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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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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USA: small study shows 17% of household cats and dogs had detectable #coronavirus sars-cov-2 neutralizing antibodies

We enrolled 37 dogs and 19 cats from 34 of 41 eligible households. All oropharyngeal, nasal, and rectal swabs tested negative by rRT-PCR; one dog’s fur swabs (2%) tested positive by rRT-PCR at the first animal sampling. Among 47 pets with serological results from 30 households, eight (17%) pets (4 dogs, 4 cats) from 6 (20%) households had detectable SARS-CoV-2 neutralizing antibodies.

Biorxiv preprint One Health Investigation of SARS-CoV-2 Infection and Seropositivity among Pets in Households with Confirmed Human COVID-19 Cases — Utah and Wisconsin, 2020

 

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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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India: double mutant coronavirus variant B.1.617 outcompeting B.1.1.7 UK variant

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

Graphs & data courtesy of Outbreak.info

France: 32 cases of Breton #coronavirus variant B.1.616 reported

On April 14, 32 cases of infection with the 20C / 655Y (B.1.616) variant were confirmed (29 in Brittany, three in other regions). All cases have a direct or indirect link with the enhanced surveillance zone by Brittany. The majority of the cases relies on the transmissions within the hospital clusters in the zone.

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, whether in Brittany or elsewhere. Epidemiological investigations are continuing to characterize the episode and monitor the spread of this variant.

French Health Department: COVID-19: epidemiological update of April 15, 2021  (PDF Download)

 

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2 Lions positive for #coronavirus at Pittsburgh Zoo

The staff at Pittsburgh Zoo say two of their lionesses have tested positive for SARS-CoV-2, the virus that causes COVID-19.

According to zookeepers, the lions were both displaying some symptoms including occasional coughing and diarrhea. The zoo reports that the two cats likely contracted the virus after an exposure to an asymptomatic zoo employee. Zookeepers say they are in contact with other zoos who have had big cats come down with the virus and using their insight to care for the two infected animals.

Pittsburgh.cbslocal.com report

 

 

France: 25 cases of Breton Variant #coronavirus B.1.616 recorded so far, 22 in Brittany, 3 elsewhere

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

 

 

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UK: Finchley in north London borough of Barnet now also surge testing for South African variant B.1.351

People living and working in Barnet, north London, are being urged to get a Covid-19 test after a case of the South African variant was found. Those in the N3 postcode area are being asked to get a test either at home or go to a mobile testing unit. Barnet Council said teams of officials will go door-to-door in areas in area to deliver PCR test kits, and a mobile testing unit will be set up in the car park of Finchley Central Station.

A statement on the council’s website said: “The South African variant of Covid-19 has been found in Barnet.  “From Thursday 15 April we will start testing people for this variant in specific postcode areas affected in N3 or those who shop on the local high street.”

LBC report

 

 

India: “Double mutant” #coronavirus strain B.1.617 evading RT-PCR tests

B.1.617, The “double mutant” coronavirus variant that is causing the current wave of Covid-19 in India is not just highly infectious but also stealthy. New Delhi hospitals say there are getting cases where a patient has typical symptoms of the disease but tests negative for the viral infection, sometimes twice or three times with RT-PCR. 

“We have received many such patients in the past few days. They had fever, cough, shortness of breath and the CT scan of the lungs showed lighter-coloured or grey patches. It is referred to as patchy ground glass opacity in medical terms. The condition is one of the defining characteristics of Covid-19,” Dr Aashish Chaudhry, managing director of Aakash Healthcare, said

He added that some of the patients underwent bronchoalveolar lavage (BAL), a diagnostic method in which a flexible scope is passed through the mouth or nose into the lungs with a measured amount of fluid introduced and then collected for examination, which confirmed the diagnosis. “All such persons who tested negative through conventional Covid-19 testing methods but had disease symptoms came positive in the lavage test,” Dr Chaudhry said.

Dr Pratibha Kale, associate professor of clinical microbiology at Institute of Liver and Biliary Sciences, said, “It is possible that in these patients the virus didn’t colonise the nasal or throat cavity because of which swab samples taken from these areas didn’t yield a positive result.” The virus, she added, attached itself to the ACE receptors — a protein found on the surface of many cell types — in the lungs and “that’s why when the fluid samples from the organ were analysed, it confirmed Covid-19 diagnosis”.

Dr Vivek Nangia, the chief of pulmonology division at Max Healthcare, said nearly 15-20% of the Covid-19 patients suffered from this problem. “They are highly symptomatic of the disease, but test negative. This is a serious problem because such patients can continue to spread the infection if they are admitted in non-Covid areas. Also, it can delay the treatment,” he added.

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Breton #Coronavirus Variant: 26 confirmed cases, 12 deaths

This Thursday, a 26th case of the Breton variant was confirmed at the Guingamp hospital center. The spread of this new form of covid-19 seems to be limited to Trégor. To date, 12 patients have died from it. Frail, elderly and / or people with co-morbidities.

However, it is impossible to conclude that there is a higher mortality caused by this variant compared to the others. The problem lies in the difficulty of detecting this mutant which often nestles deep in the respiratory system, rendering conventional nasopharyngeal PCR tests negative. “We have a surveillance bias. We have the results where we are able to find the virus. That is to say in the hospital, in people intubated in intensive care, for whom we can perform effective deep samples,” explains Alain Le Tertre, head of the Brittany unit of Public Health France.

Le telegramme report

 

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