India: Omicron BA.2 is now at 57% of genome samples, but is Delta rising again?

India has seen quite considerable growth in the BA.2 sub-lineage of Omicron recently, lifting it to about 57% of all genome samples, with BA.1 now declining steadily.

What is surprising, however, is what looks like a recent increase in Delta variant cases, which now account for about 14% of samples according to CoVSpectrum. Delta was found in almost no genome samples at the turn of the year. This apparent increase could be an anomaly caused by the low number of samples submitted in 2022, but it’s something we’ll keep an eye on.

 

A plot using Cornelius Roemer’s lineage comparison app suggests Omicron BA.2 may be heading higher in India by outcompeting BA.1 completely:

 

It’s not clear which sub-lineage, if any, is responsible for a recent rise in Delta cases in India yet.

 

India has seen a large Omicron wave in January 2022, but it hasn’t yet reached the heights of its notoriously difficult Delta wave of Spring 2021.

 

Sri Lanka has also seen a few Delta cases since the New Year:

 

According to the latest SARS-CoV-2 variant report issued by the Sri Lanka Allergy Immunology and Cell Biology Unit of the Department of Immunology and Molecular Medicine of the University of Sri Jayewardenepura, 75 new cases of Omicron and 3 new cases of Delta were detected from 78 samples.

“These 78 samples were sequenced from the 1st 2nd and 3rd weeks of January from the community.” said Dr. Chandima Jeewandara, Director of the Allergy, Immunology and Cell Biology Unit of the Faculty of Medicine. The 78 Omicron cases include a mix of the two main Omicron lineages BA.1 and BA.2.

Different Delta sublineages were detected in the following locations.1 case of AY.98 (Sri Lanka delta sub-lineage) was detected in Thalangama. 1 case of AY.104 (Sri Lanka delta sub-lineage) was detected in Kaduwela. 1 case of B.1.617.2 was detected in Wellampitiya.

Currently, 8% of the sequences of Sri Lanka are BA.2, which was named as a variant of interest by the UK Health security agency.

Newswire.lk report

 

 

Europe: Another huge Covid wave is building right across the continent

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Photo by Ravi N Jha on Unsplash

 

India: Delta variant found in the brain of a dead wild leopard

Scientists from the Indian Veterinary Research Institute have detected Covid infection in a dead wild leopard cub in Uttar Pradesh. Genomic sequencing of samples from the carcass of the cub revealed that it had been naturally infected with the Delta variant.

“Though the necropsy findings suggested traumatic injuries as the immediate cause of death; detection of virus in various tissues indicates systemic SARS-CoV-2 infection of the animal prior to sudden death due to trauma inflicted by another carnivore. Presence of virus in the brain section suggests infection of central nervous system in wild felid which has previously been demonstrated in humans only”

Preprint: Systemic infection of SARS-CoV-2 in free ranging Leopard (Panthera pardus fusca) in India

 

South Africa: Puma and 3 lions infected with Delta variant in Pretoria Zoo

 

Image by Tati Halabi from Pixabay

India: Sars-CoV-2 remains active in a dead infected person for up to nine days

“Coronavirus, according to scientific evidence that has emerged so far, can survive on a dead body, in bodily fluids, secretions and moist cells of the dead body for up to nine days.”

The Indian government has declared that, as Sars-CoV-2 remains active in a dead infected person for up to nine days, its standard operating procedure provided only for cremation and burial of the dead infected persons, which excluded Parsi ritual of leaving the dead in Tower of Silence to get decayed by natural elements and birds.

The ministry, in its affidavit through advocate Rajat Nair, said the basic elements of the standard operating procedure is that the body should be fully covered and not exposed so that people who are handling the bodies of the persons who died of Covid, which may or may not include family members, must not come in contact with bodily fluids or secretions.

“Coronavirus, according to scientific evidence that has emerged so far, can survive on a dead body, in bodily fluids, secretions and moist cells of the dead body for up to nine days. A dead body will be considered as an inanimate surface and secretions from orifices will carry infected cells and will remain smeared on the body surfaces after death. An increased risk of Covid infection from a dead body to health workers or family members is unlikely when they follow standard precautions and SOPs while handling a dead body,” the Centre said.

