Virus World

Scientists have found several strains of highly pathogenic avian influenza in a small number of NYC’s wild birds. A recent study has found a very small number of wild urban birds that either live in or migrate through New York City are carrying an unexpected hitchhiker: the highly pathogenic avian influenza virus H5N1 (ref). This worrying discovery demonstrates that potentially serious human health risks are not limited to rural environments or to commercial factory farms as most people believe, but can also be found lurking in large cities. Thus, this study — the first of its kind — highlights the dangers of close contact between animals and humans because they may end up sharing infections — or even pandemics. “To my knowledge, this is the first large-scale U.S. study of avian influenza in an urban area, and the first with active community involvement,” the study’s senior author, microbiologist and geneticist Christine Marizzi, an Adjunct Assistant Professor at the Icahn School of Medicine at Mount Sinai, said in a statement. Dr Marizzi also is the principal investigator of the New York City Virus Hunters (NYCVH) Program, and the director of community science at BioBus, which is an initiative to bring cutting-edge laboratory science to communities of students that have been historically underrepresented in science with the help of a converted school bus. Many migratory bird species stop over in New York City during their long journeys, which creates the ideal opportunity for different virus strains to meet and mix.

“Birds are key to finding out which influenza and other avian viruses are circulating in the New York City area, as well as important for understanding which ones can be dangerous to both other birds and humans,” Dr Marizzi explained. “And we need more eyes on the ground — that’s why community involvement is really critical.”  The findings were the result of a citizen scientist program to monitor the health of urban wild birds. Samples were collected by high school students in New York City who participate in both research and communication efforts as paid interns under Dr Marizzi’s expert mentorship. As part of their work, they’re provided with all the necessary protective gear to go out into the field and collect bird fecal samples, which they then help screen for viruses. Additional samples are also donated from local animal welfare centers, particularly the Wild Bird Fund, which is a local wild bird rescue. (Disclosure: I’ve been a $upporter of the Wild Bird Fund for many years.). To do this study, the junior scientist interns, or “Virus Hunters”, collected more than 2500 swabs and fecal samples in total from the Wild Bird Fund and from NYC’s parks and other natural areas across the boroughs of Manhattan, Brooklyn and the Bronx. The samples were then screened in a lab at the Icahn School of Medicine at Mount Sinai for the presence of two avian viruses: avian influenza and avian paramyxovirus. The Virus Hunters identified eight birds that were positive for avian paramyxovirus using Polymerase Chain Reaction (PCR). Two type 1 avian paramyxoviruses (APMV1, also known as Newcastle’s Disease Virus), were isolated from feral rock pigeons, Columba livia. These two viral isolates were named, reported to the USDA, and the whole genome sequences were published at the online data repository GenBank. APMV1 is a viral pathogen that affects pigeons and is present in most countries. It is a serious disease that can spread rapidly and cause high rates of pigeon illness and death. Other paramyxovirus strains may affect other avian species, particularly poultry.

Between January 2022 and November 2023, the Virus Hunters continued their work by collecting 1927 samples from raptors, poultry and waterfowl (Figure 1). They screened these samples specifically for H5N1, also known as bird flu. They detected the virus in six city birds representing four different species: Canada geese, Branta canadensis; red-tailed hawks, Buteo jamaicensis; peregrine falcons, Falco peregrinus; and domestic chickens, Gallus gallus domesticus. The positive samples came from the urban wildlife rehabilitation centers, highlighting the critical role that such centers can play in viral surveillance. After comparing the genomic sequences of the samples to each other and to other H5N1 viral genomes available in GenBank, the Virus Hunters found they were a mix of the Eurasian H5N1 2.3.4.4.b clade and local North American avian influenza virus genotypes. Is New York City sitting on a ticking H5N1 pandemic time bomb? “It is important to mention that, because we found H5N1 in city birds, this does not signal the start of a human influenza pandemic,” Dr Marizzi cautioned. “We know that H5N1 has been around in New York City for about 2 years and there have been no human cases reported.”

