UK #coronavirus variant B.1.1.7 may not have evolved spontaneously in the UK or within human populations

“Here we analyzed 454,443 SARS-CoV-2 spike genes/proteins and 14,427 whole-genome sequences. We demonstrated that the early variant B.1.1.7 may not have evolved spontaneously in the United Kingdom or within human populations. Our extensive analyses suggested that Canidae, Mustelidae or Felidae, especially the Canidae family (for example, dog) could be a possible host of the direct progenitor of variant B.1.1.7.”

Biorxiv preprint: Potential transmission chains of variant B.1.1.7 and co-mutations of SARS-CoV-2

 

 

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NEJM: In two #coronavirus vaccine breakthrough cases “examination of the SARS-CoV-2 sequences revealed that both patients were infected with variant viruses” .. “neither sequence precisely fit any known clade”

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”

 

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India: Doctors discuss the diagnosis and treatment of B.1.617 double mutant #coronavirus patients

“Death of fully vaccinated people”, “Increased incidence of reinfections”,  “Very infectious. Almost all near contacts are positive if traced”, “RT-PCR reports are 67-70% positive and RAT around 89%”, “RT-PCR was positive around 60% of cases”

Dr Nishith Kumar, Pulmonologist, Ranchi
I have seen 100s of cases where the patient is maintaining normal oxygen saturation & more than 2-40% lung is affected on CT scan

Dr T Rekha, MD med, Kolkata
So far, in the admitted cases, most of the age groups are between 30-40
One whole family (4 members) admitted post vaccination following 1st dose vaccination
RT-PCR was positive around 60% of cases

Dr Bijay Patni, Bhagaipur
D-Dimer is found to be elevated in most cases
Very infectious. Almost all near contacts are positive if traced

Dr Rajkamal Chaudhary, Delhi
Age group 1yrs to 30yrs
RT-PCR reports are 67-70% positive and RAT around 89%

Dr H Sharan, Ranchi
Recent samples (~300) showed B.1.617 in 30% of samples
Increased incidence of reinfections
Death of fully vaccinated people
HRCt chest should be advised to all

CMEIndia.in discussions  Please read the entire article here

 

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Brazil: First confirmed death from #coronavirus REINFECTION reported

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.

 

 

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Hong Kong: #coronavirus transmission linked to quarantine hotel door hooks used for meal deliveries

Hong Kong’s first community infection of a mutant Covid-19 strain involved the South African variant, officials revealed on Tuesday, with transmission likely to have taken place at a quarantine hotel via door hooks used by staff to deliver meal boxes to guests.

Experts found no problems with the hotel’s ventilation and drainage systems, the focus turned to S-shaped door hooks used by employees to hang meal boxes for self-isolating guests, who would later put them back there. ‘The virus could have been exchanged through contact with the hooks, which were “hard to clean”.’

SCMP.com report

 

 

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India: B.1.617 now at 61% of #coronavirus genome samples in Maharashtra – was ~20% just one month ago

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.

IndianExpress.com report

 

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India: New Indian #coronavirus variant B.1.618 with added E484K

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

Hindustan Times report

 

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Sweden: so much for Herd Immunity and Light Touch pandemic policies

“Instead of following evolving evidence, the [Swedish] FHM has doubled down and defended its approach without reconsidering the assumptions on which the failed national approach is based. It has downplayed the roles of asymptomatic spread, aerosol transmission, children as potential source of infection, and the use of face masks. It has maintained an approach that mainly builds on recommendations to take voluntary actions, guided (in our view) more by public opinion than by sound public health policy. “

Lancet article

 

If a picture is worth a thousand words, how much is one simple graph like this worth?

Graph courtesy of OurWorldinData.org

Maharashtra, India: complete lockdown from tomorrow

Maharashtra Health Minister Rajesh Tope has said all ministers have requested Chief Minister Uddhav Thackeray to impose a complete lockdown in the state from 8 pm tomorrow. “We have made our request. Now it is up to the Chief Minister to take the final call,”

India reported 259,170 new Covid-19 cases and 1,761 deaths in the last 24 hours, according to data from the Union Health Ministry.

Indian Express report

 

** Update from The Times of India: **

Maharashtra is likely to impose a “strict lockdown” in the state, senior minister Aslam Sheikh said on Monday amid an unprecedented rise in Covid-19 cases. Maharashtra has been reporting over 50,000 coronavirus cases every day in the last two weeks.

Time of India report

 

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Ireland: 24 cases of P.1, 55 cases of B.1.351 and 3 cases of B.1.617 reported

Director of the National Virus Reference Laboratory Dr Cillian de Gascun said that there have been three cases of the recent variant [B.1.617] first identified in India. Dr De Gascun said at least two of them are associated with travel. He said NPHET does not have any data to determine whether the variant is more transmissible or not, but said at this stage people need to remain vigilant and try to contain it locally.  Separately, 24 cases of the P.1 variant, which was first found in Brazil, have so far been confirmed in Ireland, while 55 cases of B.1.351 South African variant have also been confirmed.

RTE.ie report

 

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India: Gujurat doctors seeing an increasing number of #coronavirus cases where patients have negative RT-PCR tests but CT scans reveal significant infection in the lungs

The medical fraternity in Gujarat have come across an increasing number of cases where patients test negative in RT-PCR report but a high-resolution CT (HRCT) reveals significant infection in the lungs.

Vadodara Municipal Corporation has issued a notification stating that “the new strain of (novel) coronavirus [B.1.617] is highly contagious and the virus does not necessarily show a positive test on RT-PCR. In cases where RT-PCR is negative but findings in HRCT and lab investigations are suggestive of viral etiology, the claim should be treated as that of Covid unless proved otherwise,” states VMC’s order issued under the Epidemic Act.

According to Infectious disease specialist Dr Hiten Kareliya,”Covid-19 suspects should undergo RT-PCR tests and HRCT chest early instead of earlier practice where a patient would be asked to undergo CT scan only a couple of days after the test.

“We are seeing many cases where the patient has no symptoms or just mild fever and weakness but the infection spread to lungs rapidly,” he further said.

OneIndia.com report

 

 

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Israel: Indian #coronavirus variant – “The impression is that the Pfizer vaccine has efficacy against it, albeit a reduced efficacy,”

Israel has registered eight cases of a coronavirus variant first identified in India and believes that the Pfizer/BioNTech vaccine is at least partially effective against it, an Israeli health official said. “The impression is that the Pfizer vaccine has efficacy against it, albeit a reduced efficacy,” the ministry’s director-general, Hezi Levy, told Kan public radio, saying the number of cases of the variant in Israel now stood at eight.

Reuters report

UK: India is added to travel “red list” three weeks too late

India has been added to a “red list” of countries from which most travel to the UK is banned over fears of a new Covid variant [B.1.617], the health secretary has said. From 04:00 BST on Friday, most people who have travelled from India in the last 10 days will be refused entry. British or Irish passport holders, or people with UK residence rights, will be allowed in but must quarantine in a government-approved hotel for 10 days.

BBC report

 

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Brazil: novel #coronavirus variant VUI-NP13L reported along with 2 cases of coinfection with B.1.1.28

“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

 

 

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