Rapid displacement of SARS-CoV-2 variants within Japan correlates with cycle threshold values on routine RT-PCR testing
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Abstract
Background
The rapid spread of SARS-CoV-2 worldwide has led to the emergence of new variants due to the presence of mutations that alter viral characteristics, but there have been few studies on trends in viral lineages in Japan, an island country. We hypothesized that changes in cycle threshold (Ct) values on reverse transcription polymerase chain reaction (RT-PCR) reflect the prevalent variants during a given period.
Methods
We performed next-generation sequencing of positive samples to identify the viral lineages in Japan in 2021 and compared variant prevalence with the average Ct values on routine RT-PCR using 4 primer sets.
Results
Based on 3 sequencing runs, the highly transmissible Alpha variant, which prevailed over other lineages, such as R.1, from April 2021, was dominated by the even stronger Delta variant between July and August 2021 in Japan. The decrease in our routine RT-PCR Ct values with 4 primer sets correlated with these fluctuations in lineage prevalence over time.
Conclusions
We confirmed that our RT-PCR protocol reflects the trends in SARS-CoV-2 variant prevalence over time regardless of sequence mutation. This may aid in the tracking of new variants in the population.
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SciScore for 10.1101/2022.04.13.22273855: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: All experimental protocols were approved by the ethics committee of Genesis Healthcare. Sex as a biological variable not detected. Randomization not detected. Blinding Samples were anonymized, and laboratory technicians and researchers were blinded to the identity of the patients. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources All experimental protocols were approved by the ethics committee of Genesis Healthcare. Genesis Healthcaresuggested: NoneResults from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the …SciScore for 10.1101/2022.04.13.22273855: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: All experimental protocols were approved by the ethics committee of Genesis Healthcare. Sex as a biological variable not detected. Randomization not detected. Blinding Samples were anonymized, and laboratory technicians and researchers were blinded to the identity of the patients. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources All experimental protocols were approved by the ethics committee of Genesis Healthcare. Genesis Healthcaresuggested: NoneResults from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Although our study has the limitations of symptom onset data being unavailable and the timing of sample collection varying throughout the course of infection, it suggested that a rapid decrease in Ct values in routine testing indicates the introduction of a new, more infective variant, whereas an increase may indicate its fading out from a population. The R.1 variant, which was reported to have potential escape mutations in the N-terminal domain (W152L) and spike protein (E484K) (Hirotsu and Omata, 2021), was recently re-detected in the US amidst the rampant spread of Delta (Cavanaugh et al., 2021). This variant was not detected in our samples after June, suggesting that variants can reemerge in different populations worldwide. Variants harboring E484K, L452R, or N501Y are of particular concern because they are related to escape from antibody neutralization (Cherian et al., 2021; Lucas et al., 2021). As such, even after vaccination or previous infection, if these variants are reintroduced to a population, they may become dominant again. As nearly 80% of the Japanese population has received two doses of the SARS-CoV-2 vaccine as of February 2022, it will be of interest to investigate how the presence of antibodies affects the average Ct values and transmissibility of known and new variants such as Omicron. Furthermore, as the third vaccine is just now being administered in Japan at present, it is important to identify mutations in highly transmissible strains in order to preve...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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