Omicron Wave SARS-CoV-2 Diagnosis: Evaluation of Saliva, Anterior Nasal, and Nasopharyngeal Swab Samples

Abstract

Diagnostic testing for SARS-CoV-2 is an essential component of the global strategy for the prevention and control of COVID-19. Since the beginning of the pandemic, numerous studies have evaluated the diagnostic sensitivity of different respiratory and oral specimens for SARS-CoV-2 detection.

Direct comparison of clinical diagnostic sensitivity of saliva from buccal swabs versus combined oro-/nasopharyngeal swabs in the detection of SARS-CoV-2 B.1.1.529 Omicron

“…In this study, we observed reduced clinical diagnostic sensitivity of saliva collected by buccal swabs in comparison to matched combined oro-/nasopharyngeal swabs in the detection of Omicron (BA.1 and BA.2). Serval studies on the sensitivity of saliva versus respiratory tract specimens for the detection of SARS-CoV-2, including Omicron, have been conducted, leading to mixed and in parts contradictory results [5][6][7][8][11][12][13]. In this study, samples were collected from hospitalized, symptomatic individuals who had previously been confirmed to be SARS-CoV-2 positive, resulting in sample collection at median six days after initial symptom onset.…”

“…In November 2021, a new SARS-CoV-2 variant B.1.1.529 (Omicron) emerged and spread rapidly around the globe [4]. Several studies have suggested an improved sensitivity of saliva over upper respiratory tract specimens in the detection of Omicron and other SARS-CoV-2 variants by real-time PCR [5][6][7][8]. Saliva could offer an appealing alternative to oro-and/or nasopharyngeal swabs as sample collection is considered less invasive and could potentially be easily performed by untrained caretakers and patients themselves [9].…”

The emergence of SARS-CoV-2 lineages and associated antibody responses among asymptomatic individuals in a large university community

“…Since then CoV2 has continued to evolve, there now being additional Omicron variants (BA.4, BA.5, BA.2.12.1, BA.2.75, XBB) and "Scrabble" subvariants (BQ.1 and BQ1.1) with Spike protein sequences that further desensitize the virus to in vitro neutralization by many (but not all) monoclonal therapies (109)(110)(111)(112), as well as convalescent plasma (113). Since Omicron has a higher tropism for the nasopharyngeal and oral cavities than that of pre-Omicron lineages (39)(40)(41)(42)(43), saliva antibodies may be more important inhibitors of Omicron transmission than plasma or lower airway antibodies, and saliva-the collection of which is far easier than blood-may be more suitable for rapid determination of whether someone has neutralizing capacity against future CoV2 variants that have yet to emerge.…”

“…The rapidity with which Omicron took over was observed in other university settings which, like ours, were highly vaccinated at the time ( 107 ). Compared to infections caused by the Delta lineage, those by Omicron tend to cause less severe disease ( 108 ), which may be due in whole or part to its being enriched in upper airways (including the oral cavity) as opposed to the lower airways ( 39-43 ). Omicron variants BA.1 and BA.2 were the last lineages detected in our university community before our testing program ended in May 2022.…”

“…This is especially true of asymptomatic individuals who are PCR positive (PCR POS ), as they are estimated to account for 50-65% of all transmission (36,37). Here, we describe the relationships between COVID incidence, CoV2 lineage, viral load, CoV2-specific Ig responses (IgM, IgA & IgG) and inhibitory capacity in the saliva of asymptomatic PCR POS individuals, as the oral cavity and saliva-in addition to being readily accessible-are important sites of CoV2 infection and transmission (38) (especially newer Omicron variants (39)(40)(41)(42)(43)). CoV2-specific Ig responses were similarly assessed in PCR NEG individuals with a history of CoV2 infection and/or COVID vaccination with pre-Omicron vaccines.…”