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In this Journal, Christopher Kandel et al. analyzed the viral dynamics of the Omicron variant and found that vaccination has no impact on viral load, regardless of peak concentration and positive duration (
). However, as Christopher Kandel et al. discussed in the limitation section, they used self-collected swabs outcome, which could be easily affected by such factors as the not standardized operators or even the external environment (
Generation of False-Positive SARS-CoV-2 Antigen Results with Testing Conditions outside Manufacturer Recommendations: a Scientific Approach to Pandemic Misinformation.
Microbiol Spectr.2021 Oct 31; 9 (PubMed PMID: 34668722. Pubmed Central PMCID: PMC8528119. Epub 2021/10/21)e0068321
To address this concern, we designed a cohort study among contacts of Omicron BA.2.76 variants infections to describe the dynamics of the Omicron variant. Difference from self-collected swabs and self-retrieved, our study used contact data provided by eligible hospitals and public health laboratories according to Guidelines for Coronavirus Testing (second edition) (
). This not only could reduce the risk of contamination and decrease activity but also avoided the impact of operating and environmental factors as much as possible because all specimens were sampled, transferred, and tested by professionals. Pre-symptomatic viral dynamics were observed in this study because oropharyngeal and nasopharyngeal swabs were collected from each participant daily before onset or test positive.
From August 6 to August 19, 2022, a total of 15,730 contacts were introduced by 69 cases, of whom 61 were infected with the Omicron BA.2.76 variant before September 3, 2022 (Fig. 1A), and 1 infection was excluded because of unclear vaccination. Patients were identified and classified according to the Diagnosis and treatment plan for COVID-19 (
) and were described in Supplementary materials 1. The analytic population included 60 symptomatic COVID-19 cases (median age: 44 years [IQR: 28–52]); 32 (53%) were male, and none with immunocompromising or any common chronic medical conditions.
Fig. 1The Ct value distribution reflects viral dynamics across the outbreak of Omicron BA.2.76 of SARS-CoV-2. (A) Daily incidence of infections in the outbreak. (B) Observed Ct value of N gene of each infection. (C) Observed Ct value of ORF gene of each infection. (D) Fitting Ct value of N gene and ORF gene, respectively. (E) and (F) Fitting Ct value under varied vaccination status of N gene and ORF gene, respectively.
Among 60 COVID-19 symptomatic patients, 23 received 2 doses of inactivated vaccine (CoronaVac and COVILO) or 1 dose of the CanSino vaccine, and 27 further received the booster dose. Compared with unfully vaccinated patients (unvaccinated or received 1 dose inactivated vaccine patients), fully vaccinated and booster-vaccinated patients tended to be older (median age: 38 vs. 44 vs. 46 years). Still, the difference did not attain statistical significance (P = 0.357) (Table 1). Among 23 fully vaccinated patients, 22 (96%) received inactivated vaccine, and only 1 received the CanSino vaccine. Among 27 booster-vaccinated patients, 24 (89%) received inactivated vaccine, and 3 (11%) received the CanSino vaccine. All specimens collected from patients were tested by polymerase chain reaction (PCR) and recorded the expression of the N gene (Fig. 1B) and ORF gene (Fig. 1C) when positive test. For N gene expression, peak virus load was identified at 2–3 days after onset with the median of cycle threshold (Ct) value of 16–17, regardless of whether patients received the booster dose. This is consistent with the previous study that there is no difference in viral trajectories between fully vaccinated and booster-vaccinated patients (
). However, the median range between onset and negative test after receiving a booster dose was 8 days (IQR: 7–11 days), which was shorter than 10 days (IQR: 8–11 days) for fully vaccinated patients and 12 days (IQR: 10–13 days) for unfully vaccinated patients. ORF gene expression was normalized to that of the N gene.
Table 1Characteristics of symptomatic patients with COVID-19 by vaccination status.
