| Literature DB >> 35642439 |
Tina Uršič1, Rok Kogoj1, Jaka Šikonja1, Damijana Roškarič1, Monika Jevšnik Virant1, Petra Bogovič2, Miroslav Petrovec1.
Abstract
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.Entities:
Keywords: COVID-19; SARS-CoV-2 diagnostics; nasopharyngeal swab; real-time RT-PCR; saliva
Mesh:
Year: 2022 PMID: 35642439 PMCID: PMC9348014 DOI: 10.1002/jmv.27898
Source DB: PubMed Journal: J Med Virol ISSN: 0146-6615 Impact factor: 20.693
Descriptive characteristics of Delta and Omicron wave patients
| Study participant characteristics | Delta wave | Omicron wave |
|
|---|---|---|---|
| Female | 181/298 (60.7) | 169/326 (51.8) | 0.025 |
| Median age (years) | 35.5 | 29.0 | <0.001 |
| Known vaccination status | 240/298 (80.5) | 309/324 (95.4) | |
| Vaccinated | 107/240 (44.6) | 155/309 (50.2) | 0.729 |
| One dose | 20/240 (8.3) | 17/309 (5.5) | |
| Two doses | 87/240 (36.3) | 95/309 (30.7) | |
| Three doses | 0/240 (0.0) | 43/309 (13.9) |
Note: For the vaccination status, values are presented as participants reporting as vaccinated with one, two, or three doses/participants with at least one vaccination dose.
Comparison of symptoms experienced by patients from both waves
| Symptoms | Delta wave | Omicron wave |
|
|---|---|---|---|
| Symptom presence | 239/249 (96) | 289/312 (92.6) | 0.093 |
| Rhinorrhea | 172/249 (69.1) | 162/312 (51.9) | <0.001 |
| Cough | 173/249 (69.5) | 182/312 (58.3) | 0.007 |
| Sneezing | 112/249 (45) | 123/312 (39.4) | 0.185 |
| Sore throat | 103/249 (41.4) | 158/312 (50.6) | 0.029 |
| Headache | 161/249 (64.7) | 186/312 (59.6) | 0.222 |
| Fever | 101/249 (40.6) | 126/312 (40.4) | 0.966 |
| Hoarseness | 73/249 (29.3) | 73/312 (23.4) | 0.112 |
| Dyspnea | 38/249 (15.3) | 28/312 (9) | 0.022 |
| Chest pain | 39/249 (15.7) | 32/312 (10.3) | 0.056 |
| Other symptoms | 6/249 (2.4) | 7/312 (2.2) | 0.897 |
Note: Values are presented as participants reporting a symptom/participants with known symptoms (percent of participants with symptoms)
Other symptoms: Muscle and joint pain, nausea, vomiting, sinusitis, diarrhea, and loss of smell or taste.
Head‐to‐head comparison of rtRT‐PCR results obtained after testing NP swab and saliva samples from Delta and Omicron wave patients
| Delta wave | LightMix nasopharynx | ||
|---|---|---|---|
| POS | NEG | ||
| LightMix saliva | POS | 158 | 4 |
| NEG | 5 | 131 | |
| 163 | 135 | ||
|
| |||
| LightMix saliva | POS | 221 | 15 |
| NEG | 12 | 78 | |
| 233 | 93 | ||
Abbreviations: NEG, negative; NP, nasopharyngeal; POS, positive; rtRT‐PCR, real‐time reverse‐transcription polymerase chain reaction.
FIGURE 1Comparison of viral loads in nasopharyngeal (NP) swabs (blue) and saliva (S) samples (red) between Delta and Omicron waves. Non‐normalized (A) and normalized (B) viral loads are presented as log10 (SARS‐CoV‐2 RNA copies/µl) or as log10 (SARS‐CoV‐2 RNA copies/1000 cell copies), respectively. The box represents the first and third quartile, the line in the box, the median, the cross, the mean value, and the whiskers, the minimal and maximal value, excluding outliers that are presented as individual dots. Outliers are defined as values that deviate >1.5 times the interquartile range from the box limits. Statistical significance for individual comparisons is shown as p‐values. SARS‐CoV‐2, severe acute respiratory syndrome coronavirus 2.
FIGURE 2Viral loads at respective days after symptom onset in Delta (A and C) and Omicron (B and D) wave patients. Nasopharynx (nasopharyngeal, NP) samples are presented in blue and saliva (S) samples in red. Non‐normalized (A and B) and normalized (C and D) viral loads are presented as log10 (SARS‐CoV‐2 RNA copies/µl) or as log10 (SARS‐CoV‐2 RNA copies/1000 cell copies), respectively. The box represents the first and third quartile, the line in the box the median, the cross the mean value, and the whiskers the minimal and maximal value, excluding outliers that are presented as individual dots. Outliers are defined as values that deviate >1.5 times the interquartile range from the box limits. A trend line connects the means of viral loads across days of symptom duration. The number of participants on respective days after symptom onset included in calculations is presented below each graph. SARS‐CoV‐2, severe acute respiratory syndrome coronavirus 2.
Mean log RNA copies/µl in NPS and saliva samples according to the number of symptoms reported in the Delta and Omicron waves
| Wave | No. of symptoms | NP mean log RNA | S mean log RNA |
|
|
|---|---|---|---|---|---|
| Delta | 0–2 | 5.16 | 3.77 | 0.635 | 0.431 |
| 3–5 | 5.32 | 3.91 | |||
| ≥6 | 5.40 | 4.20 | |||
| Omicron | 0–2 | 4.40 | 3.13 | 0.052 | 0.081 |
| 3–5 | 4.69 | 3.32 | |||
| ≥6 | 4.93 | 3.60 |
Note: The Kruskal‐Wallis H test was used to compare viral loads across symptom groups individually for sample type and epidemic wave.
Abbreviations: NP, nasopharyngeal; NPS, nasopharyngeal swab; S, saliva.