Molecular characterization, phylogenetic and variation analyses of SARS-CoV-2 strains in Turkey.

Aims: We present the sequence and single-nucleotide polymorphism (SNP) analysis for 47 complete genomes for SARS-CoV-2 isolates on Turkish patients. Methods: The Illumina MiSeq platform was used for sequencing the libraries. The SNPs were detected by using Genome Analysis Toolkit - HaplotypeCaller v.3.8.0 and were inspected on GenomeBrowse v2.1.2. Results: All viral genome sequences of our isolates were located in lineage B under the different clusters, such as B.1 (n = 3), B.1.1 (n = 28) and B.1.9 (n = 16). According to the Global Initiative on Sharing All Influenza Data nomenclature, all of our complete genomes were placed in G, GR and GH clades. In our study, 549 total and 53 unique SNPs were detected. Conclusion: The results indicate that the SARS-CoV-2 sequences of our isolates have great similarity with all Turkish and European sequences.

Prevalence of COVID-19 in 10,000 samples from 7853 patients in Eastern Turkey by positive real-time PCR.

Aim: COVID-19, caused by SARS-CoV-2, started in December 2019 and has spread across the world. Materials & methods: We analyzed real-time PCR results of 10,000 samples from 2 April to 30 May 2020 in three neighbor cities located in the East of Turkey. The final study population was 7853 cases, after excluding screening tests. Results: Real-time PCR was performed to detect the SARS-CoV-2-specific RNA-dependent-RNA-polymerase gene fragment. The number of total positive samples out of 7853 were 487; however, the number of nonrepeating positive patient was 373 (4.8%). Cough and fever were the most common symptoms in positive cases. Conclusion: Epidemiologic studies should be performed about the prevalence of SARS-CoV-2 infection to better understand the effect of the virus across the world.

Saliva samples for detection of SARS-CoV-2 in mildly symptomatic and asymptomatic patients.

BACKGROUND: The ongoing coronavirus disease 2019 (Covid-19) pandemic has been rapidly spreading throughout the world with confirmed case numbers already exceeding 75 million. Although nasopharyngeal swabs are the most commonly utilized samples for based severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA detection, collecting these specimens requires healthcare workers and necessitates the use of personal protective equipment as it presents a nosocomial transmission risk. We aimed to assess the diagnostic value of saliva samples in mildly symptomatic and asymptomatic patients with confirmed Covid-19. METHODS: We performed a cohort study to validate the use of saliva for SARS-CoV-2 detection in mildly symptomatic and asymptomatic patients with a confirmed diagnosis of Covid-19. Saliva samples of the patients were analyzed by reverse-transcriptase polymerase chain reaction (RT-PCR). RESULTS: In May 2020, 28 asymptomatic and 25 mildly symptomatic patients were enrolled in the study. The median age was 37 years (range 4-70). None of the patients had a fever on presentation. Among 53 patients with SARS-CoV-2 detected in the nasopharyngeal sample, the real-time RT-PCR was positive in the saliva specimens in 48 (90.56%) patients. The mean cycle threshold (CT) values for nasopharyngeal and saliva specimens (27.80 ± 3.44 and 30.64 ± 2.83, respectively) were significantly correlated between the two sample types (p = .016). The mean CT values of nasopharyngeal and saliva samples in mildly symptomatic and asymptomatic patients (27.18 ± 3.53 and 30.24 ± 3.29 vs. 28.36 ± 3.31 and 30.98 ± 2.39, respectively) were not significantly different (p = .236 and p = .733, respectively). CONCLUSIONS: Saliva specimens can be considered as a reliable and less resource-intensive alternative to nasopharyngeal specimens for screening asymptomatic SARS-CoV-2 infections.