SARS-CoV-2 Variants and RT-PCR
Can RT-PCR Detect Omicron ?
A short thread on the topic. 👇
RT-PCR is a sensitive molecular method widely used for the detection of SARS-CoV-2 in biological samples. This is based on the principle that short pieces of DNA (aka primers) can specifically target DNA/RNA and amplify them using a polymerase protein
Typically COVID-19 RT-PCR kits use 2 or more sets of primers which target the virus nucleic acid at 2 or more genes/sites in the genome. This is to improve the specificity of the detection. Combinations between N, E, RdRP and S genes are typically used.
Mutations in the target sites can affect the efficiency of the kit. Since 2 sites are used, it is rare that both sites are lost due to mutations (but rarely does happen). An early analysis from our lab on mutations in primer target sites can be read here…
A number of variants (incl. Alpha and Omicron) have mutations in the spike gene which can adversely impact the efficiency of the primers widely used. This is called a spike-drop out on a Spike Gene Target Failure (SGTF). This is usually not an issue, since the 2nd primer works.
This property can be therefore be used as a surrogate to screen for specific variants. While they are only suggestive (since the mutations can also occur in other variants) for the variants, they can be useful for quick screening.
Confirmation is usually by genome sequencing.
Whether a kit can detect a variant is therefore dependent on the primers used.
More importantly, given a set of primers, one could also ascertain whether a kit is good depending on prevalent mutations.
AssayM is a useful resource in this regard
Unfortunately, the primer details for the majority of kits used in India is not publicly disclosed / available, which limits the possibility to ascertain which ones can detect specific variants or which ones are likely to fail for a given variant or mutations which are prevalent.
In summary
🔴 RT PCR tests which have SGTF can be used to tentatively screen for Omicron
🔴 Variants are confirmed by sequencing
🔴 Mutations can affect the efficiency of RT PCR kits
🔴 Efforts are required to ensure the primers used are disclosed for PublicHealth decision-making
Also linking the #explainer on this topic which appeared in @IndianExpress by @runaanu…

• • •

Missing some Tweet in this thread? You can try to force a refresh

Keep Current with Vinod Scaria

Vinod Scaria Profile picture

Stay in touch and get notified when new unrolls are available from this author!

Read all threads

This Thread may be Removed Anytime!


Twitter may remove this content at anytime! Save it as PDF for later use!

Try unrolling a thread yourself!

how to unroll video
  1. Follow @ThreadReaderApp to mention us!

  2. From a Twitter thread mention us with a keyword "unroll"
@threadreaderapp unroll

Practice here first or read more on our help page!

More from @vinodscaria

25 Nov
What do we know about the B.1.1.529 variant of SARS-CoV-2 with a very large number of mutations
An updated thread on emerging evidence. Image
B.1.1.529 is a newly designated variant of SARS-CoV-2…
This would not have been possible without the exemplary work of researchers in Africa who have sequenced and deposited the genomes in public domain which forms the basis of this variant designation.
The lineage (variant) is characterized by 32 conserved spike mutations A67V Δ69-70 T95I G142D/Δ143-145, Δ211/L212I ins214EPE G339D S371L S373P S375F K417N N440K G446S S477N T478K E484A Q493K G496S Q498R N501Y Y505H T547K D614G H655Y N679K P681H N764K D796Y N856K Q954H N969K L981F
Read 28 tweets
24 Nov
Real-world data on effectiveness of BBV152 / Covaxin whole inactivated #COVID19 vaccine against symptomatic infection
👥Healthcare Workers at @aiims_newdelhi
🗓 Coincided with the 2nd wave in #Delhi majorly driven by VoCs…

#MedTwitter #vaccines #India
Adjusted effectiveness of BBV152 against symptomatic COVID-19 after 2 doses adm at least
🔸️14d before testing was 50% (95% CI 33–62; p<0·0001).
🔸️28d before testing was 46% (95% CI 22–62) 
🔸️after excluding previous COVID19 cases, 14d before testing was 47% (95% CI 29–61)
In summary
🔸️Vaccine effectiveness requires at least 2 doses and 14 days after 2nd dose

What this means for #PublicHealth
🔸️ Underscores the need for completing vaccine schedule of 2doses
🔸️ Continued non-pharmacological measures in the face of a wave of infections
Read 4 tweets
3 Nov
Insights on the recent wave of COVID-19 infections in @Singapore
The present wave in Singapore is of interest since a significant large proportion (82.7%) of population has received 2 doses of #COVID19 #vaccines but nevertheless have a wave of infections and deaths.
With respect to COVID-19 variants and VoCs, clearly Delta (and 2 prominent sublineages AY.23 and AY.23.1) dominate the present wave of infections.
Data: @DiseaseOutbreak
There are some interesting insights, thanks to the data made available at
While on first look there is a significant number of cases spread across all age-groups.
The community cases are largely dominated by the younger age-groups (59 years and above)
Read 8 tweets
20 Oct
What do we know and don't about the Delta sub-lineage AY.4.2
ℹ️ AY.4.2 is a sub-lineage Delta (B.1.617.2) in the UK which has shown consistent increase over the past few months and has caught attention.
Plot: Sanger COVID-19 Genomic Surveillance Dashboard Image
The background:
Delta had significant advantage over other lineages, in almost all regions, practically eliminating all other lineages as they spread widely.
The continued evolution of delta provided a number of sublineages
There are now ~55 sublineages (AY.1 - AY.41) of Delta
Some of the AY.x sublineages have geographical preponderance, due to mutations present at the time of introductions. For example, UK has a AY.4 sublineage. More about the lineages and distribution is available at… Image
Read 9 tweets
24 Jul
Closely tracking the delta+ lineages now across the world, one of the lineages AY.3 seems to be emerging in the United States of America. This tweetorial is to summarise the observations. I will be updating this thread as new evidence emerges.
Thanks Image
The interest in looking at this lineage closely comes from the fact that this lineage has been on the rise in USA in recent weeks.
Thanks @Unusual_Times for pointing this. Image
AY.3 seems to be localized to some states, like #Mississippi and #Missouri with nearby states slowly picking up. Image
Read 15 tweets
13 Jul
The recent outbreaks of #Zika Virus in #Kerala has renewed interest in this virus. This tweetorial explains some key aspects about the virus and why we should be actively using #genomics for #GeneticEpidemiology Image
The disease in most people is mild. Majority of people infected with Zika virus DO NOT develop symptoms. Symptoms are generally mild including fever, rash, conjunctivitis, muscle and joint pain, malaise, and headache, and usually last for 2–7 days.
Source: @CDCgov Image
Death is RARE
Infection during pregnancy can cause microcephaly & congential malformations.
Neurological complications like Guillain-Barré syndrome, neuropathy and myelitis are seen in some.
Read 13 tweets

Did Thread Reader help you today?

Support us! We are indie developers!

This site is made by just two indie developers on a laptop doing marketing, support and development! Read more about the story.

Become a Premium Member ($3/month or $30/year) and get exclusive features!

Become Premium

Too expensive? Make a small donation by buying us coffee ($5) or help with server cost ($10)

Donate via Paypal

Thank you for your support!

Follow Us on Twitter!