Study finds Omicron BA.2 responsible for more but fewer infectious breakthroughs


In a recent study published on medRxiv* preprint server, researchers assessed the severity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron (B.1.1.529) infections between December 23, 2021 and February 20, 2022 in Qatar to understand how Omicron subvariants, vaccination, and prior infection status impacted these cases.

Study: Effects of BA.1/BA.2 subvariant, vaccination and prior infection on the infectivity of SARS-CoV-2 Omicron infections. Image Credit: Kuki Ladron of Guevara/Shutterstock

Qatar has an exceptionally young and diverse demographic, where only 9% of its residents are over the age of 50 and 89% are expats from over 150 other countries. Unfortunately, from December 19, 2021, Qatar experienced a resurgence of Coronavirus disease 2019 (COVID-19) cases due to Omicron which peaked in mid-January 2022. During this time, initially, more cases have been reported due to the BA subvariant of Omicron. 1, but within days the other BA.2 subvariant became dominant.

During Omicron’s pandemic wave, quantitative reverse-transcription polymerase chain reaction (RT-qPCR) testing, carried out on a large scale in Qatar, helped them diagnose 75% of COVID-19 infections. Each RT-qPCR test recorded the reason for the test, such as contact tracing, random testing campaigns, clinical symptoms, individual requests, routine health tests, pre-travel, port of entry or other. Almost all residents of Qatar have been fully vaccinated against COVID-19 during this time, and the government of Qatar has recorded all COVID-19 related information in its health system. Qatar’s federated SARS-CoV-2 databases even contained information on vaccinations performed elsewhere at the port of entry upon arrival in Qatar.

About the study

In the current cross-sectional study, the researchers used the real-time RT-qPCR cycle threshold (Cyou) value as an indicator of SARS-CoV-2 infectivity to study the effects of Omicron infections in all residents of Qatar who had SARS-CoV-2 infection confirmed by RT-qPCR on December 23, 2021 and on February 20, 2022.

The researchers obtained all demographic data from Qatar’s national COVID-19 databases, including reported clinical infections, vaccinations, RT-qPCR tests and related demographic details since the start of the pandemic.

They used the TaqPath COVID-19 Combo Kit for subvariant status – a SARS-CoV-2 infection with the Omicron BA.1 subvariant was shown as a case of gene target failure peak (S) (SGTF) and with the BA.2 the subvariant was represented as a non-SGTF case.

For each study participant, the researchers selected the first positive test confirmed by RT-qPCR. Later they derived Middle Cyou value (to be used as dependent variable) by averaging the Cyou values ​​of nucleocapsid (N), open reading frame 1ab (ORF1ab) and S genes.

Overall, they investigated the extent of spread of COVID-19 during the study period based on information about the subvariant causing the infection (BA.1 versus BA .2), type of vaccination (BNT162b2 or mRNA-1273), vaccination status (doses, time since vaccination), previous infection status, reason for RT-qPCR test, week of study period testing and demographic factors, including gender, age and nationality.

They used univariate linear regression analyzes to assess the association of each of these factors with Cyou assess. Multivariate linear regression analyzes accounting for all covariates estimated associated 95% confidence intervals (CI) and p-values. The researchers estimated the differences between BA.1 and BA.2 infections using standardized mean differences (SMDs).

Study results

The study’s analyzes included 156,202 people infected with Omicron. Recital Cyou values ​​as a measure of SARS-CoV-2 infectivity, the authors noted that with 3.53 fewer cycles, the BA.2 subvariant appeared to be significantly more infectious than the BA.1 subvariant.

Proportion of BA.1 (versus BA.2) Omicron infections in positive PCR tests assessed using the TaqPath COVID-19 Combo Kit during the study period.

Proportion of BA.1 (versus BA.2) Omicron infections in positive PCR tests assessed using the TaqPath COVID-19 Combo Kit during the study period.

VS you values ​​decreased as time since vaccination increased, a trend seen for the second and third doses of vaccination, reflecting the decline in vaccine effectiveness over time.

VS you values ​​were 0.86 cycles higher for people who received booster doses in the months before the RT-qPCR test than for unvaccinated people. Similarly, the 1.30 upper cycles C you values ​​among those with a history of SARS-CoV-2 infection compared to those without prior infection signified lower infectivity of the Omicron variant.

C descending you the values ​​(with age) reflected a decrease in the ability to eliminate SARS-CoV-2 with age. Although there were differences based on gender and nationality in C you value, these likely reflected the test-seeking behaviors of Qatar’s diverse population, with different socio-economic status and cases of undocumented infections.

The authors observed the lowest C you values ​​among those requesting the RT-PCR test due to COVID-19 symptoms and highest among those who took the test for travel-related purposes. Likewise, they observed the lowest C you values ​​when COVID-19 cases increased exponentially during the December 2021 Omicron wave and were highest after the peak of the wave. Later, C. you values ​​have declined, as only a small proportion of COVID-19 infections have remained recent.


Overall, the study demonstrated that compared to the Omicron BA.1 subvariant, the BA.2 subvariant was more contagious. It quickly spread in Qatar to cause more SARS-CoV-2 infections as evidenced by higher viral load and longer duration of COVID-19. However, as observed for other SARS-CoV-2 variants, natural immunity induced by prior infection and vaccine-induced immunity resulted in less infectious breakthrough due to Omicron.

*Important Notice

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

Journal reference:

  • Effects of BA.1/BA.2 subvariant, vaccination, and prior infection on the infectivity of SARS-CoV-2 infections Omicron, Suelen H. Qassim, Hiam Chemaitelly, Houssein Ayoub, Sawsan AlMukdad , Patrick Tang, Mohammad R. Hasan, HADI M. YASSINE, Hebah A. Al-Khatib, Maria K. Smatti, Hanan F. Abdul Rahim, Gheyath Nasrallah, Mohamed Ghaith Al-Kuwari, Abdullatif Al Khal, Peter Coyle, Anvar Hassan Kaleeckal, Riyazuddin Mohammad Shaik, Ali Nizar Latif, Einas Al-Kuwari, Andrew Jeremijenko, Adeel A Butt, Roberto Bertollini, Hamad Eid Al Romaihi, Mohamed H. Al-Thani, Laith J Abu-Raddad, medRxiv, 2022.03.02.22271771; doi:,

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