H5N1

COVID-19 in Brazil: 27,804 new cases, 618 deaths today

A screenshot from the CONASS PANEL | COVID-19 dashboard:

Cases and deaths are low, but weekend counts usually are. The tally for epi-week 25, which ended Saturday, was 503,144—higher than any but three previous weeks in Brazil's panemic. The week's deaths, 11,935, were lower than the spring spike weeks, but still higher than any week in the pandemic before epi-week 10:

Profound brain changes found in patients who died of COVID-19

Via Medscape.comProfound Brain Changes Found in Patients Who Died of COVID-19.

The most comprehensive molecular study to date of brain tissue from people who died of COVID-19 provides clear evidence that SARS-CoV-2 causes profound molecular changes in the brain, despite no molecular trace of the virus in brain tissue. 

"The signature the virus leaves in the brain speaks of strong inflammation and disrupted brain circuits and resembles signatures the field has observed in Alzheimer's or other neurodegenerative diseases," senior author Tony Wyss-Coray, PhD, professor of neurology and neurological sciences, Stanford University School of Medicine, Stanford, California, told Medscape Medical News. 

The study was published online June 21 in Nature. 

Signs of Distress 

"We know that up to a third of SARS-CoV-2-infected people show brain symptoms including brain fog, memory problems, and fatigue, and a growing number of people have such symptoms long after they seemingly recovered from virus infection," said Wyss-Coray. 

"However, we have very little understanding of how the virus causes these symptoms and what its effects are on the brain at a molecular level," he added. 

Using single-cell RNA sequencing, the researchers profiled the transcriptomes of 65,309 nuclei isolated from frontal cortex and choroid plexus samples from eight patients who died of COVID-19 and 14 controls who died of other causes. 

There was no molecular evidence of SARS-CoV-2 in brain tissue samples from the patients who died of COVID-19.

Yet, "we were very surprised to learn that no matter which type of cell we studied (different types of nerve cells, immune cells, or different support cells in the brain) there were prominent changes" compared with brain tissue samples from controls who died of other causes, said Wyss-Coray. 

The changes in the COVID-19 brains showed signatures of inflammation, abnormal nerve cell communication, and chronic neurodegeneration. 

"Across cell types, COVID-19 perturbations overlap with those in chronic brain disorders and reside in genetic variants associated with cognition, schizophrenia, and depression," the researchers report. 

"Viral infection appears to trigger inflammatory responses throughout the body that may cause inflammatory signaling across the blood–brain barrier, which in turn could 'trip off' neuroinflammation in the brain," Wyss-Coray said. 

The findings may help explain the brain fog, fatigue, and other neurological and psychiatric symptoms of long COVID. 

"While we studied only brains from people who died of COVID-19, we believe it is likely that similar, but hopefully weaker, signs of inflammation and chronic neurodegeneration will be found in COVID-19 survivors, especially those with chronic brain symptoms," Wyss-Coray said.

COVID-19 in Russia: 21,650 new cases, 611 deaths today

Via The Moscow Times: Coronavirus in Russia: The Latest News | June 28. Excerpt:

Russia has confirmed 5,451,291 cases of coronavirus and 133,282 deaths, according to the national coronavirus information center. Russia’s total excess fatality count since the start of the coronavirus pandemic is around 475,000. 

June 28: What you need to know today 

• Russia on Monday confirmed 21,650 new coronavirus cases, the highest number since January, and 611 deaths. Moscow recorded 7,246 cases and 124 deaths, a new daily mortality record for the capital. St. Petersburg recorded 1,335 new cases and a new record of 110 deaths. 

• Starting Monday, all restaurant and cafes in Moscow will require patrons to present an official QR code confirming their vaccination status, immunity or negative PCR test results. 

• All Russian travelers, vaccinated or not, will have to present a negative PCR or rapid test result on arrival in Greece, Athens announced Sunday. Travelers from Russia will also have to undergo another test as soon as they arrive.

