“We also observed that the spike protein of the Lambda variant presented increased infectivity when compared with the spike protein of the Alpha and Gamma variants, both of them with reported increased infectivity and transmissibility. Together, our data show for the first time that mutations present in the spike protein of the Lambda variant confer escape to neutralizing antibodies and increased infectivity.”
“The evidence presented here reinforces the idea that massive vaccination campaigns in countries with high SARS-CoV-2 circulation rates must be accompanied by strict genomic surveillance aimed to rapidly identify new viral isolates carrying spike mutations as well as studies aimed to analyze the impact of these mutations in immune escape and vaccines breakthrough.”
We report the emergence of a novel lineage of SARS-CoV-2 in South America, termed C.37. It presents seven nonsynonymous mutations in the Spike gene (Δ247-253, G75V, T76I, L452Q, F490S, T859N) and a deletion in the ORF1a gene (Δ3675-3677) also found in variants of concern (VOCs) Alpha, Beta, and Gamma. Initially reported in Lima, Peru, in late December 2020, it now accounts for 97% of Peruvian public genomes in April 2021. It is expanding in Chile and Argentina, and there is evidence of onward transmission in Colombia, Ecuador, Mexico, the USA, Germany, and Israel. On June 15, 2021, the World Health Organization designated C.37 as Variant of Interest (VOI) Lambda.
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 World Health Organization (WHO) said Wednesday that the coronavirus variant of COVID-19, commonly known as C.37, has been named Lambda. Lambda has been identified in 29 countries, most notably in South America where it is believed to have originated.
First identified in Peru, the Lambda lineage was classified as a global Variant of Interest on Monday due to an “elevated prevalence” in South America, the WHO said in its weekly update.
Lambda has been rampant in Peru where 81 percent of COVID-19 cases since April 2021 were associated with this variant, authorities reported.
In Chile, it was detected in 32 percent of all submitted sequences in the last 60 days, and only outclassed by the Gamma (P.1) variant which was first identified in Brazil. Other countries such as Argentina and Ecuador have also reported elevated prevalence of the new variant.
The WHO reported that the Lambda lineage carries mutations that might increase transmissibility or strengthen the virus’s resistance to antibodies.
However, evidence is too limited for the moment, the Geneva-based organization said, and more studies are required to understand better the Lambda variant.
** Our opinion: At the moment, the Sars-CoV-2 infection numbers in South America seem to be declining after peaking in June 2021. The Delta variant seems to be more of a threat internationally when you compare Latin America infection figures with the UK figures for example **
Lineage prevalence in Peru: