Co-circulation of SARS-CoV-2 Alpha and Gamma variants in Italy, February and March 2021
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Abstract
Several SARS-CoV-2 variants of concern (VOC) have emerged through 2020 and 2021. There is need for tools to estimate the relative transmissibility of emerging variants of SARS-CoV-2 with respect to circulating strains.
Aim
We aimed to assess the prevalence of co-circulating VOC in Italy and estimate their relative transmissibility.
Methods
We conducted two genomic surveillance surveys on 18 February and 18 March 2021 across the whole Italian territory covering 3,243 clinical samples and developed a mathematical model that describes the dynamics of co-circulating strains.
Results
The Alpha variant was already dominant on 18 February in a majority of regions/autonomous provinces (national prevalence: 54%) and almost completely replaced historical lineages by 18 March (dominant across Italy, national prevalence: 86%). We found a substantial proportion of the Gamma variant on 18 February, almost exclusively in central Italy (prevalence: 19%), which remained similar on 18 March. Nationally, the mean relative transmissibility of Alpha ranged at 1.55–1.57 times the level of historical lineages (95% CrI: 1.45–1.66). The relative transmissibility of Gamma varied according to the assumed degree of cross-protection from infection with other lineages and ranged from 1.12 (95% CrI: 1.03–1.23) with complete immune evasion to 1.39 (95% CrI: 1.26–1.56) for complete cross-protection.
Conclusion
We assessed the relative advantage of competing viral strains, using a mathematical model assuming different degrees of cross-protection. We found substantial co-circulation of Alpha and Gamma in Italy. Gamma was not able to outcompete Alpha, probably because of its lower transmissibility.
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SciScore for 10.1101/2021.04.06.21254923: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis The sample size was calculated to have the statistical power to detect a prevalence of 1%, with 0,8% error within each macro-area, based on the number of cases notified on the day preceding each of the two surveys. Sex as a biological variable not detected. Table 2: Resources
No key resources detected.
Results 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:We acknowledge a number of …
SciScore for 10.1101/2021.04.06.21254923: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis The sample size was calculated to have the statistical power to detect a prevalence of 1%, with 0,8% error within each macro-area, based on the number of cases notified on the day preceding each of the two surveys. Sex as a biological variable not detected. Table 2: Resources
No key resources detected.
Results 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:We acknowledge a number of limitations for this study. The sample size was calculated to have the statistical power to detect different lineages at the macro-area level. As such, regional estimates of prevalence should be taken with caution due to the small number of sequenced samples. Samples were randomly selected for sequencing among cases diagnosed by the labs, but some degree of correlation between them (e.g., cases belonging to an over-represented cluster on that day) cannot be completely excluded, especially in regions with lower sample sizes. Due to the different laboratory methodology of one region in the second survey, those data were excluded from the computation of the national prevalence of the variants. Possible biases in the estimate are expected to be minimal, since cases from this region represented only about 1.5% of the total. For what concerns model estimates on transmissibility, we could not take into account possible differences across strains in the duration of viral shedding [28], age-specific susceptibility or transmissibility [29], the proportion of asymptomatic individuals and their relative transmissibility [29], or other major determinants of the transmission dynamics of SARS-CoV-2, due to the lack of available data on the variants. Similarly, we could not distinguish the potential lineage-specific impact of existing mitigation measures in Italy, nor factor in the potential impact of vaccinations. These factors will likely shape the outcome of the...
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.
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