Archive for ‘virologist’

31/05/2020

India coronavirus: Why is India reopening amid a spike in cases?

A rush of people and motorists in a marketplace area as shops start opening in the city under specific guidelines, on May 20, 2020 in Jammu, IndiaImage copyright GETTY IMAGES
Image caption Within a week of reopening, India has seen a sharp spike in cases

India is roaring – rather than inching – back to life amid a record spike in Covid-19 infections. The BBC’s Aparna Alluri finds out why.

On Saturday, India’s government announced plans to end a national lockdown that began on 25 March.

This was expected – the roads, and even the skies, have been busy for the last 10 days since restrictions started to ease for the first time in two months. Many businesses and workplaces are already open, construction has re-started, markets are crowded and parks are filling up. Soon, hotels, restaurants, malls, places of worship, schools and colleges will also reopen.

But the pandemic continues to rage. When India went into lockdown, it had reported 519 confirmed cases and 10 deaths. Now, its case tally has crossed 173,000, with 4,971 deaths. It added nearly 8,000 new cases on Saturday alone – the latest in a slew of record single-day spikes.

A worker cleans the mascot of fast-food company McDonald's for the reopening of the outlet in Hyderabad on May 20.Image copyright GETTY IMAGES
Image caption Fast food chains like McDonald’s have begun reopening outlets in parts of India.

So, why the rush to reopen?

The lockdown is simply unaffordable

“It’s certainly time to lift the lockdown,” says Gautam Menon, a professor and researcher on models of infectious diseases.

“Beyond a point, it’s hard to sustain a lockdown that has gone on for so long – economically, socially and psychologically.”

From day one, India’s lockdown came at a huge cost, especially since so many of its people live on a daily wage or close to it. It put food supply chains at risk, cost millions their livelihood, and throttled every kind of business – from car manufacturers to high-end fashion to the corner shop selling tobacco. As the economy sputtered and unemployment rose, India’s growth forecast tumbled to a 30-year-low.

Raghuram Rajan, an economist and former central bank governor, said at the end of April that the country needed to open up quickly, and any further lockdowns would be “devastating”.

The opinion is shared by global consultant Mckinsey, whose report from earlier this month said India’s economy must be “managed alongside persistent infection risks”.

Passengers maintaining social distance as they are on board in a DTC Bus after government eased lockdown restriction, at AIIMS on May 20, 2020 in New Delhi, India.Image copyright GETTY IMAGES
Image caption As restrictions ease, Indians are slowly getting used to the new normal

“The original purpose of the lockdowns was to delay the spike so we can put health services and systems in place, so we are able handle the spike [when it comes],” says Dr N Devadasan, a public health expert. “That objective, to a large extent, has been met.”

In the last two months, India has turned stadia, schools and even train coaches into quarantine centres, added and expanded Covid-19 wards in hospitals, and ramped up testing as well as production of protective gear. While grave challenges remain and shortages persist, the consensus seems to be that the government has bought as much time as possible.

“We have used the lockdown period to prepare ourselves… Now is the time to revive the economy,” Delhi Chief Minister Arvind Kejriwal said last week.

The silver lining

For weeks, India’s relatively low Covid-19 numbers baffled experts everywhere. Despite the dense population, disease burden and underfunded public hospitals, there was no deluge of infections or fatalities. Low testing rates explain the former, but not the latter.

In fact, India made global headlines not for its caseload but for its botched handling of the lockdown – millions of informal workers, largely migrants, were left jobless overnight. Scared and unsure, many tried to return home, often desperate enough to walk, cycle or hitchhike across hundreds of kilometres.

Perhaps the choice – between a virus that didn’t appear to be wreaking havoc yet, and a lockdown that certainly was – seemed obvious to the government.

But that is changing quickly as cases shoot up. “I suspect we will keep finding more and more cases, but they will mostly be asymptomatic or will have mild symptoms,” Dr Devadasan says.

The hope – which is also encouraging the government to reopen – is that most of India’s undetected infections are not severe enough to require hospitalisation. And so far, except in Mumbai city, there has been no dearth of hospital beds.

India’s Covid-19 data is spotty and sparse, but what it does have suggests that it hasn’t been as badly hit by the virus as some other countries.

The government, for instance, has been touting India’s mortality rate as a silver lining – at nearly 3%, it’s among the lowest in the world.

But some are unconvinced by that. Dr Jacob John, a prominent virologist, says India has never had, and still doesn’t have, a robust system for recording deaths – in his view, the government is certainly missing Covid-19 deaths because they have no way of knowing of every fatality.

