Virus World

Background

The COVID-19 pandemic, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 virus, emerged in late 2019 and spready globally. Many effects of infection with this pathogen are still unknown, with both chronic and repeated COVID-19 infection producing novel pathologies.

Case presentation

An immunocompromised patient presented with chronic COVID-19 infection. The patient had history of Hodgkin’s lymphoma, treated with chemotherapy and stem cell transplant. During the course of their treatment, eleven respiratory samples from the patient were analyzed by whole-genome sequencing followed by lineage identification. Whole-genome sequencing of the virus present in the patient over time revealed that the patient at various timepoints harboured three different lineages of the virus. The patient was initially infected with the B.1.1.176 lineage before coinfection with BA.1. When the patient was coinfected with both B.1.1.176 and BA.1, the viral populations were found in approximately equal proportions within the patient based on sequencing read abundance. Upon further sampling, the lineage present within the patient during the final two timepoints was found to be BA.2.9. The patient eventually developed respiratory failure and died.

Conclusions

This case study shows an example of the changes that can happen within an immunocompromised patient who is infected with COVID-19 multiple times. Furthermore, this case demonstrates how simultaneous coinfection with two lineages of COVID-19 can lead to unclear lineage assignment by standard methods, which are resolved by further investigation. When analyzing chronic COVID-19 infection and reinfection cases, care must be taken to properly identify the lineages of the virus present.

Key points

How does COVID-19 compare to the 1918 flu pandemic? In New York City, deaths rose a comparable amount during COVID when compared to the 1918 Spanish flu. When the coronavirus swept through New York City in the spring, it brought with it a staggering surge in deaths — one that was comparable, researchers say, to the 1918 flu pandemic in the city. That’s according to a study published Thursday in JAMA Network Open that drew on death statistics from public databases to compare the toll during the two outbreaks.  When the coronavirus swept through New York City in the spring, it brought with it a staggering surge in deaths — one that was comparable, researchers say, to the 1918 flu pandemic in the city. That’s according to a study published Thursday in JAMA Network Open that drew on death statistics from public databases to compare the toll during the two outbreaks.  The study found that during the peak of the 1918 pandemic, 287 per 100,000 New Yorkers died per month, while for this year's pandemic, 202 per 100,000 New Yorkers died per month. The rate seen during the early months of the COVID-19 pandemic was 70 percent of that seen during the peak of the 1918 flu pandemic, said Dr. Jeremy Faust, an emergency medicine physician at Brigham & Women’s Hospital in Boston and the study's lead author. “This tells us that these are comparable in terms of their impact,” Faust said. "This virus has 1918 capacity."

In fact, the relative increase in deaths seen during COVID-19 was greater than what was observed during the peak of the 1918 flu, the study found. Compared to the same two-month period in the four years leading up to 1918, there were 2.8 times as many deaths among New Yorkers in October and November 1918. Looking at death rates in the spring in the three years leading up 2020, there were 4.15 times as many deaths in March through May. That larger relative increase reflects the fact that fewer New Yorkers were dying before COVID-19 than in the years leading up to the 1918 flu, thanks to improvements in public health and modern medicine. All told, a total of 33,465 New Yorkers out of a population of more than 8 million died during the COVID-19 time period, the study found. During the peak of the 1918 flu, a total of 31,589 New Yorkers died, out of a population of 5.5 million. Maimuna Majumder, a computational epidemiologist at Harvard Medical School, noted that determining the exact cause for the increased deaths seen in the spring needs further research.

“Some of these deaths are almost assuredly due to the fact that our health care system has been overwhelmed by the pandemic, thus making otherwise treatable conditions less treatable,” she said in an email. To emergency room physicians who treated COVID-19 patients in New York in the spring, the findings made sense. “I don't think this was surprising to anyone who worked in an emergency department or in an ICU in March, April or really in May in New York City,” Dr. Craig Spencer, an emergency room physician at Columbia University, said. “The level of death was really just unbelievable."