COVID-19: Research investigates the evolution of lethality worldwide

A June 25 news release from Fiocruz: COVID-19: research investigates the evolution of lethality worldwide. The Google translation:

A study developed in partnership between Fiocruz Pernambuco, the Federal Rural University of Pernambuco (UFRPE) and the Federal Institute of Paraíba (IFPB) carried out an investigation on the evolution over time of the daily numbers of deaths by COVID-19, taking into account the scenario in 43 countries. 

Using physical approaches and information theory techniques, the researchers achieved results that give scientific evidence as for the efficiency of measures such as the use of face masks, social distancing, quarantines, mass testing, and education on hygiene, to restrict the impacts of the disease. The research showed that countries that behaved in a proactive fashion in the implementation of these public health measures presented higher predictability (less entropy) to lethality by COVID-19. 

Conversely, countries that were reactive in the implementation of these measures had less predictability (more entropy). “In face of this, our findings show that these preventive measures are efficient in the fight against the lethality of COVID-19”, say the scientists of the article Predictability of COVID-19 worldwide lethality using permutation-information theory quantifiers, published in Results in Physics of the Elsevier platform. 

The methodology adopted in the study used the quantifiers of information theory, more specifically permutation entropy and Fisher’s information. The figures cover the approximate period of a year, between February 19th, 2020, and January 6th, 2021. 

“The use of permutation entropy and of Fisher’s information to quantify the disorder of time series of deaths by COVID-19 is an innovative approach, bringing together the physics of biological phenomenon and bringing to light the understanding of the ongoing pandemic. This approach places our group in the vanguard of the comprehension of COVID-19 dynamics”, explains Fiocruz researcher Bartolomeu Acioli, coordinator of the study. 

“Based on a perspective of public health, our methodology is a robust approach to subsidize decision-making by public agents on efficient measures to address the current pandemic”, declares UFRPE professor Leonardo Fernandes, a partner in the research and lead author of the paper. The research group also includes IFPB professors Fernando Araújo and Angélica Silva.

 The nine countries best ranked in the research are Taiwan, Vietnam, New Zealand, Singapore, Iceland, Thailand, Cyprus, Estonia, and Norway. Throughout the period under analysis, these places had a few common characteristics, such as less than 25 accumulated deaths per 100 inhabitants and no peak of deaths that could be characterized as a wave, as occurred in other countries. 

 The countries with the highest entropy, i.e. those located the lowest in the ranking, were Argentina, South Africa, Belgium, Iran, Czech Republic, India, Peru, Colombia, and Italy. The authors explain that all these countries experienced some moment of explosion in the number of deaths, characterized as one, two, or even three contamination waves. In the case of Italy, the first Western country to experience the new coronavirus epidemic and the lowest-ranking country in this study, the growth in the number of cases and deaths was exponential as early as in the first months. 

In spite of the high number of deaths by COVID-19 recorded in the interval under study, the United States and Brazil are in an intermediate position in this ranking - 15th and 16th, respectively.

COVID-19 in Russia: 20,583 new cases, 599 deaths today

Our World in Data

Via The Moscow Times: Coronavirus in Russia: The Latest News | June 27. Excerpt:

Russia has confirmed 5,451,291 cases of coronavirus and 133,282 deaths, according to the national coronavirus information center. Russia’s total excess fatality count since the start of the coronavirus pandemic is around 475,000. 

June 27: What you need to know today 

• Russia on Sunday confirmed 20,538 new coronavirus cases, the highest number since January, and 599 deaths. Moscow recorded 6723 cases and 114 deaths, a new daily mortality record.

Chinese city of Guangzhou to build giant Covid-19 quarantine facility with 5,000 spaces for international travellers

Via the South China Morning Post: Chinese city of Guangzhou to build giant Covid-19 quarantine facility with 5,000 spaces for international travellers. If Dr. Zhong Nanshan is backing this, it will happen. Excerpt:

The southern Chinese city of Guangzhou is planning to build a massive quarantine complex for international travellers and local residents from high-risk areas because local hotels cannot cope with highly transmissible Covid-19 mutations such as the Delta variant, according to leading respiratory expert Zhong Nanshan. 

