A small-scale study on 113 healthcare workers who had received at least one vaccine dose at a private hospital in Delhi found that 18 tested positive for Covid but all except one had mild symptoms. Of the 113 in the study, 107 had received the second dose of the vaccine.
Taken in percentage form, the study found that breakthrough infections — Covid infection in vaccinated individuals — occurred in 15.9 per cent (18 persons) of the vaccinated individuals and 95 per cent had mild symptoms. Of these, 17 incurred the infection after the second dose. According to the study, of the breakthrough infections in 18 persons, 17 incurred the infection after the second dose. These 17 had got their second dose after a mean of 34.8 days following the first jab.
A World Health Organization official said Monday it is reclassifying the Indian Sars-Cov-2 variant B.1.617 as a “variant of concern,” indicating that it’s become a global health threat. Maria Van Kerkhove, the WHO’s technical lead for Covid-19, said the agency will provide more details in its weekly situation report on the pandemic Tuesday but added that the variant, known as B.1.617, has been found in preliminary studies to spread more easily than the original virus and there is some evidence it may able to evade vaccines.
“as such we are classifying this as a variant of concern at the global level,” she said during a press conference. “Even though there is increased transmissibility demonstrated by some preliminary studies, we need much more information about this virus variant in this lineage in all of the sub lineages, so we need more sequencing, targeted sequencing to be done.”
Five residents of a care home in Borsbeek in Antwerp province have been infected with the so-called Indian variants of Covid-19, according to the Flemish Agency for Health and Care. One of those affected has died. All of the home’s residents have been fully vaccinated.
In three of the cases involved in the new outbreak, the Indian variant has been confirmed, and it is supposed the same goes for the other two. One has since died, and another is in hospital.
Early indications from an analysis of the growth of the B.1.617 variant of the Covid-19 virus has shown it to be at least twice as infectious as the UK variant and thrice as infectious as the variant behind last year’s Covid-19 wave.
Scientists involved in the whole genome sequencing as part of the Centre’s Covid-19 genomic surveillance exercise told The New Indian Express that this conclusion is based on the growth of this mutant, as compared to others, in districts where B.1.617 has been identified along with other variants in samples collected from infected individuals.
“We have been examining this data carefully and the way this lineage of virus, also called the double mutant, is growing as compared to others is remarkable,” said a senior scientist involved in the INSACOG project, a consortium of several institutions under the National Centre for Disease Control that carry out an extensive genomic surveillance. “For the public, what needs to be communicated very clearly is that there is a greater need to double mask and maintain social distancing as this virus is highly infectious.
** Update ** Tom Wenseleers: “Based on this data, the new variant from India has a very big transmission or growth advantage,” even over B.1.1.7, he says. “It’s kind of like the U.K. variant squared.”
The UK government is thought to have detected more than 40 clusters of the Indian Covid variant B.1.617 in the UK, and is on the verge of declaring it a “variant of concern”. The mutant strain is thought to be driving the massive surge of infections in India.
Professor Christina Pagel: [B.1.617] rapidly became dominant in India and, again the sequenced data there is sparse, but early modelling shows that it might well be more transmissible than our B.117 Kent strain. ‘What we have also seen in India is that B.1.617.2 is becoming the dominant subtype – exactly the same pattern we see here in the UK. ‘While this could reflect the situation in India through importation, the Sanger data tries to exclude travel related cases or surge testing and we still see the rise of B.1.617.2 in that’.
** NOTE: B.1.617.2 carries the T478K mutation according to the European Centre for Disease Prevention and Control
See also Bioxriv preprint: Preliminary report on SARS-CoV-2 Spike mutation T478K
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). Whole viral genome sequencing revealed several additional substitutions, including D796H, present in a guanine–cytosine–rich region not identified by targeted PCR. These substitutions may decrease sensitivity to convalescent serum11 and may have some unique noncoding changes as compared with the clades first identified in Wuhan, the United Kingdom, and New York City.
Although more detailed analysis of whole-genome sequencing from Patient 1 was undertaken, we could not conclude that the variant in this patient was a Pango lineage because it was only present in a single person.
Its closest links on the phylogenetic tree were the variant first identified in the United Kingdom (B.1.1.7) and the variant first identified in New York City (B.1.526), but with considerable differences. It will be of interest to determine whether this may have resulted from a recombination event between B.1.1.7 and B.1.526, as has been recently reported for recombination between the B.1.1.7 lineage and the “wild-type” lineage first identified in Wuhan. Alternatively, shared substitutions may be the result of convergent evolution.
Sujeet Singh, director of the Indian National Centre for Disease Control (NCDC), said that in Maharashtra, the B.1.617 variant was found in proportions of over 50% in many cities. Nearly 64 cases of the UK strain were found in Maharashtra, six cases of the South African strain, one of the Brazilian strain and 427 cases of the Indian double mutant variant. Over 1,770 samples were sequenced for variants in Maharashtra.
The Covid-19 surge in Delhi, however, seems to be driven mainly by the UK variant B.1.1.7. In Delhi, there are primarily two types of variants — B.1.617 and the UK strain — found in the genome sequenced samples, the NCDC director said. The B.1.617 variant of coronavirus is also known as the double mutant strain. The UK variant was found in 28% of samples in the second week of March. In the last week of the month, 50% of samples had this variant, Singh added.
West Bengal had 40 cases of the UK strain B.1.1.7, nine cases of the South African strain B.1.351 and 124 cases of the Indian double mutant B.1.617.
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.
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.
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”