Morning SARS-CoV-2 Testing Yields Better Detection of Infection Due to Higher Viral Loads in Saliva and Nasal Swabs upon Waking

The ratio between SARS-CoV-2 RNA viral load and culturable viral titre differs depending on the stage of infection: a case study of household transmission in an adult male

Effective public health measures for communicable diseases rely on the ability to identify infectious individuals and prevent transmission from those individuals. For severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the presence of replication-competent virus in specimens from an individual is the gold standard for confirming infectiousness. However, viral culture from clinical specimens is difficult and infrequently performed. Instead, infectiousness may be inferred based on the abundance of viral RNA (or viral load) in a specimen, which is more easily assessed. For this reason, understanding the relationship between RNA viral load and infectious viral titre has important implications for public health strategy. In this case report, we quantified incident, longitudinal SARS-CoV-2 viral loads collected from saliva and nasal-swab specimens, and viral titre from nasal-swab specimens. We observed that the relationship between viral load and viral titre decreases by over five orders of magnitude throughout the course of the infection. Our work demonstrates the potential for infectious virus even in specimens with low viral loads collected during the early phases of infection.

Efficient and accurate detection of viral sequences at single-cell resolution reveals putative novel viruses perturbing host gene expression

There are an estimated 300,000 mammalian viruses from which infectious diseases in humans may arise. They inhabit human tissues such as the lungs, blood, and brain and often remain undetected. Efficient and accurate detection of viral infection is vital to understanding its impact on human health and to make accurate predictions to limit adverse effects, such as future epidemics. The increasing use of high-throughput sequencing methods in research, agriculture, and healthcare provides an opportunity for the cost-effective surveillance of viral diversity and investigation of virus-disease correlation. However, existing methods for identifying viruses in sequencing data rely on and are limited to reference genomes or cannot retain single-cell resolution through cell barcode tracking. We introduce a method that accurately and rapidly detects viral sequences in bulk and single-cell transcriptomics data based on highly conserved amino acid domains, which enables the detection of RNA viruses covering over 100,000 virus species. The analysis of viral presence and host gene expression in parallel at single-cell resolution allows for the characterization of host viromes and the identification of viral tropism and host responses. We applied our method to identify putative novel viruses in rhesus macaque PBMC data that display cell type specificity and whose presence correlates with altered host gene expression.

Comparison of SARS-CoV-2 RNA detection in different types of clinical specimens among suspected COVID-19 patients in Addis Ababa, Ethiopia

Although nasopharyngeal swabs (NPSs) are superior to saliva specimens, saliva can be used as an alternative specimen for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing. Moreover, studies have reported contradicting findings on whether SARS-CoV-2 can be detected in urine or not. Thus, we aimed to evaluate the diagnostic utility of NPSs, saliva and urine specimens in suspected COVID-19 patients. We conducted a cross-sectional study among a total of 604 specimens collected from 219 individuals suspected for COVID-19 from February to July 2022. We recruited participants from two COVID-19 isolation and treatment centers in Addis Ababa. We analyzed the specimens by real-time reverse transcriptase polymerase chain reaction (RT-PCR) with a Cobas 8800 automated system. The presence of SARS-CoV-2 in NPS, saliva, and urine samples was measured by cycle threshold (Ct) values. Descriptive statistics such as frequency, percent, and mean with standard deviation were used to summarize participants characteristics. We conducted chi-square test to compare RT‒PCR results of NPS, saliva and urine specimens. All data was analyzed by SPSS version 27, and the level of significance was set at a p value ≤ 0.05. Of the 219 participants, 126 (57.5%) were positive for SARS-CoV-2 either from NPS, saliva, urine or all specimens. The rate of SARS-CoV-2 detection was significantly higher in NPS (53.9%) than in saliva (35.2%; p = 0.001) and urine (9.0%; p = 0.001) specimens. The percentage of positive agreement between NPS and saliva was 92.2%, while negative agreement was 66.9%. The overall agreement between NPS and saliva was 75.8% (K = 0.53, p < 0.001). In addition, there was a significant correlation in Ct values of both ORF1ab and E genes between the paired NPS and saliva specimens. There was significant positive correlation between NPS and saliva specimens Ct values of both ORF1ab and E genes and days from onset of symptoms to specimen collection. SARS-CoV-2 was significantly detected in NPS than in saliva and urine specimens. Although NPS is better for SARS-CoV-2 detection, saliva specimen can be used as an alternative clinical specimen in resource-limited settings where access to swabs is limited. Both saliva and urine could be sources of viral transmission.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13337-024-00892-9.

