At least 138 of the 151 Covid-19 samples sent by Tripura for genome sequencing have tested positive for the Delta Plus variant, State Health Surveillance Officer Dr Deep Kumar Debbarma said. Tripura, thus, is the first state in the northeast to have recorded a case of the Delta Plus variant.
Addressing reporters on Friday evening, Debbarma said the samples were sent to a laboratory at Kalyani, West Bengal, for the virological test. “Delta Plus variant was found in 138 of the 151 samples. 10 others tested positive for the Delta variant while three cases of alpha variant were found,” Debbarma added.
PHE England have recently published new reports on the SARS-COV-2 variants circulating in Britain: Alpha, Beta, Gamma, Zeta, Eta, B.1.1.318, Theta, Kappa, B.1.617.3, AV.1, C.36.3, Lambda, C.37
Variants under surveillance
Secondary attack rates
SARS-CoV-2 Immunity and Reinfection Evaluation (the SIREN study) cohort monitoring
Part 2: Delta (B.1.617.2) surveillance
Surveillance through genomic data
Delta with K417N (Delta-AY.1)
Data on individual variants
Lambda (C.37, VUI-21JUN-01)
Through routine scanning of variation in Delta, a small number of sequences were detected which had acquired the spike protein mutation K417N. Information suggests that there are at least 2 separate clades of Delta with K417N. One clade is large and internationally distributed with PANGO lineage designation AY.1. A second clade found in sequences uploaded to GISAID from the USA, now designated AY.2.
As of 16 June 2021, 161 genomes of Delta-AY.1 have been identified on GISAID. from Canada (1), India (8), Japan (15), Nepal (3), Poland (9), Portugal (22), Russia (1), Switzerland (18), Turkey (1), USA (83).
There are currently 38 cases of Delta-AY.1 in England (36 confirmed sequencing and 2 probable genotyping). Cases have been detected in 6 different regions in England. Delta-AY.2 has not been detected in England.
UK Variants of Concern Technical Briefing 15 (PDF download)
According to Bani Jolly of the Institute of Genomics and Integrative Biology, the phylogeny of Delta has two separate clades. While AY.1 is found in a few countries including the UK, India and Nepal, the other clade (AY.2), is largely from the sequences from California (USA).
“The split between the two clades seems to be based on two spike mutations — A222V and T95I. While all sequences in the California cluster share spike A222V, all sequences in the larger international cluster share spike T95I,” Jolly tweeted.
Stating that AY.1 has arisen independently a number of times and could be more prevalent than observed in countries with limited genomic surveillance, she tweeted that given that Delta is a variant of concern, it is important to take note of any sub-lineages that may emerge.
The Nepalese Ministry of Health and Population (MoHP) said that out of 47 confirmed delta variant samples, nine were found to have K417N mutations.
According to the ministry, the new mutation has also been named AY.1 (aka Delta-AY.1 or “Mountaineers” variant).
Issuing a press statement on Monday, the MoHP revealed that AY.1 mutation has been confirmed in more than 10 countries, including Nepal.
With this, Nepal has witnessed Alpha and Delta as the variant of concern and Kappa variant of concern, the Ministry said.
The Ministry had selected 48 samples from the National Public Health Laboratory from the people of all age groups from April 29 to June 3 and tested them in WHO identified Center for Excellence in Genomics, The Institute of Genomics and Integrative Biology (IGIB).
Out of them 47 samples had come with delta variant B.1.617.2 and one had come with alpha variant B.1.1.7. Among the 47 delta variant samples nine had shown K417N mutation, the Ministry said.
By Step 4 which will take place no earlier than 21 June, the UK government hopes to be in a position to remove all legal limits on social contact. We hope to reopen remaining premises, including nightclubs, and ease the restrictions on large events and performances that apply in Step 3.
Prague COVID-19 Response – July 2020:
“Those who cannot remember the past are condemned to repeat it”
“Here we report the discovery of 24 recent B.1.1.482 pango lineage SARS-CoV-2 viruses in South Yorkshire that have acquired approximately 23 additional mutations when compared to the majority of other samples of this lineage. Nine of these additional mutations are found in the spike gene and six represent changes which are found in variants of interest and concern across the world and/or associated with reduced antibody binding (T95I, G142D, △144, N439K, E484K, P681H). Similar mutation profiles were also seen in B.1.1.482 samples from other regions in the UK. We recommended the monitoring of samples of this lineage which is now designated AV.1.”
Virological.org – Detection of Spike Mutations; D80G, T95I, G142D, △144, N439K, E484K, P681H, I1130V, and D1139H, in B.1.1.482 Lineage (AV.1) Samples from South Yorkshire, UK (UK Variant under investigation VUI-21MAY-01)
Public Health England has revealed that it had detected another Covid variant in Yorkshire and the Humber which it has assigned as a ‘Variant Under Investigation’ VUI-21MAY-01. The strain, temporarily named AV.1, has been spotted 49 times so far.
New Variant Under Investigation
“A further variant, VUI-21MAY-01, has been designated as a Variant Under Investigation (VUI) by PHE.
The variant is from a lineage which was designated a signal in monitoring on 6 May 2021 based on an unusual mutation profile. PHE has been monitoring the variant since April.
There have been 49 cases of VUI-21MAY-01 across the country to date, mainly concentrated in Yorkshire and the Humber.
There is currently no evidence that this variant causes more severe disease or renders the vaccines currently deployed any less effective. PHE is carrying out increased laboratory testing to better understand the impact of the mutations on the behaviour of the virus.”