Examination of the SARS-CoV-2 sequences revealed that both patients were infected with variant viruses. Rapid identification of sequence variants by targeted PCR amplification showed that neither sequence precisely fit any known clade. Some of the substitutions in Patient 1 (T95I, del144, E484K, A570D, D614G, P681H, and D796H) were shared with B.1.526 (T95I, E484K, and D614G6), and three substitutions were shared with Patient 2 (in whom the variants T95I, G142V and del144, F220I, R190T, R237K, R246T, and D614G were detected).
NEJM article “Vaccine Breakthrough Infections with SARS-CoV-2 Variants”
A 39-year-old Brazilian man who died of COVID-19 last month was suffering from a second bout of the illness, researchers said on Tuesday, making it the country’s first confirmed death from coronavirus reinfection. Both episodes involved variants with the E484K mutation.
The man, from Campo Bom in the southern state of Rio Grande do Sul, had a history of chronic cardiovascular disease and diabetes. He first tested positive on November 30 but details about his symptoms – if any – are unclear. Genomic sequencing revealed the P.1 variant.
The patient fell ill a second time about 3 months later and tested positive on March 11, according to researchers at Feevale University. His initial symptoms were fatigue and respiratory distress, but his condition worsened and he was transferred to the ICU, where he was intubated and died on March 19.
Genomic sequencing of the sample from the second episode revealed the P.2 variant, which is classified as a Variant of Interest.
The National Institute of Virology (NIV), Pune, has shared data with laboratories in Maharashtra showing that of 361 Covid-19 samples taken in Maharashtra from January to March and genome sequenced, 61% or 220 had the double mutation E484Q and L452R, now classified as B.1.617 lineage.
On March 24, the Central government had announced the detection of a double mutant variant in “15-20% samples in Maharashtra” but did not link the variant with the second surge in the state.
E484K has been found in a new Sars-Cov-2 variant labelled as B.1.618, which has been reported in West Bengal, India.
Data submitted from India to the global repository GISAID shows the B.1.618, at 12%, is the third most common variant sequenced in the last 60 days. The B.1.617, at 28%, is the most common among sequences, followed by B.1.1.7 (the UK variant), the India Mutation Report by Scripps Research showed, citing the GISAID data
“Our results show that one of two antibodies from an antibody cocktail used for COVID-19 therapy no longer efficiently inhibits the viral variant with the Y453F mutation. Furthermore, our study demonstrates that the Y453F mutation reduces inhibition of the virus by antibodies produced by COVID-19 patients. This means that people who were infected with SARS-CoV-2 may have reduced protection against mink variants of the virus,” says Markus Hoffmann
“We were the first to identify two independent events of co-infection caused by the occurrence of B.1.1.28 (E484K) with either B.1.1.248 or B.1.91 lineages. Also, clustering analysis revealed the occurrence of a novel cluster of samples circulating in the state (named VUI-NP13L) characterized by 12 lineage-defining mutations.”
ScienceDirect.com preprint: Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil
Data from Outbreak.info suggests that the B.1.617 “double mutant” variant is outcompeting the UK variant B.1.1.7 in India – the B1617 variant is now being detected in nearly twice as many sequences as the UK variant in 7 day rolling average of percent sequences with mutations
Professor Paul Hunter, an epidemiologist at the University of East Anglia, analysed publicly available information on new variant numbers last Saturday and again yesterday and found that the number of genetically-confirmed Indian strain cases had risen in a week from 79 to 160. ‘That’s a big jump,’ he said.
Because only around a quarter of identified Covid cases undergo genomic sequencing to identify the strain, he feared the true figure was at least 400.
Anders Fomsgaard, virus researcher and chief physician at SSI, Statens Serum Institut, tells TV2 that there are now 11 cases of B1617 in Denmark, and that they are all connected to countries where the variant is already known. “So there are not 11 different chains of infection and that reassures us. It would not have been so good,” he says.
Here, we report the first natural infection case of SARS-CoV-2 in dogs in Connecticut. On February 12, 2021, a 3-months-old, female German Shepard dog was presented for postmortem examination at Connecticut Veterinary Medical Diagnostic Laboratory due to sudden death with no signs of illness, as reported by the owner.
