Growth advantage of SARS-CoV-2 Omicron variant found to be partly due to shorter serial interval

In a recent study posted to the medRxiv* pre-print server, a team of researchers assessed how serial intervals of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron and Delta variants varied during the same time period in the Netherlands.

Epidemiological factors, such as immune evasion and higher intrinsic transmission potential, contribute to the faster relative growth rate of Omicron, as shown by previous studies. However, not many studies have investigated the role of serial interval in Omicron’s growth advantage.

A serial interval, measured as the difference between the day of symptom onset of a coronavirus disease 2019 (COVID-19) case and its infector, contributes significantly to the growth advantage of Omicron over the Delta variant.

About the study

In the Netherlands, symptom onset dates and postal codes of all the diagnosed COVID-19 cases are recorded in the national surveillance database, where, using  source and contact tracing, a record of a unique identifier of an infector of a COVID-19 case is also maintained, when available.

In the present study, the researchers used the national surveillance database to identify pairs of primary and secondary COVID-19 cases and included transmission pairs with a symptom onset date for the infector between December 13 and December 19, 2021.

The specimens were tested with the TaqPath COVID-19 reverse transcriptase-polymerase chain reaction (RT-PCR) kit that targeted three genes – spike (S), Orf1ab, and nucleocapsid (N).

S-gene target failure (SGTF), also referred to as S-dropout, identified the presence of a deletion in the S-gene associated with the Omicron variant, and non-SGTF predicted the Delta variant. The overall share of Omicron cases in test-positive cases was 9% during the study period.

In addition, the researchers included transmission pairs with a minimum and maximum serial interval of five and 15 days, respectively. Further, to infer incubation periods of the Omicron and the Delta variants, the researchers included cases for which SARS-CoV-2 exposure information was available. The cohort approach minimized the impact of data truncation and variations introduced by a variant on the final outcome.

Study findings

Of all the transmission pairs identified in the study, there were 220 SGTF (includes either an SGTF case or an SGTF infector) and 869 non-SGTF transmission pairs. Between 1 and 26 December 2021, 117 SGTF cases and 163 non-SGTF cases were reported, with median incubation periods of 3.4 days and four days, respectively.

The observed difference of 0.5 days corresponds to the difference in the incubation period of the two variants, supporting the hypothesis that the recent rapid growth of the Omicron variant was partially driven by their shortened serial interval as compared to Delta infections.

Among within-household transmission pairs (transmission pairs with a case and infector with the same postal code), the mean serial interval of 150 SGTF and 728 non-SGTF pairs were 3.4 days and 3.9 days, respectively, indicating a significantly shorter mean serial interval of the SGTF pairs.

During this time, the researchers excluded 11 pairs with opposing SGTF results and six pairs without postal code from the final analysis.

In the Netherlands, guidelines for the Omicron variant were stricter than for Delta cases until 23 December 2021. In addition, contact tracing guidelines for contacts outside the household were different for Omicron and Delta cases.

Omicron-infected individuals and their contacts were isolated and quarantined longer than the Delta variant cases. Most likely, the observed serial interval of the SGTF transmission pairs between households must have been due to Omicron and hence was shorter.

However, this does not reasonably explain a shorter serial interval and incubation period observed for SGTF transmission pairs within households. To completely generalize the observed differences, implemented control measures and other confounding factors, such as age and vaccination status of the case and its infector, are required.

A previous study performed in South Korea showed a mean serial interval of 2.8 days (range 1-7 days) for Omicron. Similarly, reports from Norway and Nebraska showed a median incubation period of 3 days for Omicron. The findings of the current study reported strikingly similar values of mean serial interval and median incubation period for the Omicron variant.

However, unlike the previous studies, the present study directly compared the mean serial interval and the median incubation period between the Omicron and Delta variant during the same time frame, further suggesting that the reported shorter values for Omicron did not vary significantly in different settings.

Conclusions

To summarize, Omicron’s short serial interval offers, along with immune evasion and higher transmissibility, are an explanation for the growth advantage of the Omicron over the Delta variant.

A short serial interval and incubation period of Omicron cases make timely contact tracing difficult, thus making it challenging to slow down or reduce the onward transmission of Omicron.

In addition, manifold interventions such as case finding, contact tracing, booster vaccination, and non-pharmaceutical interventions will be needed to control Omicron cases.

*Important notice

medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.