“There will be 5,000 isolated spaces and the people there will be isolated according to strict rules to make sure they do not infect each other,” Zhong told a group interview on Friday. 

Zhong said that after observing the transmissibility of the Delta variant in Guangdong province during the past month, he was convinced that using hotels as quarantine facilities would not be enough to stop the spread of the disease given it was a lot more transmissible than other pre-existing variants. 

The mutations of the coronavirus also mean that other transmissible variants may also emerge in future.  

“In the long term, Guangzhou and Shenzhen must build these kinds of facilities. Otherwise when there are lots of cases in the future and we have to quarantine them in hotels, it will affect the economy and we cannot isolate them in a real sense.” 

Zhong said the new facility would cover 250,000 square metres, or 25 hectares – about the size of 46 football pitches. 

China has assigned Guangdong as the major portal to receive and quarantine international travellers before they go on to other parts of the country. Zhong said 80 to 90 per cent of international travellers entered the country via the southern province. 

Guangdong had also been asked to prevent the Delta variant from spreading to other provinces during the recent outbreak by reducing the number of travellers, Zhong said. People travelling from several cities in Guangdong have been asked to produce negative test results before they were allowed to leave. 

Zhong, who also played a leading role in tackling the severe acute respiratory disease outbreak in 2003, said so far no local cases of the Delta variant had been found outside Guangdong, but it was hard to guarantee there would be no cases outside the province because of the transmissibility of the variant. 

Zhong said the definition of “close contacts” and how they should be isolated should be revised. 

China has pursued a zero-tolerance strategy towards tracking and testing all close contacts of a positive case. Expanding the definition means the number of people being tested and quarantined would be increased after a positive case is found. 

“In the past, close contacts were defined as the families of a patient, or people who had meals or meetings with the patient in an office or within one metre in the two days before the symptom onset,” Zhong said. 

“But with the Delta variant, close contacts should be defined as those who stayed in the same space, same unit, or even in the same building in the four days before the onset of symptoms.”

Finland: 120 confirmed coronavirus infections linked to St. Petersburg travel

Via Yle Uutiset: THL: 120 confirmed coronavirus infections linked to St. Petersburg travel.

The Finnish Institute for Health and Welfare THL has stated that the number of lab-confirmed coronavirus infections linked to tourist trips to St. Petersburg has now risen to 120. 

"By yesterday [Friday] afternoon, more than 120 cases had been detected among travellers returning from St. Petersburg. Most of the infections have been detected in travellers who have returned from the European Football Championships," director of THL's Department for Health Security Mika Salminen said. 

Although public debate in Finland has revolved around returning football fans, Salminen said the THL's call to undergo a coronavirus test applies to all tourists returning from St. Petersburg. There are so many infections that anyone who travelled in a bus or minivan should take precautions, he added. 

"Everyone who has travelled on a bus or in a minivan could have been exposed. People need to apply for a coronavirus test as early as this week, and not wait until next week," Salmimen said. 

According to THL's assessment, it is possible that some of the infections may be the Delta variant, previously known as the variant first detected in India. 

"The assessment is slow and technical, and it can take up to two weeks to get results from these tests. You have to act on the assumption that these can be it [the Delta variant]. The measures are exactly the same regardless of which variant is involved," he said, adding that authorities are continuing efforts to contact all people who may have been exposed to the virus. 

"We have received lists of people who were there at the border crossing, and with the help of these lists, municipalities are trying to reach people. There are always some challenges, some people may not have even gone on the trip, have changed buses or returned via a different route. It can never be 100 percent accurate, but the municipalities are doing their best," he said. 

THL further recommends that anyone who may have been in contact with tourists who returned from St. Petersburg to Finland should also apply for a coronavirus test. 