“We report the first detection of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus from a dog in Connecticut during February 2021. Complete genome sequencing and phylo-genetic analysis of the hCoV-19/USA/CT-CVMDL-Dog-1/2021 (CT_Dog/2021) virus were con-ducted to identify the origin and lineage of the virus. The CT_Dog/2021 virus belonged to the GH/B1.2. genetic lineage and was genetically close to SARS-CoV-2 identified from humans in the U.S. during the winter of 2020-2021. However, it was not related to other SARS-CoV-2 identified from companion animals in the U.S. It contained both D614G in spike and P323L in nsp12 substitutions which have become the dominant mutations in the United States. The continued sporadic detections of SARS-CoV-2 in companion animals warrant public health concerns about their potential to become a new reservoir species of SARS-CoV-2.”
The so-called double mutant coronavirus found in Maharashtra, India may be becoming the most prevalent among all mutant variants in India, genome sequencing data submitted by Indian scientists to a global database indicates, according to a recent analysis that takes into account when they were detected. The double mutant virus – now classified as B.1.617 – was the most common in the samples sequenced in the 60 days prior to April 2 at 24%.
The variant was first detected on October 5 and was relatively obscure till it began popping up on increasing number of samples January onwards, the India situation report on outbreak.info showed. On April 1, it accounted for 80% of all analysed genome sequences of mutant variants sent by India to the global repository GISAID.
Prof Paul Hunter, professor in medicine at the University of East Anglia, told the Guardian that the arrival of the India variant was potentially worrying. He said: “These two escape mutations working together could be a lot more problematic than the South African and Brazilian variants which have only got one escape mutation. “It might be even less controlled by vaccine than the Brazilian and South African variants.”
The variant featured two “escape mutations” – E484Q and L452R – that “are causing people to be concerned. “There’s laboratory evidence that both of these are escape mutations. Basically, applying what we know about other human coronaviruses would suggest that this is going to be even less controlled by vaccine. But we don’t know that for certain at the moment”
Forbes are carrying an interesting about the recently discovered coronavirus variant found in Tanzania, Africa in travellers arriving from Angola. The variant is from “From An Entirely New Branch Of SARS-CoV-2”, and carries Spike mutations E484K, P681H, T478R, Q957H, H655Y, D215G, D80Y. L210N, W258L, R246I. “An additional 18 amino acid changes occur in proteins outside the spike protein. These include 14 in the orf1ab proteins that specify the replication complex. “
“This is a remarkable illustration of convergent evolution,” say’s Forbes
Clade 20C variant that emerged in Brittany. A cluster of infections with a 20C clade variant (“20C / 655Y variant” or B.1.616), was detected in the Côtes d´Armor, with cases occurring between January and March 2021. The particularity associated with the cases confirmed infections with this variant is the possibility of presenting symptoms suggestive of COVID-19 with negative RT-PCR on usual nasopharyngeal swabs.
The virus is nevertheless detectable by the usual PCR techniques but seems to be found in a preferential in the lower airways. To date, it has not been shown that this variant would be more transmissible or lead to more severe forms. Reinforced surveillance has been put in place in the geographical area concerned in Brittany. A national case investigation protocol suggestive of infection with the 20C / 655Y variant has been disseminated to identify and describe the cases that may occur outside this geographic area. In case of suspicion of infection with this variant (investigation protocol available on the website of Public Health France), samples beyond the nasal sphere pharyngeal gland should be offered whenever possible to increase the sensitivity of the diagnosis by RT-PCR.
As of April 07, 25 cases of infection with the 20C / 655Y variant have been confirmed by the CNR (22 in Brittany, 3 in other regions). All cases have a direct or indirect link with the enhanced surveillance zone by Brittany. The majority of cases are linked to transmissions within hospital clusters in the area. A few cases have been reported in connection with a chain of transmission in the community but, to date, there are significant dissemination of this variant in the population has not been documented, either in Brittany or elsewhere. Epidemiological investigations are continuing to characterize the episode and monitor the spread of this variant.
French Public Health Document: COVID-19: epidemiological update of April 8, 2021