A woman jogs at Lodhi Garden after the local government eased restrictions imposed as a preventive measure against the spread of the COVID-19 coronavirus in New Delhi on May 21, 2020.Image copyright GETTY IMAGES
Image caption Indians are venturing out again but it’s unclear how many of them are asymptomatic.

And, he says, “what we must aim for is flattening the mortality curve, not necessarily the epidemic curve”.

Dr John, like several other experts, also predicts a peak in July or August, and believes the country is reopening so quickly because the “government realised the futility of such leaky lockdowns”.

A shift in strategy

So is the government gearing up for another lockdown when the peak comes?

While Dr Menon believes the lockdown was well-timed, he says it was too focused on cases coming from abroad.

“There was a hope that by controlling that, we could prevent epidemic spread, but how effective was our screening [at airports]?”

Now, he adds, is the time for “localised lockdowns”.

Media caption Coronavirus: Death and despair for migrants on Indian roads

The federal government has left it to states to decide where, how and to what extent to lift the lockdown as the virus’ progression varies wildly across India.

Maharashtra alone accounts for more than a third of India’s active cases. Add Tamil Nadu, Gujarat and Delhi, and that makes up 67% of the national total.

But other states – such as Bihar – are already seeing a sharp uptick as migrant workers return home.

“Initially, most of your cases were in the cities,” Dr Devadasan says. “But we kept the migrant workers in cities and didn’t allow them to go home. Now, we are sending them back. We have facilitated transporting the virus from urban areas to rural areas.”

While the government has said how many infections have been avoided – up to 300,000 – and lives saved – up to 71,000 – by the lockdown, there is no indication of what lies ahead.

There is only advice: The day the government began to ease restrictions, Mr Kejriwal tweeted, urging people to “follow discipline and control the coronavirus disease” as it was their “responsibility”.

The famous Paranthe wali gali (bylane of fried bread) in Chandni Chowk, on August 20, 2014 in New Delhi, India.Image copyright GETTY IMAGES
Image caption Social distancing will prove to be India’s biggest post-lockdown challenge

Because the alternative – of curfews and constant policing – is unsustainable.

“My worry is more the circumstances of people – it’s not as though they have an option to practise social distancing,” Dr Menon says.

And they don’t – not in joint family homes or one-room hovels packed together in slums, not in crowded markets or busy streets where jostling is second nature, or in temples, mosques, weddings or religious processions where more is always merrier.

The overwhelming message is that the virus is here to stay, and we have to learn to live with it – and the only way to do that, it appears, is to let people live with it.

Source: The BBC

28/05/2020

India coronavirus: Trouble ahead for India’s fight against infections

Coronavirus in IndiaImage copyright GETTY IMAGES
Image caption India has more than 150,000 reported infections

On the face of it, things may not look bad.

Since the first case of coronavirus at the end of January, India has reported more than 150,000 Covid-19 infections. More than 4,000 people have died of the infection.

To put this in some context, as of 22 May, India’s testing positivity rate was around 4%, the death rate from the infection around 3% and the doubling rate of infection – or the amount of time it takes for the number of coronavirus cases to double – was 13 days. The recovery rate of infected patients was around 40%.

All this is markedly lower than in the countries badly hit by the pandemic.

Like elsewhere in the world, there are hotspots and clusters of infection.

More than 80% of the active cases are in five states – Maharashtra, Tamil Nadu, Delhi, Gujarat and Madhya Pradesh – and more than 60% of the cases in five cities, including Mumbai, Delhi and Ahmedabad, according to official data.

More than half of people who have died of the disease have been aged 60 and older and many have underlying conditions, hewing to the international data about elderly people being more vulnerable to the disease.

The more than two-month-long grinding lockdown, official data suggests, has prevented the loss of between 37,000 and 78,000 lives. A paper published in Harvard Data Science Review appears to support that – it shows an eight-week lockdown can prevent about two million cases and, at a 3% fatality rate, prevent some 60,000 deaths.

“Infection has remained limited to certain areas. This also gives us confidence to open up other areas. It is so far an urban disease,” says VK Paul, who heads the medical emergency management plan on Covid-19.

This is where such claims enter uncertain territory.

India testingImage copyright GETTY IMAGES
Image caption India has conducted some 180,000 tests so far

India is now among the top 10 countries worldwide in terms of total reported infections, and among the top five in the number of new cases.

Infections are rising sharply, up from 536 cases on 25 March when the first phase of the world’s harshest lockdown was imposed. The growth of infections is outpacing growth in testing – tests have doubled since April but cases have leapt fourfold.

