Covid-19 Delta Variant Mutates to “Delta Plus” as California Fully Reopens

As California fully reopens in the midst of rise of the B.1.617.2 strain or Delta variant of COVID-19 that has devastated India, China, UK and is now spreading in the US. The delta variant has now further mutated to “Delta Plus’ or ‘AY.1’ variant, which is very concerning. In an interview with indica News Dr. Prasun J. Mishra on this topic.

Dr. Mishra (Ex-Genentech, Ex-NCI, Ex-NIH) is the founding president and CEO of American Association for Precision Medicine (AAPM) and chair of ACT: AAPM Coronavirus Taskforce, leading research efforts focused on preventing and curing COVID-19, cancer, and other chronic diseases; not only treating the sick but also providing knowledge/tools to individuals to live longer, healthier lives.

Widely recognized as a Technology and Healthcare thought leader, Dr. Mishra has keynoted, chaired, and organized numerous successful international conferences. His research work has been recognized globally by over 40 prestigious awards and honors. Dr. Mishra also served as a Scientist and Principal Investigator at Genentech, Roche. Moreover, his passion for drug development and precision medicine has led to identification of new drug targets, biomarkers, companion diagnostics, and several drugs/ combinations in the clinic. Due to his unique perspective and selfless service, he is highly respected and sought-after mentor to many.

Please share your observations about B.1.617.2 strain and who are infected?

COVID-19 B.1.617.2 variant carries over a dozen mutations (see Figure 1), earlier was referred to as “double mutant” due to the presence of the prominent E484Q and L452R mutations. On May 10 the World Health Organization (WHO) has classified the Delta variant as a “variant of concern”.

Originally identified in India, the delta variant is now the most transmissible variant yet that has spread around the world to at least 65 countries and in 49 US states (see Figure 4). The delta variant has recently fueled the second wave of cases that has crippled health systems, and caused havoc, in India. The delta strain now makes up more than 46 percent of new cases in the U.K. (Figure 2).

Figure 1: Characteristic mutations in the COVID-19 delta lineage (

Figure 2: The delta strain now makes up more than 46 percent of new cases in the U.K.


Recently, the ‘Delta’ variant has further mutated to a ‘Delta plus’ or ‘AY.1’ variant with signs of resistance against the monoclonal antibody cocktail (Casirivimab and Imdevimab, received EUA by CDSCO). “A small number of sequences of Delta (B.1.617.2) having spike mutation K417N can be found on GISAID. As of June 15, these sequences have been identified in genomes from 10 countries.” (quote by Bani Jolly Twitter)

Public Health England, in its latest report on coronavirus variants, said the Delta plus variant was identified in six genomes from India as of June 7. The health agency has confirmed the presence of a total of 63 genomes of the Delta variant with the new K417N mutation (India Today).



Figure 3: Nextstrain for Delta+K417N sequences showing phylogeny (A) bifurcating in to two clades of AY.1. The bottom small cluster is composed largely of sequences from California. The top larger cluster with sequences from 8 countries including UK, India and Nepal (A and B).

Is it a matter of concern though slow, the number is rising, there are 286 B.1.617.2 strains in California alone?

It is very concerning that this highly transmissible delta variant has a higher hospitalization risk, making it the most dangerous of all. Moreover, research suggests that the delta variant may be up to 50 percent more transmissible than the original U.K./Alpha variant.

Figure 4: Average daily prevalence of the delta variant in the US (Based on reported sample collection date, source:

As per CDC, the delta variant now constitutes over ~10% of all COVID-19 infections in the US (as per June 5) and over 18% of cases in some Western U.S. states (Figure 4)( source To date, California has a total of 291 documented variants of the B.1.617 lineage (source

Figure 5: Delta variant comprises around ~10 percent of total new covid-19 infections in the U.S. (, image:

What are some of the other variants out there? Does it impact people who are already vaccinated?

Table 1 summarizes some of the common variants that are now being circulated globally and how they compare to the delta variant. The good news is that the vaccines more or less work on all strains (source Eric Topol Twitter). Moreover, a recent study conducted by the UK government, suggested that the full vaccination is still largely effective against the Delta strain. Two doses of a COVID vaccine provided 81 percent protection against the delta variant (compared with 87 percent protection against the UK/Alpha variant). Whereas a single dose provided only 33 percent protection against symptomatic infection from delta (compared with 51 percent protection against UK/Alpha). Suggesting that the delta variant is the biggest threat to all of the partially vaccinated people worldwide (source:

No alt text provided for this image

Table 1. A table showing key properties of the major variants as compared to the delta variant (source Eric Topol Twitter).

And do you expect the surge after California opens fully tomorrow?

During the dawn of the pandemic, California was among the first to act fast to implement stringent regulations to contain the disease. However, despite the precautions, we lost over 50,000 more lives, which is highest than any other state in the US (source NY Times). Although the COVID-19 cases are down now due to successful vaccination campaigns, the highly transmissible delta strain has now spread to 65 countries and in 49 US states (see figure 5). We have to be prepared for a possible third wave (see figure 6).

No alt text provided for this image

Figure 6. There were 3 different waves of illness during the Spanish Flue pandemic, starting in March 1918 and subsiding by the summer of 1919 (source

I applaud CA Gov. Gavin Newsom’s decision to continue California’s COVID-19 state of emergency order beyond June 15 when the state will fully open. The emergency order gives state health officials broad authority to implement restrictions in case of another outbreak. I would like to quote Gov Newsom who said “We’re still in a state of emergency. This disease has not been extinguished. It’s not vanished. It’s not taking the summer months off.”(LA Times).

As we open, let us all continue taking all the precautions to contain the spread of these highly infectious and deadly COVID variants and a possible third wave of the ongoing COVID-19 pandemic.

Interview by Ritu Jha, Indica News, June 15 2021

Leave a Reply

Your email address will not be published. Required fields are marked *