Study published in JAMA (August 13, 2020):

https://doi.org/10.1001/jamanetworkopen.2020.17527

More than 1,900 people are dying in the US daily on average – the highest level since early March. Covid-19 has now killed as many Americans as the 1918-19 flu pandemic, with more than 675,000 reported deaths. The US population a century ago was just a third of what it is today, meaning the flu cut a much bigger, more lethal swath through the country. But the Covid-19 crisis is by any measure a colossal tragedy in its own right, especially given major advances in scientific knowledge and the failure to take maximum advantage of vaccines. Unlike a century ago, vaccines have been made widely available. However, an extensive reticence to be inoculated, fueled in part by baseless fears about safety and efficacy, means that 36% of people in the US aged 12 and over have yet to be fully vaccinated, according to data from the federal Centers for Disease Control and Prevention (CDC).  “Big pockets of American society – and, worse, their leaders – have thrown this away,” said Dr Howard Markel a medical historian at the University of Michigan.

The White House initially forecast 100,000 to 240,000 deaths from Covid-19, if people socially distanced. Donald Trump, who erroneously predicted the coronavirus would simply vanish, oversaw the lower end of this forecast being reached in May last year, the latter death toll arriving in November. A surge in deaths in the spring of 2020 was surpassed by a larger wave of deaths over winter, with a record 4,197 people dying on a single day, 13 January, according to Johns Hopkins University. Since Joe Biden became president, the rollout of vaccines has helped push the rate of deaths down, although it started climbing again in August due to the spread of the Delta variant. The true death toll may be much higher than the official total because, like the previous pandemic, it is estimated. Also similar to the 1918-19 flu, the coronavirus may never entirely disappear. Scientists hope it will become a mild seasonal bug as human immunity strengthens through vaccination and repeated infection.  “We hope it will be like getting a cold, but there’s no guarantee,” said Rustom Antia, a biologist at Emory University, suggesting an optimistic scenario in which this could happen over a few years. For now, the pandemic still has the US and other parts of the world firmly in its jaws. While the Delta variant-fueled surge in infections may have peaked, US deaths are more than 1,900 a day on average – the highest level since early March – and the overall toll topped 675,000 on Monday, according to the count kept by Johns Hopkins.

Winter may bring a new surge, with the University of Washington’s influential model projecting an additional 100,000 or so Covid-19 deaths by 1 January, which would bring the overall US toll to 776,000.  The 1918-19 influenza pandemic killed 50 million globally, at a time when the world had a quarter the population it does now. Global deaths from Covid-19 stand at more than 4.6 million. The 1918-19 flu’s US death toll is a rough guess, given incomplete records of the era and the poor scientific understanding of what caused the illness. The 675,000 figure comes from the CDC. Before Covid-19, the 1918-19 flu was universally considered the worst pandemic in history. Whether the current scourge ultimately proves deadlier is unclear.  In many ways, the 1918-19 flu – which was wrongly named Spanish flu because it first received widespread news coverage in Spain – was worse. Spread by the mobility of the first world war, it killed young, healthy adults in vast numbers. No vaccine existed and there were no antibiotics to treat secondary infections.  Jet travel and mass migrations threaten to increase the toll of the current pandemic. Much of the world is unvaccinated. And the coronavirus has been full of surprises. Just under 64% of the US population has received as least one dose of the vaccine, with state rates ranging from a high of approximately 77% in Vermont and Massachusetts to lows around 46% to 49% in Idaho, Wyoming, West Virginia and Mississippi. Globally, about 43% of the population has received at least one dose, according to Our World in Data, with some African countries just beginning to give their first shots. “We know that all pandemics come to an end,” said Dr Jeremy Brown, director of emergency care research at the National Institutes of Health, who wrote a book on influenza. “They can do terrible things while they’re raging.” Covid-19 could have been far less lethal in the US if more people had gotten vaccinated faster, “and we still have an opportunity to turn it around”, Brown said. “We often lose sight of how lucky we are to take these things for granted.”