Currently, only one person has so far been infected by the H5N1 virus in the United States — a dairy worker in Texas. And yet despite the rarity of human H5N1 infections, this virus worries scientists that as bird flu spreads worldwide, the risk of it “jumping” the species barrier into humans continues to grow. For this reason, it’s important that people know what they can do to protect themselves from an infection with H5N1. “It’s smart to stay alert and stay away from wildlife,” Dr Marizzi advised. “This also includes preventing your pets from getting in close contact with wildlife.” Domestic cats are particularly susceptible. For example, out of 24 cats known to have contracted H5N1 on a single Texas dairy farm last month, twelve of them have died so far. If one must handle sick or injured birds or other wildlife, it is important to always use safe practices. These practices include placing a towel, blanket, jumper or pillowcase gently over the stricken animal. This will help keep it calm and aid with safe handling. If dealing with a sick or wounded bird, it is best to gently wrap it in a towel or hold the wings close to its body and place it into a paper bag or box for transport to bird rescue center.

Research Published in  Journal of Virology (May 15, 2024):

The new coronavirus tears through areas where residents generally keep to their own small, close-knit communities. But the virus takes its time spreading in crowded cities where residents of different neighbourhoods tend to intermingle, ultimately infecting more people than in the relatively isolated areas. Moritz Kraemer at the University of Oxford, UK, and his colleagues modelled the spread of SARS-CoV-2 through communities of various sizes and population densities(B. Rader et al. Nature Med. https://doi.org/fcjk; 2020).

The researchers validated their model by comparing its output with known data on individual movements and infection rates in crowded Chinese cities such as Wuhan and less densely packed provinces in Italy. The team’s model predicts relatively short, intense spikes in COVID-19 cases in relatively uncrowded cities where residents stick to their own neighbourhoods rather than mingling freely. In crowded cities, however, people are more likely to have to cope with outbreaks that last longer than do those in the countryside. The researchers applied their model to 310 cities worldwide, and predict that those with relatively even population distributions, such as Ulaanbaatar in Mongolia, could expect a short-term explosion in cases. But more densely settled urban centres, such as Madrid, can expect more protracted outbreaks.

Published in Nature Medicine (October 5, 2020):

https://doi.org/10.1038/s41591-020-1104-0

NEARLY 14% of people tested in the first phase of a coronavirus antibody study in New York tested positive, Gov. Andrew Cuomo announced Thursday. The governor said 13.9% of the 3,000 people who were screened tested positive for coronavirus antibodies, indicating that they had previously contracted the virus and have since recovered. Nearly 16 percent of males tested positive for the virus while 12 percent of females did. About one-fifth, 21.2%, of positive results were throughout New York City. Downstate, including Long Island, Westchester and Rockland counties, accounted for 28.4% of cases.

Approximately 3,000 antibody samples were collected from 40 locations in 19 counties among people who were out of their homes and not self-isolating or quarantining. Health officials report more than 263,750 cases of COVID-19 in New York and more than 19,450 deaths. Throughout New York City's five boroughs there are more than 147,295 cases and 15,074 deaths. The daily death toll continues to decline, with 438 people dying from the virus on Wednesday. However, Cuomo said the numbers aren't "coming down as fast as we'd like to see."

According to the results, Cuomo said, the infection rate means that 2.7 million people could be infected across the state, which has a population of about 19 million. Based on the data, the death rate could be lower than some experts have estimated....

The health department said it is still investigating the virus' origin, after finding eight of the positive wastewater samples are genetically linked. New York state health officials have found indications of additional cases of polio virus in wastewater samples from two different counties, leading them to warn that hundreds of people may be infected with the potentially serious virus.  Just two weeks ago, the New York Health Department reported the nation's first case of polio in almost a decade, in Rockland County, north of New York City. Officials said that case occurred in a previously healthy young adult who was unvaccinated and developed paralysis in their legs. Since then, three positive wastewater samples from Rockland County and four from neighboring Orange County were discovered and genetically linked to the first case, the health department said in a press release on Thursday, suggesting that the polio virus is being spread within local communities. The newest samples were taken from two locations in Orange County in June and July and one location in Rockland County in July. "Based on earlier polio outbreaks, New Yorkers should know that for every one case of paralytic polio observed, there may be hundreds of other people infected," State Health Commissioner Dr. Mary T. Bassett said. "Coupled with the latest wastewater findings, the Department is treating the single case of polio as just the tip of the iceberg of much greater potential spread. As we learn more, what we do know is clear: the danger of polio is present in New York today."  The health department reiterated that it is still investigating the virus' origin, and said that it is not yet clear whether the infected person in Rockland County was linked to the other cases.