Epidemiologists say the increase in reported infections is possibly because of increased testing. India has been testing up to 100,000 samples a day in the past week. Testing criteria has been expanded to include asymptomatic contacts of positive patients.

Yet, India’s testing remains one of the lowest in the world per head of population – 2,198 tests per million people.

The bungled lockdown at the end of March triggered an exodus of millions of informal workers who lost their jobs in the cities and began returning home in droves, first on foot and then by train. Some four million workers have travelled by rail from cities to their villages in more than half a dozen states in the past three weeks.

There is mounting evidence that this has already led to the spread of infection from the cities to the villages. And with the messy easing of the lockdown earlier this month, there are growing fears of infections spreading further in the cities.

Rising infections and a still-low fatality rate possibly points to milder infection in a younger population and a large number of asymptomatic cases. The focus, says Amitabh Kant, CEO of the government think-tank NITI Aayog, should be “bringing down fatalities and improving the recovery rate”.

But if the infection rate continues to grow, “things are going to get pretty grim in a few weeks time,” a leading virologist told me.

India lockdownImage copyright GETTY IMAGES
Image caption Millions of workers have fled the cities and returned to their villages after the lockdown

Doctors in the capital, Delhi, and the western city of Mumbai tell me they are already seeing a steady surge in Covid-19 admissions and worry about a looming shortage of hospital beds, including in critical care.

When the infection peaks in July, as is expected, a spike in infections could easily lead to many avoidable deaths as hospitals run out of beds for, or delay treatment to, infected patients who need timely oxygen support and clinical care to recover.

“That is the real worry. A critical-care bed needs an oxygen line, a ventilator, doctors, nursing staff. Everything will be under pressure,” Dr Ravi Dosi, who is heading a Covid-19 ward at a hospital in Indore, told me. His 50-bed ICU is already full of patients battling the infection.

With the lockdown easing, doctors are feeling jittery. “It’s a tactical nightmare because some people have begun going to work but there is a lot of fear”, says Dr Dosi.

“One co-worker sneezed in the office and 10-15 of his colleagues panicked and came to the hospital and demanded they get tested. These are the pressures that are building up.”

One reason for the confusion is the lack of – or the opacity of – adequate data on the pandemic to help frame a strategic and granular response.

Most experts say a one-size-fits-all strategy to contain the pandemic and impose and lift lockdowns will not work in India where different states will see infection peaks at different times. The reported infection rate – the number of infections for every 100 tests – in Maharashtra state, for example, is three times the national average.

“The infection is not spreading uniformly. India will see staggered waves,” a leading virologist, who insisted on anonymity, told me.

The lack of data means questions abound.

What about some 3,000 cases, which are not being assigned to any state because these people were found infected in places where they don’t live? (To put this into context, nine states in India have more than 3,000 cases.) How many of these cases have died or recovered?

Also, it is not clear whether the current data – sparse, and sporadic – is sufficient to map the future trajectory of the disease.

There is, for example, no robust estimate of carriers of the virus who have no symptoms – last month a senior government scientist said at least “80 out of every 100 Covid-19 patients may be asymptomatic or could be showing mild symptoms”.

coronavirus victim burial in IndiaImage copyright GETTY IMAGES
Image caption More than 4,000 people have died of Covid-19 in India

If that is indeed true, then India’s fatality rate is bound to be lower. Atanu Biswas, a professor of statistics, says the predicted trajectory could change “with the huge inclusion of asymptomatic cases”. But, in the absence of data, India cannot be sure.

Also, epidemiologists say, measures like the doubling time of the infections and the reproduction number or R0 have their limitations. R0, or simply the R value, is a way of rating a disease’s ability to spread. The new coronavirus, Sars-CoV-2, has a reproduction number of about three, but estimates vary.

“These measures are good when we are in the middle of a pandemic, less robust with fewer cases. You do need forecasting models for at least a month’s projection to anticipate healthcare needs. We should always evaluate an aggregate of evidence, not just one measure, but a cascade of measures,” Bhramar Mukherjee, a professor of biostatistics and epidemiology at the University of Michigan, told me.

Others say even calculating the number of recorded infections every day is “not always a good indicator of how an infection is spreading”.

A better option would be to look at the number of new tests and new cases every day that would provide a “degree of standardisation”, K Srinath Reddy, president of the Public Health Foundation of India, told me.

Likewise, he believes, a measure of how many Covid-19 deaths have occurred compared with the size of a country’s population – the numbers of deaths per million people – is a better indicator of the fatality rate. Reason: the denominator – the country’s population – remains stable.

