Dataset Information

Tracking the Initial Diffusion of SARS-CoV-2 Omicron Variant in Italy by RT-PCR and Comparison with Alpha and Delta Variants Spreading.

ABSTRACT: The emergence of the Omicron SARS-CoV-2 variant caused public health concerns worldwide, raising the need for the improvement of rapid monitoring strategies. The present manuscript aimed at providing evidence of the utility of a diagnostic kit for the routine testing of SARS-CoV-2 infection as a cost-effective method for tracking the Omicron variant in Italy. The study was conducted on patients' naso-oropharyngeal-swab-derived RNA samples. These samples were subjected to RT-PCR using the TaqPath COVID-19 RT PCR CE IVD kit. Nonparametric testing and polynomial models fitting were used to compare the spreading of Alpha, Delta and Omicron variants. The samples of interest were correctly amplified and displayed the presence of S gene-target failure, suggesting that these patients carry the Omicron variant. The trend of diffusion was found to be significantly different and more rapid compared with that of the Alpha and Delta variants in our cohorts. Overall, these results highlight that the S gene target failure was a very useful tool for the immediate and inexpensive tracking of Omicron variant in the three weeks from the first detection. Thus, our approach could be used as a first-line screening to reduce the time and costs of monitoring strategies, facilitating the management of preventive and counteracting measures against COVID-19.

SUBMITTER: Caputo V

PROVIDER: S-EPMC8870788 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature

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Tracking the Initial Diffusion of SARS-CoV-2 Omicron Variant in Italy by RT-PCR and Comparison with Alpha and Delta Variants Spreading.

Caputo Valerio V Calvino Giulia G Strafella Claudia C Termine Andrea A Fabrizio Carlo C Trastulli Giulia G Ingrascì Arcangela A Peconi Cristina C Bardini Silvia S Rossini Angelo A Salvia Antonino A Borsellino Giovanna G Battistini Luca L Caltagirone Carlo C Cascella Raffaella R Giardina Emiliano E

Diagnostics (Basel, Switzerland) 20220211 2

The emergence of the Omicron SARS-CoV-2 variant caused public health concerns worldwide, raising the need for the improvement of rapid monitoring strategies. The present manuscript aimed at providing evidence of the utility of a diagnostic kit for the routine testing of SARS-CoV-2 infection as a cost-effective method for tracking the Omicron variant in Italy. The study was conducted on patients' naso-oropharyngeal-swab-derived RNA samples. These samples were subjected to RT-PCR using the TaqPath ...[more]

PMID: 35204558

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Project description:ObjectivesA number of studies have shown that the airborne transmission route could spread some viruses over a distance of 2 meters from an infected person. An epidemic model based only on respiratory droplets and close contact could not fully explain the regional differences in the spread of COVID-19 in Italy. On March 16th 2020, we presented a position paper proposing a research hypothesis concerning the association between higher mortality rates due to COVID-19 observed in Northern Italy and average concentrations of PM10 exceeding a daily limit of 50 µg/m3.MethodsTo monitor the spreading of COVID-19 in Italy from February 24th to March 13th (the date of the Italian lockdown), official daily data for PM10 levels were collected from all Italian provinces between February 9th and February 29th, taking into account the maximum lag period (14 days) between the infection and diagnosis. In addition to the number of exceedances of the daily limit value of PM10, we also considered population data and daily travelling information for each province.ResultsExceedance of the daily limit value of PM10 appears to be a significant predictor of infection in univariate analyses (p<0.001). Less polluted provinces had a median of 0.03 infections over 1000 residents, while the most polluted provinces showed a median of 0.26 cases. Thirty-nine out of 41 Northern Italian provinces resulted in the category with the highest PM10 levels, while 62 out of 66 Southern provinces presented low PM10 concentrations (p<0.001). In Milan, the average growth rate before the lockdown was significantly higher than in Rome (0.34 vs 0.27 per day, with a doubling time of 2.0 days vs 2.6, respectively), thus suggesting a basic reproductive number R0>6.0, comparable with the highest values estimated for China.ConclusionA significant association has been found between the geographical distribution of daily PM10 exceedances and the initial spreading of COVID-19 in the 110 Italian provinces.

Project description:IntroductionIn November 2021, the SARS-CoV-2 Omicron variant of concern has emerged and is currently dominating the COVID-19 pandemic over the world. Omicron displays a number of mutations, particularly in the spike protein, leading to specific characteristics including a higher potential for transmission. Although Omicron has caused a significant number of deaths worldwide, it generally induces less severe clinical signs compared to earlier variants. As its impact on blood platelets remains unknown, we investigated platelet behavior in severe patients infected with Omicron in comparison to Delta.MethodsClinical and biological characteristics of severe COVID-19 patients infected with the Omicron (n=9) or Delta (n=11) variants were analyzed. Using complementary methods such as flow cytometry, confocal imaging and electron microscopy, we examined platelet activation, responsiveness and phenotype, presence of virus in platelets and induction of selective autophagy. We also explored the direct effect of spike proteins from the Omicron or Delta variants on healthy platelet signaling.ResultsSevere Omicron variant infection resulted in platelet activation and partial desensitization, presence of the virus in platelets and selective autophagy response. The intraplatelet processing of Omicron viral cargo was different from Delta as evidenced by the distribution of spike protein-positive structures near the plasma membrane and the colocalization of spike and Rab7. Moreover, spike proteins from the Omicron or Delta variants alone activated signaling pathways in healthy platelets including phosphorylation of AKT, p38MAPK, LIMK and SPL76 with different kinetics.DiscussionAlthough SARS-CoV-2 Omicron has different biological characteristics compared to prior variants, it leads to platelet activation and desensitization as previously observed with the Delta variant. Omicron is also found in platelets from severe patients where it induces selective autophagy, but the mechanisms of intraplatelet processing of Omicron cargo, as part of the innate response, differs from Delta, suggesting that mutations on spike protein modify virus to platelet interactions.

Dataset Information

Tracking the Initial Diffusion of SARS-CoV-2 Omicron Variant in Italy by RT-PCR and Comparison with Alpha and Delta Variants Spreading.

Publications

Tracking the Initial Diffusion of SARS-CoV-2 Omicron Variant in Italy by RT-PCR and Comparison with Alpha and Delta Variants Spreading.

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