SARS-CoV-2 Viral Load in the Nasopharynx at Time of First Infection Among Unvaccinated Individuals: A Secondary Cross-Protocol Analysis of 4 Randomized Trials

Importance

SARS-CoV-2 viral load (VL) in the nasopharynx is difficult to quantify and standardize across settings, but it may inform transmission potential and disease severity.

Objective

To characterize VL at COVID-19 diagnosis among previously uninfected and unvaccinated individuals by evaluating the association of demographic and clinical characteristics, viral variant, and trial with VL, as well as the ability of VL to predict severe disease.

Design, Setting, and Participants

This secondary cross-protocol analysis used individual-level data from placebo recipients from 4 harmonized, phase 3 COVID-19 vaccine efficacy trials sponsored by Moderna, AstraZeneca, Janssen, and Novavax. Participants were SARS-CoV-2 negative at baseline and acquired COVID-19 during the blinded phase of the trials. The setting included the US, Brazil, South Africa, Colombia, Argentina, Peru, Chile, and Mexico; start dates were July 27, 2020, to December 27, 2020; data cutoff dates were March 26, 2021, to July 30, 2021. Statistical analysis was performed from November 2022 to June 2023.

Main Outcomes and Measures

Linear regression was used to assess the association of demographic and clinical characteristics, viral variant, and trial with polymerase chain reaction-measured log10 VL in nasal and/or nasopharyngeal swabs taken at the time of COVID-19 diagnosis.

Results

Among 1667 participants studied (886 [53.1%] male; 995 [59.7%] enrolled in the US; mean [SD] age, 46.7 [14.7] years; 204 [12.2%] aged 65 years or older; 196 [11.8%] American Indian or Alaska Native, 150 [9%] Black or African American, 1112 [66.7%] White; 762 [45.7%] Hispanic or Latino), median (IQR) log10 VL at diagnosis was 6.18 (4.66-7.12) log10 copies/mL. Participant characteristics and viral variant explained only 5.9% of the variability in VL. The independent factor with the highest observed differences was trial: Janssen participants had 0.54 log10 copies/mL lower mean VL vs Moderna participants (95% CI, 0.20 to 0.87 log10 copies/mL lower). In the Janssen study, which captured the largest number of COVID-19 events and variants and used the most intensive post-COVID surveillance, neither VL at diagnosis nor averaged over days 1 to 28 post diagnosis was associated with COVID-19 severity.

Conclusions and Relevance

In this study of placebo recipients from 4 randomized phase 3 trials, high variability was observed in SARS-CoV-2 VL at the time of COVID-19 diagnosis, and only a fraction was explained by individual participant characteristics or viral variant. These results suggest challenges for future studies of interventions seeking to influence VL and elevates the importance of standardized methods for specimen collection and viral load quantitation.

Reduction of SARS-CoV-2 viral load in saliva after rinsing with mouthwashes containing cetylpyridinium chloride: a randomized clinical study

Background

Symptomatic patients with COVID-19 typically have a high SARS-CoV-2 viral load in their saliva. Procedures to reduce the viral load in their oral cavity are important for mitigating the viral transmission.

Methods

This randomized clinical trial investigated the impact of two mouthwashes (0.075% cetylpyridinium chloride plus 0.28% zinc lactate (CPC+Zn) (n = 32), and 0.075% cetylpyridinium chloride (CPC) (n = 31)) on the viral load of SARS-CoV-2 in saliva when compared to the distilled water negative control (n = 32). Saliva was collected before (T0) and after (5 min, T1; 30 min, T2; and 60 min, T3) the intervention. Viral load in saliva was measured by qRT-PCR assays. The data in both groups was normalized for T0 and Negative Control, resulting in fold change values.

