Brazil Researchers Identify New Recombinant Variant, This Time Involving A BA.1 Subvariant Ie BA.1.14.1 With The BA.2 Variant!
Already there are so many new recombinant variants emerging as a result of Delta and Omicron coinfections and also from the Omicron BA.1 and BA.2 coinfections.
A dynamical nomenclature system for the designation of new lineages was created by the Pango network committee, in which recombinants start with an X letter. Currently, there are 3 Delta/Omicron (XD, XF, XS) and 13 Omicron BA.1*/BA.2 (XE, XG, XH, XJ, XK, XL, XM, XN, XP, XQ, XR, XT, and XU) recombinants, according to the Pango designation, release v1.8. (https://github.com/covlineages/pango-designation
To make matters more complicated, it has now been found that recombinant events are also taking place between subvariants and main variants and even between subvariants and subvariants.
Brazilian researchers have now identified a new recombinant variant that has yet to be assigned a Pango designation that involved the BA.1 subvariant ie BA.1.14.1 and the BA.2 variant.
This putative new recombinant and along with two XE recombinants were identified in children by the GENOV surveillance program (https://dasa.com.br/en/genov/
) from Dasa, Brazil. All three children haven’t traveled abroad nor their relatives, indicating that the infections by recombinants likely occurred in São Paulo city.
According to the study team, a three years old male child from São Paulo city, Brazil, presented an unassigned lineage according to standard pipeline classification. The sample was collected on Feb 16, 2022, and the complete genome sequencing resulted in a median coverage of 1,379 (99.39% over 30x) and 99.59% of non-N bases, with no detected sign of co-infection or contamination of negative controls. The consensus sequence was deposited on GISAID under the ID EPI_ISL_12055062 (hCoV-19/Brazil/SP-DASA828822284657/2022).
Initially, a subsequent analysis with Nextclade Web (version 1.14.0) resulted in a recombinant lineage with XM Pango classification, however, a few reversions and private mutations could be identified. The presence of the labeled mutation C17410T from the 21L clade (that includes BA.2) suggested a breakpoint different from the XM lineage (https://github.com/cov-lineages/pangodesignation/issues/472
The study team then used the sc2rf tool to screen potential breakpoints and compare the putative new recombinant with XE, XM, and XJ lineages. (https://github.com/lenaschimmel/sc2rf
Interestingly, a single breakpoint was detected between positions 15714 and 17410 in the ORF1B of the new recombinant.
Further detailed search for similar sequences in the public databases and their relationship with known recombinants in the phylogenetic tree was done with the UShER utility from the UCSC Genome Browser group.
This led to the new recombinant not being clustered with XM sample
s but was allocated separately in a non-resolved and multifurcated branch containing a miscellaneous of non-designated BA.1*/BA.2 recombinants.
Other samples from Malaysia, India, Denmark, England, and Japan also presented the same estimated single breakpoint of the new recombinant, between positions 15714 and 17410 at the ORF1B. However, these samples found by UsHER diverge mostly by substitutions related to the BA.1 and may represent different potential recombinant lineages.
Instead, it was found that the Brazilian sample presented substitutions such as ORF1a:T4174I and ORF1a:A3615V that could characterize a BA.1.14.1 lineage (https://github.com/cov-lineages/pango-designation/issues/506
The subvariant BA.1.14.1 lineage has been mostly found in the Brazilian population, with an estimated 4% relative growth advantage reported by CoV-Spectrum (accession date 2022-04-27). Sample resequencing resulted in an identical consensus sequence with a median coverage of 2032 (99.56% over 30x) and 99.59% of non-N bases.
According to the PANGO designation, the minimum number of high-quality sequences to designate a new lineage is five, and at least 50 sequences are expected for significant recombinant lineages.
This newly identified SARS-CoV-2 BA.1.14.1/BA.2 recombinant will be continuously monitored by the GENOV surveillance team.
The study findings were published on a preprint server: Research Square, and is currently being peer reviewed. https://www.researchsquare.com/article/rs-1641864/v1
It is expected that more recombinant lineages will emerge as the SARS-CoV-2 virus is rapidly evolving and mutating contrary to what so called stupid American, British and Australian ‘experts’ are saying otherwise.
Considering the current kinetics of the pandemic, where many authorities and people are living in denial and are not adhering to more stringent safety measures, breakthrough coinfections and reinfections will be the new norm, each time debilitating the individual’s immune system and other cellular pathways and systems, making the even more vulnerable and susceptible and with increased mortality risk even if they do not seem to have severe symptoms upon infection. Close monitoring of excess death rates in various geolocations is crucial to also get a better perspective of how specific lineages are causing unique long term medical and health issues.
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