No.(%)
Characteristic
Unfully vaccinated
Fully vaccinated
Booster dose
P-value
(N=10)
(N=23)
(N=27)
Age, median (Q1-Q3), year
38(27–53)
44(19–50)
46(32–53)
0.357KW
Gender
0.615Fish
Male
4(40.0)
12(52.2)
16(59.3)
Female
6(60.0)
11(47.8)
11(40.7)
Type of vaccine
0.850Fish
SinoVac
2(20.0)
8(34.8)
10(37.0)
SinoPharm
1(10.0)
6(26.1)
8(29.6)
SinoVac & SinoPharm
0(0.0)
8(34.8)
6(22.2)
CanSino
0(0.0)
1(4.3)
3(11.1)
(Missing)
7(70.0)
0(0.0)
0(0.0)
Range between last vaccine and onset, median (Q1-Q3), days
387(134–443)
355(344–374)
174(142–221)
<0.001KW
N gene
Peak cycle threshold, median (Q1-Q3)
17(15–17)
16(15–17)
16(15–17)
0.483KW
Day of the peak, median (Q1-Q3)
3(2–5)
2(2–5)
3(2–3)
0.611KW
Pre-symptomatic positivity
0.702Fish
No
9(90.0)
22(95.7)
24(88.9)
Yes
1(10.0)
1(4.3)
3(11.1)
Range between onset and negative, median (Q1-Q3), days
12(10–13)
10(8–11)
8(7–11)
0.167KW
ORF gene
Peak cycle threshold, median (Q1-Q3)
17(16–21)
17(15–19)
16(15–18)
0.438KW
Day of the peak, median (Q1-Q3)
3(2–5)
2(2–5)
3(2–3)
0.566KW
Pre-symptomatic positivity
0.818Fish
No
9(90.0)
22(95.7)
25(92.6)
Yes
1(10.0)
1(4.3)
2(7.4)
Range between onset and negative, median (Q1-Q3), days
In order to reduce individual variations and estimate the positive duration (Ct value < 30), B-spline basis functions (using the 4th-degree basis function) were selected to model the change of Ct value after infected (Table S1, Supplementary materials 3). In our model, ORF gene expression was slightly higher than N gene expression, with a longer positive duration (9.85 vs. 8.80 days) (Fig. 1D). Pre-symptomatic positive duration was 0.5 days and 0.15 days for N gene and ORF gene, respectively (Fig. 1D). For N gene expression, the positive duration after receiving booster dose was 9.55 days, which was slightly shorter than fully vaccinated (10.15 days) and unfully vaccinated (10.70 days) (Fig. 1E). And similar results were observed for ORF gene expression in Fig. 1F (mean duration: 8.65 vs. 9.00 vs. 9.40 days). This is consistent with what was previously described in Table 1, completed full vaccination and received booster reduces the duration of positivity, regardless of N gene or ORF gene expression.
Our study is limited by the insufficient sample size in the cohort. Specifically, patients who received the booster dose had higher viral loads may be accused of older and individual variability. In addition, differential vaccine types between fully vaccinated and booster patients would bias the analysis of viral dynamics.
Funding
This study was partly supported by the National Key Research and Development Program of China (2021YFC2301604), the Self-supporting Program of Guangzhou Laboratory (SRPG22-007), Medical and Health Guidance Project of Xiamen (3502Z20214ZD1297) and Guidance Project of Fujian Provincial Science & Technology Department (2019D014).
Ethical statement
This study was approved by the institutional ethics committee of the Xiamen Center for Disease Control and Prevention, Fujian, China. Written consent was obtained from patients or their guardians when samples were collected.
The funder of the study had no role in study design, data collection, data analysis, data interpretation, manuscript prepared and reviewed. The corresponding authors had final responsibility for the decision to submit for publication.
Declaration of Competing Interest
The authors declare no competing interests.
Acknowledgments
We thank the staffs of the Xiamen Center for Disease Control and Prevention, China, for accessing the various data sources. The opinions expressed are those of the authors and not necessarily the institutions to which they are affiliated.
Generation of False-Positive SARS-CoV-2 Antigen Results with Testing Conditions outside Manufacturer Recommendations: a Scientific Approach to Pandemic Misinformation.
Microbiol Spectr.2021 Oct 31; 9 (PubMed PMID: 34668722. Pubmed Central PMCID: PMC8528119. Epub 2021/10/21)e0068321
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