In the absence of robust and expansive data, India appears to be struggling to predict the future trajectory of the infection.

It is not clear yet how many deaths are not being reported, although there is no evidence of large scale “hidden deaths”.

Coronavirus isolation ward in KolkataImage copyright GETTY IMAGES
Image caption A Covid-19 isolation ward in India

Epidemiologists say they would like to see clearer data on deaths due to pneumonia and influenza-like illnesses at this time over the past few years to quantify excess deaths and help with accurate reporting of Covid-19 deaths.

They would also like to see what racial disparities in infections and deaths there are to help improve containment in specific community areas. (In Louisiana, for example, African Americans accounted for 70% of Covid-19 deaths, while comprising 33% of the population.)

What is clear, say epidemiologists, is that India is as yet unable to get a grip on the extent of the spread of infection because of the still limited testing.

“We need reliable forecasting models with projection for the next few weeks for the country and the states,” says Dr Mukherjee.

Epidemiologists say India needs more testing and contact-tracing for both asymptomatic and symptomatic infections, as well as isolation and quarantine.

There’s also the need to test based on the “contact network” to stop super-spreader events – frontline workers, delivery workers, essential workers, practically anybody who interacts with a large group of people.

“We have to learn how to manage and minimise risk in our daily lives as the virus is going to be with us,” says Dr Mukherjee.

Without knowing the true number of infected cases India is, in the words of an epidemiologist, “flying blindfolded”.

That can seriously jeopardise India’s fight against the virus and hobble its response in reviving the broken economy.

Source: The BBC

09/04/2020

Pass the salt: The minute details that helped Germany build virus defences

MUNICH (Reuters) – One January lunchtime in a car parts company, a worker turned to a colleague and asked to borrow the salt.

As well as the saltshaker, in that instant, they shared the new coronavirus, scientists have since concluded.

That their exchange was documented at all is the result of intense scrutiny, part of a rare success story in the global fight against the virus.

The co-workers were early links in what was to be the first documented chain of multiple human-to-human transmissions outside Asia of COVID-19, the disease caused by the coronavirus.

They are based in Stockdorf, a German town of 4,000 near Munich in Bavaria, and they work at car parts supplier Webasto Group. The company was thrust under a global microscope after it disclosed that one of its employees, a Chinese woman, caught the virus and brought it to Webasto headquarters. There, it was passed to colleagues – including, scientists would learn, a person lunching in the canteen with whom the Chinese patient had no contact.

The Jan. 22 canteen scene was one of dozens of mundane incidents that scientists have logged in a medical manhunt to trace, test and isolate infected workers so that the regional government of Bavaria could stop the virus from spreading.

That hunt has helped Germany win crucial time to build its COVID-19 defences.

The time Germany bought may have saved lives, scientists say. Its first outbreak of locally transmitted COVID-19 began earlier than Italy’s, but Germany has had many fewer deaths. Italy’s first detected local transmission was on Feb. 21. By then Germany had kicked off a health ministry information campaign and a government strategy to tackle the virus which would hinge on widespread testing. In Germany so far, more than 2,100 people have died of COVID-19. In Italy, with a smaller population, the total exceeds 17,600.

CHART: Contrasting curves reut.rs/3c2UZA4

“We learned that we must meticulously trace chains of infection in order to interrupt them,” Clemens Wendtner, the doctor who treated the Munich patients, told Reuters.

Wendtner teamed up with some of Germany’s top scientists to tackle what became known as the ‘Munich cluster,’ and they advised the Bavarian government on how to respond. Bavaria led the way with the lockdowns, which went nationwide on March 22.

Scientists including England’s Chief Medical Officer Chris Whitty have credited Germany’s early, widespread testing with slowing the spread of the virus. “‘We all know Germany got ahead in terms of its ability to do testing for the virus and there’s a lot to learn from that,’” he said on TV earlier this week.

Christian Drosten, the top virologist at Berlin’s Charite hospital, said Germany was helped by having a clear early cluster. “Because we had this Munich cohort right at the start … it became clear that with a big push we could inhibit this spreading further,” he said in a daily podcast for NDR radio on the coronavirus.

Drosten, who declined to be interviewed for this story, was one of more than 40 scientists involved in scrutiny of the cluster. Their work was documented in preliminary form in a working paper at the end of last month, intended for The Lancet. The paper, not yet peer-reviewed, was shared on the NDR site.

