Efficacy comparison of nasopharyngeal swab and saliva samples used for detecting SARS-CoV-2 Delta and Omicron variants

Koronavirus, ki povzroča akutni respiratorni sindrom (SARS-CoV-2), se je decembra 2019 pojavil v kitajskem mestu Wuhan. Bolezen, ki jo virus povzroča, je svetovna zdravstvena organizacija poimenovala COVID-19. Virus se je hitro razširil po vsem svetu in močno spremenil naše vsakdanje življenje. Pandemija je močno pospešila razvoj novih diagnostičnih metod, saj je zgodnje odkritje okužbe s SARS CoV-2 bistvenega pomena za uspešen nadzor nad širjenjem virusa. Verižna reakcija s polimerazo v realnem času s predhodno reverzno transkripcijo trenutno velja za zlati standard v diagnostiki SARS-CoV-2. Vzorec izbire je že od začetka pandemije bris nosnega dela žrela. Zaradi pomanjkanja materialov ter neprijetnega odvzema brisa nosnega dela žrela se je pojavil interes iskanja alternativnih kužnin, kot je npr. slina. V okviru magistrskega dela smo primerjali testiranja brisov nosnega dela žrela in sline 624 preiskovancev, odvzetih med septembrom 2021 in februarjem 2022, za odkrivanje različic delta in omikron SARS-CoV-2. Ocenili smo razlike med virusnim bremenom v vzorcih, pridobljenih v posameznem valu okužbe. Poleg tega smo ugotavljali razlike v učinkovitosti metod molekularne diagnostike pri uporabi obeh vrst vzorcev, pri tem pa, v primerjavi s standardno, ovrednotili tudi novo molekularno diagnostično platformo. Dokazali smo, da povzroča genetska različica delta težji potek bolezni v primerjavi z različico omikron. Izkazalo se je, da imajo bolniki, okuženi z različico delta, višje virusno breme v obeh testiranih vzorcih. Hkrati je raziskava ovrgla hipotezo, da bi slina lahko nadomestila bris nosnega dela žrela kot kužnino izbire. Dokazali smo statistično značilno razliko v inhibiciji pomnoževanja nukleinskih kislin v vzorcih sline v primerjavi z vzorci brisov nosnega dela žrela. Pri ovrednotenju nove molekularne diagnostične platforme pa smo zaključili, da nova platforma ni primerna za odkrivanje genetske različice omikron.Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible and virulent human-infecting coronavirus that emerged in late December 2019 in Wuhan, China, causing a respiratory disease called coronavirus disease 2019 (COVID-19). SARS-CoV-2 has massively impacted global public health and caused widespread disruption to daily life. The pandemic has greatly accelerated the development of new diagnostic methods, as early detection of SARS-CoV-2 infection is essential for successful outbreak control. Real-time polymerase chain reaction with prior reverse transcription is currently considered the gold standard in SARS-CoV-2 diagnostics. Since the beginning of the pandemic nasopharyngeal swab has been the sample of choice. Due to the lack of materials and the inconvenience of nasopharyngeal swab collection, there has been a great interest in finding an alternative sample, such as saliva. We compared the usefulness of nasopharyngeal swab and saliva samples of 624 participants, collected between September 2021 and February 2022, for the detection of Delta and Omicron SARS-CoV-2 variants. The study aimed to assess if any differences among participants from both waves could be observed and if any difference in molecular diagnostic performance could be observed among the two sample types. We also evaluated a new molecular diagnostic platform. We demonstrated that the Delta variant of SARS-CoV-2 caused a more serious progress of an infection compared to the Omicron variant. Participants infected with the Delta variant were shown to have a higher viral load in both viral specimens. At the same time the research refuted the notion that a saliva sample could substitute for nasopharyngeal swab, since nasopharyngeal swab was shown to provide a better viral specimen. In saliva samples, we demonstrated a higher percentage of nucleic acid amplification inhibition, compared to nasopharyngeal swab, with the difference being statistically significant. During the evaluation of the new molecular diagnostic platform, we concluded that the new platform is not suitable for detecting the Omicron genetic variant

Performance of nasopharyngeal swab and saliva in detecting Delta and Omicron SARS-CoV-2 variants

A prospective cohort study was conducted during the Delta and Omicron severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) epidemic waves from paired nasopharyngeal swab (NPS or NP swab) and saliva samples taken from 624 participants. The study aimed to assess if any differences among participants from both waves could be observed and if any difference in molecular diagnostic performance could be observed among the two sample types. Samples were transported immediately to the laboratory to ensure the highest possible sample quality without any freezing and thawing steps before processing. Nucleic acids from saliva and NPS were prospectively extracted and SARS-CoV-2 was detected using a real-time reverse-transcription polymerase chain reaction. All observed results were statistically analyzed. Although the results obtained with NP and saliva agreed overall, higher viral loads were observed in NP swabs regardless of the day of specimen collection in both SARS-CoV-2 epidemic waves. No significant difference could be observed between the two epidemic waves characterized by Delta or Omicron SARS-CoV-2. To note, Delta infection resulted in higher viral loads both in NP and saliva and more symptoms, including rhinorrhea, cough, and dyspnea, whereas Omicron wave patients more frequently reported sore throat. An increase in the mean log RNA of SARS-CoV-2 was observed with the number of expressed symptoms in both waves, however, the difference was not significant. Data confirmed that results from saliva were concordant with those from NP swabs, although saliva proved to be a challenging sample with frequent inhibitions that required substantial retesting