Delta Growth

2022-01-18 the post updates are over because Omicron has nearly eliminated Delta.

A new Delta subvariant AY.119 has a curious mutation ORF1b:A1847S in nsp14 (ExoN/MTase).


The Delta AY subvariants reached AY.111. Noticeable are new mutations in ORF1b,  different in AY.44, AY.100, and AY.103. That means they do not convey sufficient selective advantage to the virus.


The new Delta subvariants are AY.43 and AY.44. They look like vanilla Delta, similar to AY.4 and AY.25, especially in the S-protein. AY.44 has mutations ORF1a:A2554V and ORF1b:F183V, neither of which is new, although the latter appeared in quantities only in the Delta. AY.4.2 looks like a blink on the radar now.


There is a lot of talk about AY.4.2 variant. AY.4.2 differs from AY.4 and other Delta variants by new mutations in the spike:

A222V (93% vs 0% in AY.4 and 10% in the Delta)

Y145H (74% vs <1% in AY.4 and the Delta)

Both mutations are outside of RBD and NTD, but might have impact on binding between the spike and ACE2 and/or antibodies. Also, AY.4.2 has higher frequency of this ORF1A mutation:

A2529V (98% vs 78% in AY.4 and <30% in the Delta)


Lineage Comparison. Alaa Abdel Latif, Julia L. Mullen, Manar Alkuzweny, Ginger Tsueng, Marco Cano, Emily Haag, Jerry Zhou, Mark Zeller, Emory Hufbauer, Nate Matteson, Chunlei Wu, Kristian G. Andersen, Andrew I. Su, Karthik Gangavarapu, Laura D. Hughes, and the Center for Viral Systems Biology.


The Delta variant is changing and adds new mutations. The consensus sequence according to Pango has 30 mutations now. Notice that there are multiple definitions of Delta. The W.H.O defines the Delta differently – as Pango B.1.617.2. Pango B.1.617.2 is not Delta, but the top node of multiple lineages, also included in the Delta (AY.1, AY.2, … AY.30, …). The consensus sequence of B.1.617.2 has fewer mutations.

The real world has Pango Delta. The current Delta sequence (See the Characteristic mutations of Delta), including all the characteristic mutations, is dominant in the US, UK, and worldwide.

>70% in the US

USA, snapshot 2021-10-17

>90% in the UK

>80% Worldwide

(the sampling is biased)

Characteristic mutations of Delta
gene amino acid
ORF1a A1306S
ORF1a P2046L
ORF1a P2287S
ORF1a V2930L
ORF1a T3255I
ORF1a T3646A
ORF1b P314L
ORF1b G662S
ORF1b P1000L
ORF1b A1918V
S T19R
S E156G
S del157/158
S L452R
S T478K
S D614G
S P681R
S D950N
ORF3a S26L
M I82T
ORF7a V82A
ORF7a T120I
ORF7b T40I
ORF8 del119/120
N D63G
N R203M
N G215C
N D377Y

The content of this article reflects the situation on the original publication date Oct 17, 2021. Updates are occasionally inserted at the top.