Epidemiologic characteristics of SARS-CoV-2 Omicron and Delta variant infection cases in Cantabria, Spain

By Pooja Toshniwal PahariaApr 12 2022Reviewed by Danielle Ellis, B.Sc.

In a recent study published in Emerging Infectious Diseases, researchers performed a comparative assessment of the key epidemiological characteristics such as secondary attack rates (SAR), transmission, serial interval, and incubation period of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections by the Omicron and Delta variants.

According to the Center for Disease Control and Prevention (CDC) data, 622 index cases and 455 secondary cases of Omicron infections and 1,420 close contacts were identified In December 2021 by contact tracing in the Cantabria region of Spain.

About the study

In the present study, researchers reported the key epidemiological characteristics such as the SAR, transmission, serial interval, and the incubation period of Omicron infections in Spain. They also compared these characteristics with that of the Delta infections.

A total of 63 samples obtained from real-time reverse transcription-polymerase chain reaction (RT-PCR)-diagnosed Omicron infections were subjected to single-nucleotide polymorphism (SNP) genotyping analysis that focused on the L452R and K417N mutations. Samples that were negative for L4523 and positive for K417N were considered Omicron infections and selected for further analysis.

The analysis was further validated by whole-genome sequencing. Genomic libraries were prepared and subsequently sequenced. The next-generation data were further assembled and analyzed, and the lineages were assigned using the Phylogenetic Assignment of Named Global Outbreak Lineages (PANGOLIN) software.

Data were obtained from the Contact Tracing Program of Cantabria on socio-demographic characteristics such as vaccination status (unvaccinated/fully vaccinated), age, absence or presence of symptoms, and the symptom onset date (SOD) and the diagnosis date (DD) for symptomatic and asymptomatic infections, respectively. Corresponding data were also obtained for 1,299 Delta infections (of 1,708 SARS-CoV-2 infections) in November 2021.

Close contacts (individuals present within a two-meter distance from the index case patient for >15 minutes) were identified two days prior to and ten days post index case SOD and were classified as social, household, and occupational based on the setting of SARS-CoV-2 transmission.

Global SAR was determined as the mean of secondary cases in close contact. The contact setting-based and variant-based SAR differences among Omicron and Delta infections for unvaccinated and vaccinated patients by Pearson X² analysis. The mean, median, interquartile range (IQR), and mean differences were calculated for the transmission period, incubation period, and serial intervals for both variants.

Only the symptomatic index cases were considered for determining the incubation, serial intervals, and transmission periods. The transmission period was determined as the period between the index case SOD and the date of the last contact with the close contacts who were secondarily infected.

Only the symptomatic secondary cases were considered for determining the serial intervals and incubation periods. The incubation period was determined as the period between the date of the last contact and the secondary case SOD. The serial interval was determined as the period between the index case SOD and secondary case SOD.

Results

A total of 12,587 and 2,201 close contacts and secondary cases, respectively, were identified, of which 356 and 1,642 secondary cases were by Omicron and Delta variants, respectively.

Global SARs for Omicron and Delta cases were 39% and 26%, respectively. This indicated an absolute increase of 13 points (9.9 to 16.1) in SAR by the Omicron variant. The SAR was higher in social settings for Omicron than Delta variants (30.5% versus 16.2%) and occupational settings (31% versus 10.5%), but not for household settings (49.4% versus 48%).

Among Delta infections, overall, the SARs were significantly higher for unvaccinated patients (7.8%) than for vaccinated patients. Their SARs for household and occupational settings were 9.9% and 9.5%, respectively. However, for Omicron infections, no significant differences were observed between unvaccinated and vaccinated patients for any of the contact settings.

The mean and median transmission period was shorter for the Omicron variant than the Delta variant viz. 0.5 versus 0.8 and zero-day versus one day, respectively. The mean difference between the two variants was significant (-0.3 days), whereas the IQR was equal. This indicates that Omicron has higher transmissibility than Delta.

The median incubation period was three days for the Omicron and Delta variants with no significant mean differences. However, Omicron had a shorted IQR. The mean serial interval of Omicron infections was substantially shorter than Delta infections (4.8 days versus 5.4 days). The corresponding median values were four days and five days, respectively. However, there were no significant differences among the unvaccinated and vaccinated patients for the transmission, incubation, or serial interval periods.

Conclusion

The study findings showed that Omicron is more transmissible than Delta in social and occupational settings with significantly higher global SAR (about 50%) and significantly lower serial interval (IQR 3 versus 5) in Spain. Additionally, vaccination did confer some protection against secondary SARS-CoV-2 infections. However, there was no significant benefit of vaccination on the duration of incubation, transmission, or serial interval of the Omicron and Delta variants for secondary infections.

Omicron infections may transmit during the early and asymptomatic stage of SARS-CoV-2 infection, when isolation, contact tracing, and testing are impossible as the individuals are unaware of the infection. Thus, preventive measures such as social distancing and restricting public gatherings are of utmost importance to curtail the extensive and rapid spread of Omicron.