The Times of India report

 

 

 

 

Photo by Eli Solitas on Unsplash

India: Man caught trying to get a 12th dose of Covid vaccine

An 84-year-old man from Bihar in India has claimed to have been inoculated with 11 doses of Covid-19 vaccines. According to a report by IndiaToday, Brahmadev Mandal, a resident of Orai village in Madhepura district was caught before being administered the 12th dose.

“I benefitted a lot from the vaccine. This is why I have been taking it repeatedly… The government has made a wonderful thing [vaccine],” Mandal reportedly said.

Deccan Herald report (in English)

 

Image by Yogendra Singh from Pixabay

India: Covid infections twice as high in fully vaccinated than those with single dose

More positive Covid cases are reported among fully-vaccinated people in India compared to those who have only had a single dose of vaccine.

According to Indian health experts, a combination of factors such as hybrid immunity (acquired through a combination of vaccination and infection), age and testing strategy could have led to the difference. There are various studies that indicate how hybrid immunity is superior when compared to the immunity received from double dose of vaccination. 

Dr Althaf A, an epidemiologist and associate professor at Government Medical College Hospital, Manjeri, pointed out that hybrid immunity among youngsters is far better than that of fully-vaccinated adults.  “There are chances that a lot of youngsters were infected in the second wave. When they get a single dose following the infection, it will result in better immunity,” he said. 

New Indian Express report

p.s. That’s a 38% vaccine breakthrough rate for the fully vaccinated, and a 55% vaccine breakthrough rate if you combine the partially and fully vaccinated….

 

 

Decoding Sars-Cov-2: How are global Covid waves formed, and can we predict future waves?

Global Covid waves are formed by smaller continental waves combining to create the unique global sine wave pattern we have seen in 2021.

The chart below shows the global Covid wave pattern from 2021. Let’s take it apart and look at the constituent elements of each wave. We’ll be using a biweekly view for these charts as it smooths out a lot of the jitter and gives a clearer picture of wave direction.

 

The chart below shows the constituent elements of the three global Covid waves of 2020 and 2021. It shows which continents contributed to each wave.

We have included India in this chart as it was such a major factor in the second global wave. We have separated North America and South America as their respective waves are not linked, and we have excluded Africa from the chart as its recorded cases have been too low to make an impact on the global situation.

You can see from the above chart that two continents were largely responsible for the first major winter wave from October 2020 to February 2021. They were Europe and North America.

Both of the North American and European winter waves of October 2020 to February 2021 were largely blunted by national lockdowns, local lockdowns and lower case recording over the winter holidays. The first winter wave of 2020-2021 would have undoubtedly been the largest wave of the past year had it not been for those mitigating measures.

As we mentioned earlier, Asia, (notably India) was the chief contributor to the second global wave, from February 2021 to June 2021.

The third global wave from June 2021 to October 2021 largely consisted of cases from Asia, North America and Europe.

It’s already apparent that Europe will play a large role in the coming winter wave from October 2021 to February 2022, but which continents will accompany it?

Every other continent is currently on the downward slope from a wave, none have yet shown an inflexion point or upward curve in Covid cases indicating a new wave forming.

We have seen, however, increasing Covid activity in both China and Singapore this week, and news this morning of a sudden spike in Covid deaths in India attracted our attention, particularly as it seems to be occurring without a corresponding increase in Covid cases. The increase in Indian deaths also began close to the anniversary of last year’s global infection point for Covid deaths that happened on the 19th October 2020.

 

North America is a few weeks behind Asia in its exit slope. Its earlier than expected summer wave in 2021 has put it slightly out of sync with its previous waves. South America has yet to contribute to a global wave in any significant manner.

So, on the basis of the second chart above, it would seem that Europe and Asia would be the most likely contributors to a new global winter wave. A fresh wave in North America could begin within weeks though, perhaps as early as November 2021. A combination of waves from these three continents would be a repeat of the last wave. It could be the largest global wave of the pandemic so far as many of the mitigations used last year appear to have been abandoned.

In our next post, we will be trying to predict future Covid waves on a continental level and a national level by using repeating code snippets – the same method we used successfully in this post and in this post

 

Here is the interactive global biweekly case chart:

 

More in our Decoding Sars-Cov-2 series:

 

 

 

Image by Free-Photos from Pixabay

India seeing a rise in Covid deaths without a corresponding rise in cases

India has seen an unusual increase in Covid deaths over the last week without a corresponding rise in Covid cases. The sudden surge in deaths started on the 21st October 2021, a date that we have already mentioned as a possible inflexion point for Covid waves in both 2020 and 2021.

