Faster transmission of SARS-CoV-2 Delta variant in households compared to Alpha
In a recent The Lancet Infectious Diseases study, researchers are assessing how quickly the Alpha and Delta variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are transmitted by estimating the generation time of the variants from transmission data in a household study .
To study: Generation time of SARS-CoV-2 alpha and delta variants: an epidemiological analysis. Image Credit: Studio MIA / Shutterstock.com
SARS-CoV-2, the virus responsible for coronavirus disease 2019 (COVID-19), has mutated into different variants throughout the current pandemic. Prior to the emergence of the currently dominant Omicron variant (B.1.1.529), the SARS-CoV-2 Delta variant (B.1.617.2) was the dominant strain circulating in the UK and most countries in the world. Despite the protection conferred by vaccination, the Delta variant had a high risk of severe disease compared to previous strains of SARS-CoV-2.
Defining virus transmissibility
The speed and strength of a variant is a measure of its transmissibility. Variant speed refers to how fast it grows at the population level. Additionally, the rate of change is measured by the exponential growth rate, which can be inferred from infection incidence data in a given population.
Comparatively, the strength of the variant reflects its transmissibility and is measured by its time-dependent reproduction number. The reproduction number, which reflects the infectivity of a virus, refers to the number of individuals each infected person is expected to infect in a given population.
The relationship between speed and strength of a variant is determined by generation time, which is the time between infection events in infector-infected pairs. Generation time is required in most modeling studies on inheritance and variant control. Thus, this parameter is rigorously used by epidemiologists to monitor the spread of viruses and assess the effectiveness of interventions based on new cases reported daily.
Taken together, an increased number of COVID-19 cases is attributable to high transmission of the virus, a shorter generation time, or a combination of these factors.
The ever-evolving nature of SARS-CoV-2 variants
Although scientists previously estimated the central average generation time of SARS-CoV-2 at 3.44-7.5 days, the data used in this study was collected at the start of the COVID-19 pandemic. Following the emergence of new variants of SARS-CoV-2, the characteristics of viral transmission are expected to change.
To this end, a study conducted when the Alpha variant was the dominant circulating strain indicated a shorter generation time between September 2020 and November 2020. The shorter the generation time, the faster the virus is transmitted. This generation time-to-date estimate is important for estimating the reproduction number, which is essential for epidemiological studies.
To date, the effect of different variants on the generation time of SARS-CoV-2 has not been compared. In order to acquire this information, analysis of datasets of infector-infected pairs is necessary, which is possible in household studies. In the current household study, the researchers aim to determine whether the generation time of the SARS-CoV-2 Delta variant is shorter than that of the Alpha variant in the UK
About the study
The researchers provided an epidemiological analysis using data from an ongoing prospective UK Health Security Agency (UKHSA) household study between February 2021 and September 2021. The dominant circulating strain changed from the Alpha variant to the Delta variant during the period this study was conducted. .
The researchers only recruited households that had a positive index case, which was confirmed by a polymerase chain reaction (PCR) test. Because the household study also included genomic sequencing of positive cases, the researchers were able to assess the generation times of individuals infected with the Alpha and Delta variant.
Using mathematical modeling, the researchers estimated the generation time of the Alpha and Delta variants. More specifically, the Markov Monte Carlo Chain (MCMC) was used to fit the transmission model to the data with the following assumptions:
- SARS-CoV-2 has an average incubation period distribution of 5.8 days
- Asymptomatic carriers are 35% infectious compared to symptomatic people with COVID-19
- Vaccinated people are less susceptible to COVID-19 than unvaccinated people
- Vaccination status does not alter an individual’s potential for contagiousness
- There is only one primary source of infection in each focus of transmission.
Several other parameters were estimated for each variant. These included the mean latency period, which is defined as the time between when the infection became infectious, the symptomatic infectious period, and overall transmissibility (βoh).
Especially, βoh represents the expected number of household transmissions caused by a single non-symptomatic individual infected with SARS-CoV-2 in an unvaccinated household. The global transmissibility parameter also assumes that after each transmission event, the newly infected individual is replaced by another susceptible individual.
Together, these parameters were used to calculate the intrinsic generation time distribution, household generation time distribution, and posterior estimates of the percent reduction in these quantities for SARS-CoV-2 Alpha and Delta variants.
During the study period, the researchers recruited a total of 227 households consisting of 559 participants. While the Alpha variant was detected in 131 households, which included 243 infections in 334 participants, between February 2021 and May 2021, the Delta variant was found in 96 households, which accounted for 174 infections in 225 participants, between May 2021 and August 2021.
Compared to the Alpha variant, the average intrinsic generation time was around 4.7 days for the Delta variant, which was shorter than the 5.5 days for the Alpha variant. Additionally, the Delta variant also had an average household build time of 3.2 days, which was 28% shorter than the Alpha variant at 4.5 days.
Domestic transmission of the Delta variant generally occurred earlier in SARS-CoV-2 infection compared to viral transmissions that occurred with the Alpha variant. Additionally, the Delta variant had an average household serial interval of 1.8 days, which was shorter than that of the Alpha variant at 3.5 days.
Variant type had a greater impact on household generation time compared to other factors such as age and vaccination status.
The estimated transmissibility of SARS-CoV-2 variants depends on the rate of viral transmission; therefore, the effectiveness of anti-SARS-CoV-2 interventions is also determined by this viral characteristic. Thus, estimates of generation time and reproduction number are essential for epidemiological analyses, especially for newly emerging viruses and strains of SARS-CoV-2.
In the current study, the researchers applied advanced mathematical modeling techniques to estimate the generation time of the delta and alpha variants of SARS-CoV-2 using transmission data from a household study conducted in UK. Taken together, the results of the current study support the higher transmissibility of the Delta variant within households compared to the Alpha variant.
- Hart, MS, Miller, E., Andrews, NJ, et al. (2022). Generation time of SARS-CoV-2 alpha and delta variants: an epidemiological analysis. The Lancet Infectious Diseases. doi:10.1016/S1473-3099(22)00001-9.