Study suggests increased vaccine breakthrough for SARS-CoV-2 Omicron variant in Houston, Texas

A recent study by US researchers reveals early signals of substantially increased vaccine breakthrough for the Omicron variant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Houston, Texas; however, lower disease severity and decreased hospitalization rates were also noted. The study is currently available on medRxiv* preprint server while awaiting peer review.

Study: Early signals of significantly increased vaccine breakthrough, decreased hospitalization rates, and less severe disease in patients with COVID-19 caused by the Omicron variant of SARS-CoV-2 in Houston, Texas. Image Credit: WildMedia/Shutterstock

Background

Since the start of the coronavirus disease 2019 (COVID-19) pandemic, two notable SARS-CoV-2 variants of concern have caused two distinct disease surges in the United States, Europe, Southeast Asia, and elsewhere – Alpha (B.1.1.7) and Delta (B.1.617.2) variants.

As they have disrupted many societies and remodeled human behavior, it was understandable that the rise of the Omicron variant (B.1.1.529) brought many concerns worldwide. There were many question marks regarding its epidemiology and clinical characteristics.

When the pandemic started, the Houston Methodist healthcare system in the US introduced an extensively integrated population genomics project to sequence all SARS-CoV-2 samples from COVID-patients cared for at their facilities.

This was possible due to a very large diagnostic laboratory serving the entire system but adjacent to a research institute with large capacity and comprehensive expertise in population genomics. Consequently, this is one of the reasons why previous waves of SARS-CoV-2 were so meticulously described in Houston.

Now, a research team led by experts from the Houston Methodist Research Institute and Houston Methodist Hospital in Texas decided to use this rich data source to fill very important knowledge gaps with true global relevance.

Methodological approach

The overall study was based on a detailed genome sequence analysis of 862 Omicron samples that have been taken from geographically, ethnically, and socioeconomically diverse patients presenting with symptoms/signs consistent with COVID-19.

Multiple testing platforms have been used on material obtained from nasopharyngeal swabs, oropharyngeal or nasal swabs, sputum or bronchoalveolar lavage fluid. Patient metadata was obtained from electronic medical records using standard informatics methods.

Furthermore, a vaccination breakthrough case has been defined as a sample positive on reverse transcription-polymerase chain reaction (RT-PCR) – obtained from a patient more than fourteen days after full mRNA vaccination schedule (either second dose or booster).

From the initial identification of SARS-CoV-2 Omicron strain in the study population, only three weeks were enough to recognize it as a cause of 90% of all new COVID-19 cases, with a calculated case doubling time of 2.2 days.

In comparison to individuals infected with either Alpha or Delta variants, Omicron patients were substantially younger and presented with higher vaccine breakthrough rates; nonetheless, Omicron patients had lower chances for hospitalization with a lower need for respiratory support and a shorter length of hospital stay, which is in line with decreased disease severity.

Of course, certain study limitations have to be highlighted, especially a small number of study subjects and underrepresenting certain demographic groups (most notably children and homeless individuals). On the other hand, genome sequencing endeavors have been continuously pursued in a diverse Houston Methodist patient population for almost two years.

Importance

These findings are quite consistent with the data reported from the United Kingdom, South Africa, and Canada and different animal infection model data, which points towards the conclusion that Omicron can result in less severe disease in hamsters and mice.

In the aggregate, our data add critical new information to features of Omicron genomic epidemiology and patient characteristics in the US,” explain the study authors of this paper.

Further, the present study highlights the importance of analyzing SARS-CoV-2 genome data integrated with patient metadata and stresses the need to continue to do this in near-real time as the Omicron surge continues, the virus evolves, and new variants with potentially altered fitness and biomedically relevant phenotypes are generated”, they add.

Hence, analyses akin to this one are also very important in the context of future vaccine formulations and long-COVID syndrome (both noteworthy considerations during this pandemic) but may also apply to future infectious disease issues that necessitate special scrutiny.

*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.