Seeing a rise in the Covid death rate without a prior uptick in cases is a highly unusual turn of events. Indian newspapers don’t appear to have picked up on it yet.

Singapore has also reported an unusual increase in deaths and cases today, so we are publishing their Covid case and death charts for comparison.

 

Indian deaths from Covid-19 have started to rise despite a stable Covid infection rate:

 

Covid case rates in India have been stable for months following its large wave earlier in the year:

 

 

Singapore has also seen a large rise in Covid deaths over the past month. but they are firmly linked to a rise in cases:

 

UPDATE: 29th October 2021: From our reader John: “80 to 90% of the deaths are in the state of Kerala. None that I see today are in Uttar Pradesh. https://www.mohfw.gov.in/”

 

UPDATE: 29th October 2021: “India records 585 Covid-19 deaths in 24 hours, 482 of them from Kerala”

The situation in Kerala has been of concern for the central government in the last few months. Majority of the worst-affected districts across the country are in Kerala, according to central government figures.

Though the daily count of infection has come down in the southern state, it is still recording more than half of the entire country’s Covid-19 caseload every day.

Hindustantimes.com report

 

 

Published 11th October 2021:

October 19th – 23rd could be crucial in determining how bad Covid-19 will be this winter

 

 

Image by RENE RAUSCHENBERGER from Pixabay

USA: Covid-19 vaccine breakthrough case in a tiger

There’s a headline we never thought we would write.

A partially vaccinated 11-year-old tiger at the Brookfield Zoo has tested positive for COVID-19. The zoo received confirmation of Amur tiger Malena’s positive test this week after she started showing mild respiratory symptoms, including coughing and sneezing, late last week. Those symptoms are consistent with what other zoos have seen in big cats infected with COVID-19, according to a statement from the Chicago Zoological Society.

ABC7Chicago.com report

 

USA: Six African lions, a Sumatran tiger and two Amur tigers infected with Covid in Washington Zoo

 

 

 

Photo by Frida Bredesen on Unsplash

USA: Six African lions, a Sumatran tiger and two Amur tigers infected with Covid in Washington Zoo

Six African lions, a Sumatran tiger and two Amur tigers at the National Zoo in Washington have tested positive for the coronavirus, which causes Covid-19, the Smithsonian Institution said Friday.

Animal caretakers observed appetites, coughing, sneezing and lethargy in six African lions, a Sumatran tiger and two Amur tigers, and final results were expected in coming days to confirm the presumptive positive coronavirus test results, said the Smithsonian, which operates the zoo.

“All lions and tigers are being treated with anti-inflammatories and anti-nausea medication to address discomfort and decreased appetite,” the zoo said on its website, adding that they were also being treated with antibiotics for possible secondary bacterial pneumonia.

Smithsonian Magazine report

 

 

Image by Kevinsphotos from Pixabay

Global Covid-19 deaths almost TRIPLE in one day on 20th July 2021

The global death toll from Covid-19 almost tripled in one day yesterday. The global death toll had been averaging around 6,000 – 8,000 cases for the past week, but yesterday that figure rocketed to over 22,000.

It seems that Ecuador accounted for a large proportion of those new deaths, jumping from just a handful over the past week to over 8,000 deaths in one day, but that is not the entire story. India saw a sudden massive leap in deaths, as did many other countries. It’s almost as if Sars-CoV-2 went into another gear across the entire globe yesterday.

A report in yesterday’s London Times estimated that India’s death toll may be as high as four million people – ten times its current figure, but this would not have been included in the new global toll reported today.

This is a story we will try to update as more information becomes available.

 

Global: Sars-COV-2 – a virus that oscillates between killing 5,000 to 20,000 a day for an entire year?

India: children returning to hospitals with long-covid symptoms like breathlessness, headaches, say Delhi doctors

Dr Nameet Jerath, Senior Consultant, Pediatric Intensive Care, Indraprastha Apollo Hospitals, New Delhi, said most children previously infected with coronavirus have had mild Covid, but stressed that even those who were asymptomatic are having prolonged low grade fevers, weakness, headache even after recovery.

