime reverse transcription polymerase chain reaction (rRT-PCR) tests for SARS-CoV-2 referred to as the doublescreening procedure, which was adopted following the re-opening of the sea, air and land borders for passengersafter the first lockdown. The rRT-PCR double screening procedure involved reporting a negative rRT-PCR testwhich was carried in 72 to 120 h before departure whilst presenting no known symptoms of the COVID-19and performing a second rRT-PCR test at the point of arrival. This study compares the results of SARS-CoV-2rRT-PCR tests performed on incoming flight passengers from the 1st July to 9th of September 2020 to NorthernCyprus. The rRT-PCR test results collected by the Near East University (NEU) DESAM COVID-19 laboratory werecompared with the rRT-PCR test results collected by the Ministry of Health and/or private COVID-19 laboratoriesin Northern Cyprus. This comparative study was conducted using binomial distribution. In addition, by applyingthe Susceptible-Exposed-Infected-Removed (SEIR) model to Northern Cyprus, overall basic reproduction number(R0) value of the COVID-19 was analysed for the same time period to act as a threshold for this comparison.In both the statistical and SEIR mathematical model, R0 was calculated. It was assumed that, the more similarthe R0 results of NEU DESAM COVID-19 laboratory and other laboratories were with the overall R0 value ofNorthern Cyprus, the more reliable the results would be. We calculated that the median R0 values of the NEUDESAM COVID-19 laboratory and other laboratories performing the SARS-CoV-2 rRT-PCR on air passengersduring the studied period to be 0.96 and 1.29, respectively, compared to Northern Cyprus median R0 value whichwas 0.99. The rRT-PCR screening results from the NEU DESAM COVID-19 laboratory were closely aligned withthe screening results of Northern Cyprus whereas the screening results reported by other laboratories were not in afit with the regional pattern. This study also aimed to point out the importance of the rRT-PCR screening procedure since asymptomatic positive SARS-CoV-2 cases entery to Northern Cyprus was inhibited and this prevented thespread of the disease within the population.

Molecular epidemiology of HIV-1 strains in the south-east and east of Turkey

Objective:To detect the subtype characterization and drug-resistant mutations in HIV-1 strains after the refugee movement from Syria to Turkey between 2011 and 2014 in south east border lines. Methods: A total of 65 patients were included in this study, of which 57(88%) patients were antiretroviral therapy-naive patients. HIV-1 RNA was detected and quantii ed by realtime PCR assay. HIV-1 subtypes and circulating recombinant forms(CRFs) were identii ed by phylogenetic analysis(neighbor-joining method), and drug-resistant mutations were analyzed.Results: Three major HIV groups were indicated. Two of these groups were located in subtype B. The other group showed heterogeneity. Subtype B(48/65, 73.8%), followed by CRFs(12/65, 18.5%) was the most common strain. Subtype of CRFs consisted of CRF01_AE(9/65, 13.8%) and CRF02_AG(3/65, 4.6%). Subtype C(1/65, 1.5%), sub-subtypes A1(2/65, 3.1%) and F1(2/65, 3.1%) were also detected with low prevalence. The rate of overall primary antiretroviral resistance was 4.9%(3/61). Drug-resistant rate for non-nucleoside reverse transcriptase inhibitors was 4.9%. The thymidine analogue mutation rate was 13.1%(8/61).Conclusions: HIV molecular epidemiology studies are necessary to determine transmission patterns and spread. Subtype B and CRF01_AE, CRF02_AG are the most prevalent strains in the south-east of Turkey. However, subtype C, sub-subtypes A1 and F1 are of low prevalence but persist in the south-east of Turkey. In the near future, changing of HIV epidemiology will be possible in Turkey due to migration movement in border lines and resistance testing will play an important role in HIV management.

Dynamic of HIV-1 Strains Isolated from Newly Diagnosed Antiretroviral Drug Naive Turkish Patients

OBJECTIVE:Human Immunodeficiency Virus(HIV)infection is still global health issue,and lack of vaccine furthers the devastating effect.The treatment regimen is challenged by the development of resistance,thus increase the mutation and dissemination of resistance genes across the globe.This work aims to assess the nature of HIV-1 subtypes and mutations from HIV-1 positive patients who are drug-inexperienced.METHODS:The analysis of 103 new positive cases of HIV-1 involved in the study.Drug-resistant mutations,HIV-1 subtypes and circulating recombinant forms(CRFs)were assessed as per World Health Organization(2009)list of monitoring drugresistant mutation.RESULTS:The results revealed that subtype B was dominant 58(56.3%),compared to non-subtype B 34(33%)and CRF 11(10.7%).The occurrence of HIV-1 drug resistance for Nucleotide reverse transcriptase inhibitors(NRTIs),Non-nucleotide reverse transcriptase inhibitors(NNRTIs),and Protease inhibitors(PIs)were 7.8%(8/103),22.3%(23/103)and 1%(1/103)respectively and the patients had the following primary antiretroviral drug resistance mutations to NRTI,3A62V(2.9%),2 M41L(1.9%),1 F77L(1%),1 K70KR(1%),and 1 T215S(1%).In the NNRTI,13 E138A(12.6%),3 E138G(2.9%),3 K103N(2.9%),2V179D(1.9),1 K103KN(1%)and 1K103T(1%)mutations were found.While in the PI drug,1 L24LI(1%)drug resistance mutations were found.CONCLUSION:Primary drug-resistant mutations in antiretroviral therapy(ART)naive subjects were found and the information in turn will contribute to the global data collection and treatment plan of HIV-1 patients.