ELECTRONIC DIARIES

It was on Monday, Jan. 27, that Holger Engelmann, Webasto’s CEO, told the authorities that one of his employees had tested positive for the new coronavirus. The woman, who was based in Shanghai, had facilitated several days of workshops and attended meetings at Webasto’s HQ.

The woman’s parents, from Wuhan, had visited her before she travelled on Jan. 19 to Stockdorf, the paper said. While in Germany, she felt unusual chest and back aches and was tired for her whole stay. But she put the symptoms down to jet lag.

She became feverish on the return flight to China, tested positive after landing and was hospitalised. Her parents also later tested positive. She told her managers of the result and they emailed the CEO.

In Germany, Engelmann said he immediately set up a crisis team that alerted the medical authorities and started trying to trace staff members who had been in contact with their Chinese colleague.

The CEO himself was among them. “Just four or five days before I received the news, I had shaken hands with her,” he said.

Now known as Germany’s “Case #0,” the Shanghai patient is a “long-standing, proven employee from project management” who Engelmann knows personally, he told Reuters. The company has not revealed her identity or that of others involved, saying anonymity has encouraged staff to co-operate in Germany’s effort to contain the virus.

The task of finding who had contact with her was made easier by Webasto workers’ electronic calendars – for the most part, all the doctors needed was to look at staff appointments.

“It was a stroke of luck,” said Wendtner, the doctor who treated the Munich patients. “We got all the information we needed from the staff to reconstruct the chains of infection.”

For example, case #1 – the first person in Germany to be infected by the Chinese woman – sat next to her in a meeting in a small room on Jan. 20, the scientists wrote.

Where calendar data was incomplete, the scientists said, they were often able to use whole genome sequencing, which analyses differences in the genetic code of the virus from different patients, to map its spread.

By following all these links, they discovered that case #4 had been in contact several times with the Shanghai patient. Then case #4 sat back-to-back with a colleague in the canteen.

When that colleague turned to borrow the salt, the scientists deduced, the virus passed between them. The colleague became case #5.

Webasto said on Jan. 28 it was temporarily closing its Stockdorf site. Between Jan. 27 and Feb. 11, a total of 16 COVID-19 cases were identified in the Munich cluster. All but one were to develop symptoms.

All those who tested positive were sent to hospital so they could be observed and doctors could learn from the disease.

Bavaria closed down public life in mid-March. Germany has since closed schools, shops, restaurants, playgrounds and sports facilities, and many companies have shut to aid the cause.

HAMMER AND DANCE

This is not to say Germany has defeated COVID-19.

Its coronavirus death rate of 1.9%, based on data collated by Reuters, is the lowest among the countries most affected and compares with 12.6% in Italy. But experts say more deaths in Germany are inevitable.

“The death rate will rise,” said Lothar Wieler, president of Germany’s Robert Koch Institute for infectious diseases.

The difference between Germany and Italy is partly statistical: Germany’s rate seems so much lower because it has tested widely. Germany has carried out more than 1.3 million tests, according to the Robert Koch Institute. It is now carrying out up to 500,000 tests a week, Drosten said. Italy has conducted more than 807,000 tests since Feb. 21, according to its Civil Protection Agency. With a few local exceptions, Italy only tests people taken to hospital with clear and severe symptoms.

Germany’s government is using the weeks gained by the Munich experience to double the number of intensive care beds from about 28,000. The country already has Europe’s highest number of critical care beds per head of the population, according to a 2012 study.

Even that may not be enough, however. An Interior Ministry paper sent to other government departments on March 22 included a worst-case scenario with more than 1 million deaths.

Another scenario saw 12,000 deaths – with more testing after partial relaxation of restrictions. That scenario was dubbed “hammer and dance,” a term coined by blogger Tomas Pueyo. It refers to the ‘hammer’ of quick aggressive measures for some weeks, including heavy social distancing, followed by the ‘dance’ of calibrating such measures depending on the transmission rate.

The German government paper argued that in the ‘hammer and dance’ scenario, the use of big data and location tracking is inevitable. Such monitoring is already proving controversial in Germany, where memories of the East German Stasi secret police and its informants are still fresh in the minds of many.

A subsequent draft action plan compiled by the government proposes the rapid tracing of infection chains, mandatory mask-wearing in public and limits on gatherings to help enable a phased return to normal life after Germany’s lockdown. The government is backing the development of a smartphone app to help trace infections.

Germany has said it will re-evaluate the lockdown after the Easter holiday; for the car parts maker at the heart of its first outbreak, the immediate crisis is over. Webasto’s office has reopened.

All 16 people who caught COVID-19 there have recovered.

Source: Reuters

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