Updated on: Wednesday, December 15, 2021, 05:41 PM IST

Omicron scare: What is S-gene dropout test? National COVID19 Taskforce member Dr Rahul Pandit writes

What is S-gene dropout test? National COVID19 Taskforce member Dr Rahul Pandit writes  |

What is S-gene dropout test? National COVID19 Taskforce member Dr Rahul Pandit writes |


Even as the discovery of the new Omicron variant has shaken the world, the fact that it can be identified by an RT-PCR test brings a lot of hope. But there is a way in which the test may act as a surrogate marker to catch the culprit mutation. Here is what you should know.

Omicron is a heavily mutated variant with unusual constellation of mutations and is very different to other variants that have circulated in the past two years. As per the Centre for Epidemic Response and Innovation in South Africa, Omicron was found to have 50 mutations overall and more than 30 on the spike protein. Another unusual discovery is that the variant has a missing S-gene. Researchers in South Africa and around the world are conducting studies to better understand many aspects of Omicron and will continue to share the findings of these studies as they become available.


Transmissibility: It is not yet clear whether Omicron is more transmissible (e.g., more easily spread from person to person) compared to other variants, including Delta. The number of people testing positive has risen in areas of South Africa affected by this variant, but epidemiologic studies are underway to understand if it is because of Omicron or other factors

Severity of disease: It is not yet clear whether infection with Omicron causes more severe disease compared to infections with other variants, including Delta. Preliminary data suggests that there are increasing rates of hospitalization in South Africa, but more evidence is required. Moreover, there is currently no information to suggest that symptoms associated with Omicron are different from other variants. Initially reported infections were among university students—younger individuals who tend to have the more mild disease—but understanding the level of severity of the Omicron variant will take a few days to several weeks

WHY STRENGTHENING TESTING IS CRITICAL? The ability of diagnostic tests to detect the Omicron variant is critical to tracking its spread and putting in place measures to curb transmission. Analyses so far suggest that the rapid antigen (lateral flow) and gold-standard PCR tests should still detect the variant, but more comprehensive verification of this is ongoing.

Moreover, the new variant contains a deletion in its S gene, one of the three common target genes of many PCR tests. This can cause what’s known as “S gene dropout”, where the PCR S-gene target is not detected, while the other PCR gene targets are still recognized. Therefore, the overall PCR accuracy for tests with multiple genetic targets is not likely to be impacted. The missing S gene target can even act as a surrogate marker for the new variant in tests that target this gene, as the currently dominant Delta variant is S-gene positive on PCR. The S gene dropout has made possible timely screening for the Omicron variant in some regions of South Africa & Botswana, and gives the countries a way to track the variant’s spread without genomic sequencing, which is usually only performed for a subset of PCR-positive samples.

In India, the Ministry of Health and Family Welfare & public health experts have asked laboratories to conduct RT-PCR tests in whole for all the three genes - N’, ‘S’, ‘E’ and ‘ORF’, particularly on international travelers to help detect the absence of S gene. If the ‘S’ gene is absent in a person and the other genes are positive, it is a way to know that the Omicron variant may be present. Therefore, in my view increasing testing and genome sequencing is critical to being at the top of this situation and tackling it on time. While these measures are being put in place and the governing bodies are working round-the clock to track & trace international travellers from ‘at risk’ countries, masking, social distancing & hand hygiene should continue to be our thumb rule.

(Authored by Dr Rahul Pandit, Director-Critical Care, Fortis Hospitals Mumbai, Member-National COVID19 Taskforce & Maharashtra’s COVID19 Taskforce)

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Published on: Wednesday, December 15, 2021, 05:41 PM IST