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

China: man tests positive after 3 weeks in quarantine and 9 negative Covid tests

A man who completed 21 days of mandatory quarantine upon returning to China from overseas has been identified as the likely source of a new Covid outbreak.  The man underwent 14 days of compulsory hotel quarantine, another 7 days in centralized quarantine and then a further week of health monitoring. He had tested negative for the virus nine times during 21 days of quarantine, before testing positive 37 days after entering China.

Putian’s locally-transmitted epidemic mainly has two chains of transmission – the one relating to Putou Primary School and one relating to Xiesheng shoe-making factory. The total infections from the school increased to at least 15 and at least 10 other infections from the Xiesheng shoe-making factory as of press time.

Preliminary studies suggest the outbreak may be traced to father of a student at the school who recently returned to Putian from Singapore. The person surnamed Lin tested positive on September 10, 38 days after returning from Singapore on August 4, during which he took nine nucleic acid and serologic tests, which were all negative.

Globaltimes.cn report

 

 

 

 

Photo by Nuno Alberto on Unsplash

Singapore: 1,096 new infections of which 484 were fully vaccinated, 333 were partially vaccinated and 279 unvaccinated

In its daily update on Thursday night (July 22), the Singapore Ministry of Health (MOH) revealed that of 1,096 locally transmitted infections over the last 28 days, 484 were fully vaccinated, 333 cases were partially vaccinated and 279 were unvaccinated.

StraitsTimes.com report

Editors note:  484 out of 1,096 infections is 44 per cent of the total. If you add the 333 partially vaccinated, the percentage of vaccine breakthroughs is nearly 75% of total infections.

Singapore: significant risk of vaccine breakthrough with the Sinovac #coronavirus vaccine

There is a significant risk of “vaccine breakthrough” with the Sinovac vaccine, or CoronaVac, with international evidence showing that many who had taken it were later infected with COVID-19, said the Ministry of Health’s (MOH) director of medical services Kenneth Mak on Friday, 18 June 2021.

Associate Professor Kenneth Mak said that Singapore has been assessing the experience of countries such as Indonesia, which has vaccinated a “larger proportion” of the population using CoronaVac.

Yahoo News report

 

 

Seychelles: a population of 100,000 that has 900 #coronavirus vaccine breakthrough cases

 

Chile: Santiago goes back into lockdown despite 60% #coronavirus vaccination rate

Photo by Xiaoxin Shen on Unsplash

UK: Delta with K417N – the “mountaineers” variant – PHE #coronavirus Delta-AY.1 update

Of the 36 cases of Delta-AY.1 (mountaineers) variant, 27 cases were known to have a vaccination status within the National Immunisation Management System (NIMS). 

“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. There is limited epidemiological information available at present.

International Epidemiology
As of 7 June 2021, 63 genomes of Delta with K417N have been identified on GISAID. from Canada (1) Germany (1), Russia (1), Nepal (2), Switzerland (4), India (6), Poland (9), Portugal (12), Japan (13), USA (14).

Epidemiology
There are currently 36 cases of Delta-AY.1 in England (35 confirmed sequencing and 1 probable genotyping) plus an additional 10 sequences which include some cases in other UK nations and some genomes for which case data is being sought. The first 5 cases were sequenced on 26 April 2021 and were contacts of travellers to Nepal and Turkey. All these cases were detected in the West Midlands. Cases have been detected in 6 different regions in England (Table 21, Figure 26). The majority of cases are in younger individuals, with 2 cases of age 60 or over (Figure 27). Out of the 36 cases, there were 11 travel associated cases (6 travellers and 5 cases amongst contacts of travellers). Twelve cases have no history of travel or contact with travellers. Countries of travel included red-list countries (Nepal and Turkey), amber-list countries (Malaysia) and green-list countries (Singapore).

Of the 36 cases, 27 cases were known to have a vaccination status within the National Immunisation Management System (NIMS), when linked on NHS number. Of these, 18 cases occurred in people who were not vaccinated, 2 cases in people who had received their first dose within 21 days of specimen date, 5 cases in people who had received their  first dose more than 21 days after specimen date. There was a total of 2 cases where there were more than 14 days between the second dose of vaccine and a positive specimen. No deaths have been recorded amongst the 36 cases.”

PHE download – SARS-CoV-2 variants of concern and variants under investigation in England  – Technical briefing 15 (PDF)

 

UK: The “mountaineers variant” – B.1.617.2 with K417N mutation

 

UK: “Everest climbers could have spread potentially more infectious and vaccine resistant’ variant

 

 

Image by Simon from Pixabay

Singapore: 78 #coronavirus cases in current outbreak were vaccinated compared to about 300 unvaccinated cases

A total of 78 Covid-19 cases in the current outbreak in Singapore have been vaccinated – many of whom are frontline workers – compared to about 300 unvaccinated cases, said Health Minister Ong Ye Kung.  The numbers represent a ratio of about 79 per cent unvaccinated cases versus 21 per cent vaccinated ones. It’s “not quite” true that the situation in Singapore is “getting very bad”, he said.

ChannelNewsAsia.com report

Singapore is currently battling a fresh wave of B.1.617.2 infections introduced through Changi airport despite strict anti-covid protocols including regular antigen and RT-PCR testing for the workforce. About one quarter of the population of Singapore have been fully vaccinated and over one third have been partially vaccinated. Singapore has only approved the use of the Pfizer and Moderna Covid-19 vaccines for use in the country. It’s a stark warning about the difficulty of controlling the spread of the new variant first discovered in India.

 

Singapore: Changi Airport #coronavirus cluster – 18 patients with 61% vaccine breakthrough rate

 

 

Image by Pexels from Pixabay

Singapore: B.1.617.2 Delta has a higher viral load in the respiratory tract of patients and stays for longer

On May 19, the director of Singapore’s National Center for Infectious Diseases, Professor Liang Yuxin, said in an exclusive interview with Singapore’s mainstream media, Lianhe Zaobao, that Singapore’s research shows that the recent local transmission of the mutant new coronavirus B.1.617.2 remains in the respiratory tract of patients in a higher amount. It also stays for longer, causing the virus to spread more easily.  A study found that patients infected with the B.1.617.2 virus had a higher amount and discharge of the virus in the respiratory tract than the original, longer time in the body, and a slower rate of decline.

Professor Liang Yuxin said that the lower the circulation threshold, the more viruses in the body. The circulation threshold of a common virus is about 20, while that of a variant virus is 15, so it may be easier to spread. She also said that the recent outbreaks of multiple infection groups in Singapore are all related to the B.1.617.2 variant virus that was first discovered in India.

Huanqiu.com report

 

Singapore: Changi Airport #coronavirus cluster – 18 patients with 61% vaccine breakthrough rate

 

 

Image by Jason Goh from Pixabay

Singapore: Changi Airport #coronavirus cluster – 18 patients with 61% vaccine breakthrough rate

 Eleven out of 18 positive patients were vaccinated, at least 6 are infected with the B.1.617 variant.

 

UK: eleven vaccine breakthrough cases reported for B.1.617.2

 

 

 

Image by David Mak from Pixabay