Polio is "a serious and life-threatening disease," the state health department said. It is highly contagious and can be spread by people who aren't yet symptomatic. Symptoms usually appear within 30 days of infection, and can be mild or flu-like. Some people who are infected may become paralyzed or die. Before the polio vaccine was introduced in the 1950s, thousands of Americans died in polio outbreaks and tens of thousands, many of them children, were left with paralysis. After a successful vaccination campaign, polio was officially declared eradicated in the U.S. in 1979.   Unvaccinated New Yorkers are encouraged to get immunized right away, the health department said. Unvaccinated people who live, work or spend time in Rockland County, Orange County and the greater New York metropolitan area are at the greatest risk. Most school-aged children have received the polio vaccine, which is a four-dose course, started between 6 weeks and 2 months of age and followed by one shot at 4 months, one at 6 to 12 months, and one between the ages of 4 and 6. According to the health department, about 60% of children in Rockland County have received three polio shots before their second birthday, as have about 59% in Orange County — both below the 79% statewide figure.  According to the CDC's most recent childhood vaccination data, about 93% of 2-year-olds in the U.S. had received at least three doses of polio vaccine. Meanwhile, adults who are not vaccinated would receive a three-dose immunization, and those who are vaccinated but at high risk can receive a lifetime booster shot, according to the health department.  The vaccine is 99% effective in children who receive the full four-dose regime, health officials said. "It is concerning that polio, a disease that has been largely eradicated through vaccination, is now circulating in our community, especially given the low rates of vaccination for this debilitating disease in certain areas of our County," Orange County Health Commissioner Dr. Irina Gelman said. "I urge all unvaccinated Orange County residents to get vaccinated as soon as medically feasible." Rockland County Department of Health Commissioner Dr. Patricia Schnabel Ruppert issued a similar statement, calling on people who are not vaccinated to get the shots "immediately." Polio has rarely appeared in the U.S. since it was declared eradicated over 40 years ago. The last reported case was brought by a traveler in 2013, according to The Associated Press.

In what may be the world’s most important math puzzle, researchers are trying to figure out how many people in a community must be immune before the coronavirus fades. We’ve known from the beginning how the end will arrive. Eventually, the coronavirus will be unable to find enough susceptible hosts to survive, fading out wherever it briefly emerges. To achieve so-called herd immunity — the point at which the virus can no longer spread because there are not enough vulnerable humans — scientists have suggested that perhaps 70 percent of a given population must be immune, through vaccination or because they survived the infection. Now some researchers are wrestling with a hopeful possibility. In interviews with The New York Times, more than a dozen scientists said that the threshold is likely to be much lower: just 50 percent, perhaps even less. If that’s true, then it may be possible to turn back the coronavirus more quickly than once thought. The new estimates result from complicated statistical modeling of the pandemic, and the models have all taken divergent approaches, yielding inconsistent estimates. It is not certain that any community in the world has enough residents now immune to the virus to resist a second wave.

But in parts of New York, London and Mumbai, for example, it is not inconceivable that there is already substantial immunity to the coronavirus, scientists said. “I’m quite prepared to believe that there are pockets in New York City and London which have substantial immunity,” said Bill Hanage, an epidemiologist at the Harvard T.H. Chan School of Public Health. “What happens this winter will reflect that.”  “The question of what it means for the population as a whole, however, is much more fraught,” he added.

An emergency room doctor in Elmhurst, Queens, gives a rare look inside a hospital at the center of the coronavirus pandemic. “We don’t have the tools that we need.