Results

CPC+Zn oral solution reduced the viral load in saliva by 6.34-fold at T1, 3.6-fold at T2 and 1.9-fold at T3. Rinsing with the CPC mouthwash reduced the viral load in saliva by 2.5-fold at T1, 1.9-fold at T2 and 2.0-fold at T3.

Conclusion

CPC+Zn mouthwash or with the CPC mouthwash reduced the viral load in saliva of COVID-19 patients immediately after rinsing. These reductions extended up to 60 min.

The potential of saliva as an accessible and sensitive sample type for the detection of respiratory pathogens and host immunity

Despite its prominence in early scientific records, the usefulness of saliva as a respiratory specimen has been de-emphasised over the past century. However, due to its low cost and reliance on specific supply chains and the non-invasive nature of its collection, its benefits over swab-based specimens are again becoming increasingly recognised. These benefits were highlighted over the course of the COVID-19 pandemic, where saliva emerged as a more practical, clinically non-inferior sample type for the detection of SARS-CoV-2 and saw numerous saliva-based diagnostic tests approved for clinical use. Looking forward, as saliva uniquely contains both respiratory secretions and immunological components, it has potentially wide applications, ranging from clinical diagnostics to post-vaccine disease burden and immunity surveillance. This Personal View seeks to summarise the existing evidence for the use of saliva in detecting respiratory pathogens, beyond SARS-CoV-2, as well as detailing methodological factors that can influence sample quality and thus, clinical utility.

Extreme differences in SARS-CoV-2 viral loads among respiratory specimen types during presumed pre-infectious and infectious periods

SARS-CoV-2 viral-load measurements from a single-specimen type are used to establish diagnostic strategies, interpret clinical-trial results for vaccines and therapeutics, model viral transmission, and understand virus-host interactions. However, measurements from a single-specimen type are implicitly assumed to be representative of other specimen types. We quantified viral-load timecourses from individuals who began daily self-sampling of saliva, anterior-nares (nasal), and oropharyngeal (throat) swabs before or at the incidence of infection with the Omicron variant. Viral loads in different specimen types from the same person at the same timepoint exhibited extreme differences, up to 10⁹ copies/mL. These differences were not due to variation in sample self-collection, which was consistent. For most individuals, longitudinal viral-load timecourses in different specimen types did not correlate. Throat-swab and saliva viral loads began to rise as many as 7 days earlier than nasal-swab viral loads in most individuals, leading to very low clinical sensitivity of nasal swabs during the first days of infection. Individuals frequently exhibited presumably infectious viral loads in one specimen type while viral loads were low or undetectable in other specimen types. Therefore, defining an individual as infectious based on assessment of a single-specimen type underestimates the infectious period, and overestimates the ability of that specimen type to detect infectious individuals. For diagnostic COVID-19 testing, these three single-specimen types have low clinical sensitivity, whereas a combined throat-nasal swab, and assays with high analytical sensitivity, was inferred to have significantly better clinical sensitivity to detect presumed pre-infectious and infectious individuals.

An overview of the most important preanalytical factors influencing the clinical performance of SARS-CoV-2 antigen rapid diagnostic tests (Ag-RDTs)

Due to the many technical limitations of molecular biology, the possibility to sustain enormous volumes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostic testing relies strongly on the use of antigen rapid diagnostic tests (Ag-RDTs). Besides a limited analytical sensitivity, the manually intensive test procedures needed for performing these tests, very often performed by unskilled personnel or by the patients themselves, may contribute to considerably impair their diagnostic accuracy. We provide here an updated overview on the leading preanalytical drawbacks that may impair SARS-CoV-2 Ag-RDT accuracy, and which encompass lower diagnostic sensitivity in certain age groups, in asymptomatic subjects and those with a longer time from symptoms onset, in vaccine recipients, in individuals not appropriately trained to their usage, in those recently using oral or nasal virucidal agents, in oropharyngeal swabs and saliva, as well as in circumstances when instructions provided by the manufacturers are unclear, incomplete or scarcely readable and intelligible. Acknowledging these important preanalytical limitations will lead the way to a better, more clinically efficient and even safer use of this important technology, which represents an extremely valuable resource for management of the ongoing pandemic.