Genomic Diversity of the SARS-CoV-2 in Turkey and the Impact of Virus Genome Mutations on Clinical Outcomes

COVID-19 is a viral respiratory disease caused by SARS-CoV-2 infection. Global efforts of genomic surveillance of the virus give chance to track the spread of the pandemic. Global emergence of some viral mutations called attention and various studies have been suggested about increased infectivity of the virus. Herein, we sequenced viral genomes isolated from 184 patients in Istanbul and analyzed clinical metadata for the investigation of any viral mutation which affects the disease course of the host. We did not detect any viral mutations affecting the disease outcome in our cohort. Besides, we observed intra-host mutations in 76% of the isolates. Insertion/deletion and stop-gain mutations are also significantly less common among intra-host variants compared to consensus viral genome mutations. Longitudinal genomic surveillance is essential for timely detection of any lineages that might affect clinical outcome, the performance of diagnostic assays, or even the immunological escape of the virus.

Does sampling saliva increase detection of SARS-CoV-2 by RT-PCR? Comparing saliva with oro-nasopharyngeal swabs

The gold standard method in the diagnosis of SARS-CoV-2 infection is the detection of viral RNA in nasopharyngeal sample by RT-PCR. Recently, saliva samples has been suggested as an alternative due to being fast, reliable and non-invasive, rather than nasopharyngeal samples. We compared RT-PCR results in nasopharyngeal, oro-nasopharyngeal and saliva samples of COVID-19 patients. 98 of 200 patients were positive in RT-PCR analysis performed before the hospitalization. In day 0, at least one sample was positive in 67% of 98 patients. Positivity rate was 83% for both oro-nasopharyngeal and nasopharyngeal samples, while it was 63% for saliva samples (p<0.001). On day 5, RT-PCR was performed in 59 patients, 34% had at least one positive result. The positivity rate was 55% for saliva and nasopharyngeal samples, while it was 60% for oro-nasopharyngeal samples. Our study shows that the sampling saliva does not increase the sensitivity of RT-PCR tests at early stages of infection. However, on 5th day, viral RNA detection rates in saliva were similar to nasopharyngeal and oro-nasopharyngeal samples. In conclusion, we suggest that, in patients receiving treatment, virus presence in saliva, in addition to the standard samples, is important to determine the isolation period and to control the transmission.

COVID-19 PCR Test Performance For Samples Stored At Ambient Temperature

BackgroundThe new type of Coronavirus infection had become a pandemic in a very short period since it was first seen in Wuhan. The outbreak had a negative impact on all health care systems throughout the world and overwhelmed the diagnostic laboratories as well. During the pandemic, handling patient specimens in accordance with the universal guidelines was troublesome as WHO, CDC and ECDC required cold chain compliance during transporting and storing the swap samples. Materials and methodsIn this study, we tested diagnostic performance of RT-PCR on 30 swab samples stored at ambient temperature and compared them with the samples stored at +4{degrees}C. ResultsOur results revealed that all the samples stored at ambient temperature remain PCR positive for at least five days. We did not see any false negativity. ConclusionIn conclusion, we report that transferring and storing of nasopharyngeal/oropharyngeal samples at ambient temperature could be possible in the resource-limited conditions like pandemic.