COVID-19 UPDATE / Immunity and Vaccine Development


In this edition:

1.     The main SARS-CoV-2 variants

2.     The number of sequences of sequences of each variant recorded by country

3.     B.1.1.7 outbreak in long-term care facility in Ontario

4.     P1 now accounts for 42% of new infections in city of Manaus

5.     COVID-19 vaccine doses administered per 100 people, 25 January

6.     Moderna vaccine protects against UK and South African variants

7.     Israel reports only 20 positive COVID tests from 128K who had their second Pfizer shot

8.     Israel sees 60% drop in hospitalisations for age 60+ three weeks after first shot

9.     EU vaccine delivery delays

1. The main SARS-CoV-2 variants

Chart: Eric Topol

2.     The number of sequences of each variant recorded by country

2.1 The number of sequences of the B.1.1.7 (UK) lineage recorded in each country

Percentage of lineage detection by country: UK 57.0%, USA 6.0%, Russia 3.0%, Italy 3.0%, Switzerland 3.0%

2.2 The number of sequences of the B.1.351 (SA) lineage recorded in each country.

Percentage of lineage detection by country: South Africa 79.0%, UK 12.0%, Germany 1.0%, Australia 1.0%, France 1.0%

2.3 The number of sequences of the P.1 (Brazil) lineage recorded in each country.

Charts and percentages:

International SOS Comment: These results are indicative as results may be biased by the amount of genomic testing being conducted by each country.

3.     Is B.1.1.7 more lethal?

In addition to being more transmissible, the variant now dominant in the UK may be about 30 percent more deadly than previous strains, but much uncertainty remains,” reports The Scientist.

“The evidence comes from two analyses reviewed by a government committee called the New and Emerging Respiratory Virus Threats, or NERVTAG. Patrick Vallance, Prime Minister Boris Johnson’s Chief Scientific Adviser, said at the news conference that the 30% would mean that, for example, where before about 10 of every 1,000 60-year-olds who contracted COVID-19 would die, the rate for those with a B.1.1.7 infection would go up to 13 or 14 deaths per 1,000 cases. However, he urged caution in interpreting the numbers.

“Maria Van Kerkhove, the World Health Organization’s technical lead on COVID-19, told the Associated Press on 23 January that the contagiousness and deadliness of new variants are being studied, and that so far her team hasn’t observed that they are more likely to cause severe disease, but that more-transmissible variants could lead to overwhelmed healthcare systems and thus, indirectly, to more deaths.”

4.     B.1.1.7 outbreak in long-term care facility in Ontario

Roberta Place, a long-term care facility in Barrie ON (110 km north of Toronto) has suffered a serious outbreak of B.1.1.7 (UK) variant.

The outbreak started on 8 January.  The virus probably introduced into the facility by a staff member; a family member had travelled internationally, however quarantine rules were followed.

The local health district reports: B.1.1.7 has been confirmed at Roberta Place in Barrie, where all but three of 127 residents have tested positive and 29 have died. Of the staff, 84 have tested positive and a 19-year-old staff member has died.

Cara Ferguson tweeted: One of those residents was my mother. It happened shockingly fast. She had a positive test and hospital admittance yesterday morning and died just before 1 pm today.

Investigation shows that:

·       COVID +ve and COVID -ve residents shared rooms

·       Staff were caring for both COVID +ve and COVID -ve residents

·       Residents had not yet had their first dose of vaccine

International SOS Comment: 

This outbreak describes the rapid spread of B.1.1.7 in a long-term care facility; however, failure of non-pharmaceutical precautions (NPIs) undoubtedly also played a role. 

Postscript: All residents of long-term care homes in Ontario have received the first dose of vaccine.

5.     P1 now accounts for 42% of new infections in city of Manaus

The P1 (Brazilian) variant already accounts for about half of new infections in the Brazilian Amazonian city of Manaus, raising concerns about a greater risk of spread, said Professor Ester Sabino from the University of Sao Paulo, whose team’s preliminary results have been published on the forum.  The P1 variant accounted for 42% of new infections in Manaus during the period15-23 December. It was 0% in November.

International SOS Comment:  The increasing frequency of the detection of the P1 variant may indicate increased transmissibility.

6.     COVID-19 vaccine doses administered per 100 people, 25 Jan 2021

7.     Moderna vaccine protects against UK and South African variants

A non-peer-reviewed study published on the pre-print server BioRix has shown that the Moderna COVID-19 vaccine triggers an immune response that protected in laboratory tests against the two variants of the virus first detected in Britain and South Africa. 

There was full protection against the UK (B.1.1.7) variant however the antibodies produced were six times less efficient at neutralizing the South African B.1.351 variant in the  laboratory tests.

As a precaution, Moderna announced that it will begin two new studies. The company will:

1.     Test adding a third shot of its current vaccine to boost its two-dose regimen.

2.     Conduct early human tests of an all-new vaccine specific to the South African variant

Note: Eric Topol tweeted: “variant has the reduced antibody neutralisation (>5X) projected not enough to interfere with the Moderna vaccine. We make “a ton” of antibodies.”

8.     Israel reports only 20 positive COVID tests from 128K who had their 2nd Pfizer shot

Ynetnews reports that just 20 positive coronavirus tests out of 128,000 people who had their second Pfizer shot a week or more ago. None of the 20 were serious cases.

“The Maccabi HMO said most of the 20 were tested due to a known exposure to a confirmed COVID-19 case. Most were over 55. Half had a preexisting condition. None had a fever over 38.5°C. None needed hospitalisation.

“Not all 128,000 were tested, only people with known exposures or symptoms. So, the real number is probably a little higher. But most of the 128,000 will be over 60, because they got vaccinated first. This suggests the vaccine is extremely effective.

“Currently more than 2.6 million Israelis have received a single dose of the vaccine and about 1.2 million have been given both shots, out of a population of about 9 million.”

9.     Israel sees 60% drop in hospitalisations for age 60+ 3 weeks after 1st shot

Maccabi Healthcare Services reported earlier this month that it has seen a 60% reduction in coronavirus infections three weeks after the first shot was administered, says The Times of Israel.

“The decrease in hospital admissions is swift after vaccination, Maccabi suggests in its latest data, finding that hospitalizations start to fall sharply from Day 18 after people receive the first shot. By Day 23, which is two days after the second shot, there is a 60% drop in hospitalizations among vaccinated people aged 60-plus.

However, Professor Rahav said that some of the drop may be due to a tendency of newly vaccinated people to adhere to lockdown rules, which causes a drop in infection and hospitalization.

Chart, line chart, histogram

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10.  EU vaccine delivery delays

BBC News reports that AstraZeneca has said a production problem means the number of initial doses available would be lower than expected. This comes after some nations’ vaccination programs were slowed due to a cut in deliveries of the Pfizer-BioNTech vaccine.