Dr Shuchin Bajaj, Founder-Director, Ujala Cygnus Group of Hospitals, said that children are facing the issue of brain fogging and are unable to remember what they studied.

“They do not have much energy left, are stressed, anxious. Parents might confuse brain fogging with children trying to make excuses to not study or attend online classes, but these are real symptoms,” he said.

Bajaj also said that in children who had severe Covid, symptoms like shortness of breath, developing severe heart rate even while going to toilet, severe headaches were found.

“These symptoms were found to be persisting for three to four months,” he added.

ThePrint.in report

 

 

 

Image by AkshayaPatra Foundation from Pixabay

India: Delta Plus Delta-AY.1 dominant in Tripura – found in 138 out of 151 coronavirus sequences

At least 138 of the 151 Covid-19 samples sent by Tripura for genome sequencing have tested positive for the Delta Plus variant, State Health Surveillance Officer Dr Deep Kumar Debbarma said. Tripura, thus, is the first state in the northeast to have recorded a case of the Delta Plus variant.

Addressing reporters on Friday evening, Debbarma said the samples were sent to a laboratory at Kalyani, West Bengal, for the virological test. “Delta Plus variant was found in 138 of the 151 samples. 10 others tested positive for the Delta variant while three cases of alpha variant were found,” Debbarma added.

Indian Express Report

USA/UK: 2 separate clades of Delta #coronavirus variant with K417N – AY.1 and AY.2

Through routine scanning of variation in Delta, a small number of sequences were detected which had acquired the spike protein mutation K417N. Information suggests that there are at least 2 separate clades of Delta with K417N. One clade is large and internationally distributed with PANGO lineage designation AY.1.  A second clade found in sequences uploaded to GISAID from the USA, now designated AY.2.

As of 16 June 2021, 161 genomes of Delta-AY.1 have been identified on GISAID. from Canada (1), India (8), Japan (15), Nepal (3), Poland (9), Portugal (22), Russia (1), Switzerland (18), Turkey (1), USA (83).

There are currently 38 cases of Delta-AY.1 in England (36 confirmed sequencing and 2 probable genotyping). Cases have been detected in 6 different regions in England. Delta-AY.2 has not been detected in England.

UK Variants of Concern Technical Briefing 15 (PDF download)

 

According to Bani Jolly of the Institute of Genomics and Integrative Biology, the phylogeny of Delta has two separate clades. While AY.1 is found in a few countries including the UK, India and Nepal, the other clade (AY.2), is largely from the sequences from California (USA).

“The split between the two clades seems to be based on two spike mutations — A222V and T95I. While all sequences in the California cluster share spike A222V, all sequences in the larger international cluster share spike T95I,” Jolly tweeted.

Stating that AY.1 has arisen independently a number of times and could be more prevalent than observed in countries with limited genomic surveillance, she tweeted that given that Delta is a variant of concern, it is important to take note of any sub-lineages that may emerge.

Time of India report

 

 

 

Image by PublicDomainPictures from Pixabay

India: four lions at Vandalur zoo infected with Delta variant of #coronavirus

The Genome sequencing analysis of four samples taken from lions at the Arignar Anna Zoological Park in Vandalur revealed that they were all affected by the Delta (B.1.617.2) variant of Covid.

“Genome sequencing of 4 of the samples was done at NIHSAD, Bhopal. Analysis of the sequences shows that all the 4 sequences belong to Pangolin lineage B.1.617.2 and are Delta variants as per WHO nomenclature,” an official from the release Arignar Anna Zoological Park read.

As per the report communicated on June 3 by NIHSAD, Bhopal, the samples of 9 lions had tested positive for SARS CoV-2 and the animals have been under active treatment since then.

The park authorities had requested the Institute to share the results of genome sequencing of the SARS CoV-2 virus that has infected the lions.

Two lions have recently died of Covid-19 s at the zoo, see reports below

TribuneIndia.com report

 

India: second lion dies of #coronavirus at Vandalur Zoo near Chennai

 

India: Neela the lioness dies of #coronavirus infection at Vandalur zoo – UPDATED

 

Photo by Andrea Brataas on Unsplash