Cases reported all over the country 

Infections related to travel to St. Petersburg have been detected all over Finland. 

"A large part are in the Helsinki metropolitan area, Helsinki, Espoo and Vantaa. There are also infections in Turku, Hämeenlinna, Kuopio, Jyväskylä and even Oulu. They are all over Finland," Salimen said, adding that identifying infections is a positive thing, as it reduces the risk of further cases. 

Last Tuesday, about 800 people were allowed to enter Finland at the Vaalimaa border crossing without the need for a coronavirus test or health checkup. 

Authorities decided to make an exception to the rule about testing as traffic was heavily congested at the border crossing, especially as hundreds of football fans returned from watching Finland play Belgium in the European Championship finals in St. Petersburg on Monday evening.

COVID-19 in Brazil: 79,277 new cases, 2,001 deaths today

A screenshot from the CONASS PANEL | COVID-19 dashboard:

Recovery of deleted deep sequencing data sheds more light on the early Wuhan SARS-CoV-2 epidemic

Via bioRxiv: Recovery of deleted deep sequencing data sheds more light on the early Wuhan SARS-CoV-2 epidemic. The abstract:

The origin and early spread of SARS-CoV-2 remains shrouded in mystery. Here I identify a data set containing SARS-CoV-2 sequences from early in the Wuhan epidemic that has been deleted from the NIH’s Sequence Read Archive. I recover the deleted files from the Google Cloud, and reconstruct partial sequences of 13 early epidemic viruses. 

Phylogenetic analysis of these sequences in the context of carefully annotated existing data suggests that the Huanan Seafood Market sequences that are the focus of the joint WHO-China report are not fully representative of the viruses in Wuhan early in the epidemic. Instead, the progenitor of known SARS-CoV-2 sequences likely contained three mutations relative to the market viruses that made it more similar to SARS-CoV-2’s bat coronavirus relatives.

Research suggests first cases of Covid-19 arose earlier than initially reported

Via the University of Kent: Research suggests first cases of Covid-19 arose earlier than initially reported.

Research led by Dr David Roberts at the University’s School of Anthropology and Conservation has found that the first case of Covid-19 likely arose between early October and mid-November 2019 in China, with the most likely date of origin being 17 November 2019. 

The origins of the ongoing Covid-19 pandemic remain unclear. The first officially identified case occurred in early December 2019. Yet, this research published by PLOS Pathogens supports growing evidence that the Covid-19 pandemic arose sooner and grew more rapidly than officially reported. 

Dr Roberts alongside Dr Jeremy Rossman (Honorary Senior Lecturer in Virology at Kent’s School of Biosciences and President of Research-Aid Networks, Chicago) and Dr Ivan Jarić (Biology Centre of the Czech Academy of Sciences), used a statistical modelling technique previously utilised in conservation science to establish this finding. 

The optimal linear estimation (OLE) modelling technique originally developed by Dr Roberts and a colleague to date extinctions of species, helped to clarify the timing of the onset of the pandemic. The researchers reversed the method to determine the date when Covid-19 most likely originated, according to when some of the earliest known cases occurred in 203 countries. 

The analysis also identified when Covid-19 is likely to have spread to the first five countries outside of China, as well as other continents. For instance, it estimates that the first case outside of China occurred in Japan on 3 January 2020, the first case in Europe occurred in Spain on 12 January 2020, and the first case in North America occurred in the United States on 16 January 2020. 

Dr Roberts said: ‘The novel application of OLE within the field of epidemiology offers a new opportunity to understand the emergence and spread of diseases as it only requires a small amount of data. 

‘This application could be applied to provide insights into Covid-19’s continued spread and help authorities to better understand the spread of other infectious diseases in the future.’ 

Their research paper ‘Dating first cases of COVID-19’ is published by PLOS Pathogens: doi: 10.1371/journal.ppat.1009620 Coronavirus