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):

Health department says it's working with Jerusalem 'to ensure a coordinated response' after 4 cases of virus recently detected in Safed. The State of New York’s health department called for residents to get vaccinated against polio before traveling to Israel, where several children have recently tested positive for the virus. In a statement Friday, the New York Department of Health noted the four cases diagnosed in the northern city of Safed earlier this month, a year after a small outbreak of the disease in the country. It called on New Yorkers “to get fully immunized” before flying to Israel or other countries with polio. Health officials in New York have been in touch with their Israeli counterparts “to ensure a coordinated response,” the statement said, adding that travelers should adhere to guidelines from the US Center for Disease Control. Besides Israel, the statement noted the CDC has issued precautions against polio before traveling to the United Kingdom, Ukraine, Afghanistan, Pakistan, Indonesia, Nigeria, Côte d’Ivoire and several other central African countries.

Polio is a viral disease that mainly affects children and can cause disability, paralysis and death. Today, polio vaccinations are standard for children and are an effective preventive measure, but vaccine skepticism has enabled the disease to pop up from time to time. The outbreak in Israel last March, which came after the first case of polio in 33 years was discovered in the country, prompted a vaccination drive to combat the disease. The finding landed Israel on the World Health Organization’s Polio Eradication Initiative’s list of countries with outbreaks, after it was declared polio-free in 1988. Following the cases detected earlier this month, the Health Ministry cited evidence of polio spreading in sewage systems and said over 150,000 Israeli children are unvaccinated against the virus.

New York Gov. Kathy Hochul (D) on Friday declared a state of emergency after poliovirus was detected in the sewage of a fourth county in the state in an effort to boost vaccination rates as some regions lag well behind national vaccination levels.

KEY FACTS

The following essay is reprinted with permission fromThe Conversation, an online publication covering the latest research. The first case of polio in the U.S. since 2013 was announced by New York state health officials on July 21, 2022. The U.S. resident had not been vaccinated. Polio was a common cause of paralysis in children before safe and effective vaccines were invented in the mid-20th century. Thanks to global vaccination campaigns, polio is now almost eradicated, with only 13 cases of endemic wild poliovirus reported in 2022 to date worldwide.  The New York patient reportedly contracted a form of polio that can be traced back to the live, but weakened, poliovirus used in the oral polio vaccine. This version of the vaccine has not been used in the U.S. since 2000. Health officials said the virus affecting the male patient, who has muscle weakness and paralysis, likely originated somewhere overseas, where oral vaccines are still administered. William Petri is an infectious disease specialist and chair of the World Health Organization’s Polio Research Committee. Here he explains what vaccine-derived poliovirus is and why the inactivated polio vaccine administered in the U.S. today can’t cause it. 

What are the two kinds of polio vaccine?

Vaccines introduce a harmless version of a pathogen to your body. The idea is that they train your immune system to fight off the real germ if you ever encounter it. The oral polio vaccine, originally developed by Albert Sabin, uses a live but weakened poliovirus that one swallows in a sugar cube or droplet. Scientists weaken – or attenuate – the virus so it can no longer cause disease.  The other kind of polio vaccine was originally developed by Jonas Salk. It contains inactivated, dead virus. It is administered by an injection. In the U.S., children receive the inactivated polio vaccine at 2, 4 and 6 months of age. It provides nearly complete protection from paralytic polio.

How can the live vaccine lead to a case of polio?

The weakened form of the live virus in the oral vaccine cannot cause disease. However, because the vaccine is given orally, the weakened virus is excreted in the feces and can spread from someone who is vaccinated to their close contacts. If the weakened virus circulates person to person for long enough, it can mutate and regain its ability to cause paralysis. The mutated virus can then infect people in communities with poor sanitation and low vaccination rates, causing disease and even paralysis.  This is an exceedingly rare occurrence. With more than 10 billion doses of the oral polio vaccine administered since 2000, there have been fewer than 800 cases of vaccine-derived polio reported. Apparently, the current patient in New York was somehow exposed to a mutated poliovirus that had been transmitted after vaccination overseas. Earlier this summer, routine surveillance spotted vaccine-derived poliovirus in London’s sewage system, but no cases have been reported there.

Why use the oral vaccine anywhere if it comes with this risk?

There’s a positive aspect to the fact that the weakened live virus can circulate in the community once oral vaccine recipients shed it in their feces. Traveling a feces-to-oral route, it can help induce immunity even in people who weren’t directly vaccinated. The oral polio vaccine is also cheaper and easier to administer than inactivated polio vaccines. Most importantly, the live-virus vaccine stops transmission of wild poliovirus in a way that the inactivated-virus vaccine does not. The eradication of polio in the Americas, Europe and Africa has been accomplished solely through the use of the live oral vaccine. Once polio has been wiped from a continent, then it is safe to stop using the oral live vaccine and use only the inactivated vaccine, which does prevent disease in recipients and does not pose the rare risk of vaccine-derived paralytic polio.  A new and safer oral polio vaccine that has been engineered not to mutate is now replacing the earlier live-virus vaccine. Thus, even this extremely rare complication of polio vaccination should soon become a thing of the past. 

How close is the world to eradicating polio?

Thanks to tremendous global effort, two of the three viruses that cause polio have been eradicated. The world is now on the verge of eradicating the final one, wild poliovirus 1 (WPV1). Today endemic polio is found only in Pakistan, with 12 cases of paralytic polio so far in 2022, and Afghanistan, with just one case this year. Africa has two cases, imported from overseas, which are being contained by additional vaccination campaigns. Once wild poliovirus has been eradicated from the planet, vaccination efforts may be able to switch to the inactivated polio vaccine, eliminating the risk of any future vaccine-derived cases.

This article was originally published on The Conversation. Read the original article.

New York State reported Thursday that it has detected a case of vaccine-derived polio in a person in Rockland County, north of New York City, the first such recorded case in the United States since 2013.  The unidentified individual developed paralysis, said Beth Cefalu, Rockland County’s director of strategic communications. Polio paralysis is irreversible. The area where the case was detected was the epicenter of a large measles outbreak in 2018-2019 that was fueled by low vaccination rates among communities of Hasidic Jews. The outbreak went on for so long that the country almost lost its measles-free status. The memory of that episode is provoking concern that the area might be ripe for additional vaccine-derived polio cases to occur. “I think it’s concerning because … it can spread,” said Walter Orenstein, a polio expert at Emory University. “If there are unvaccinated communities, it can cause a polio outbreak.” “The inactivated polio vaccine we have is very effective and very safe and could have prevented this,” he said. “We need to restore our confidence in vaccines.” The Centers for Disease Control and Prevention said in a statement that while the risk is low for people who are vaccinated, there is risk for those who have not had the recommended three doses of injectable polio vaccine. “Most of the U.S. population has protection against polio because they were vaccinated during childhood, but in some communities with low vaccine coverage, there are unvaccinated people at risk,” the statement said. “Polio and its neurologic effects cannot be cured, but can be prevented through vaccination.” 

The New York State department of health said in a statement that the person was infected with a type 2 vaccine-derived poliovirus, which would have come from oral polio vaccine used in a number of countries, but not the United States. The U.S. stopped using oral polio vaccine in 2000. Cefalu told STAT the case is still being investigated, but it is believed the individual had not recently traveled outside the country to a place where type 2 vaccine-derived polio viruses are spreading. If that is the case, that would indicate someone else inadvertently imported the virus, suggesting there may be additional undetected transmission. Only a small portion of people infected with polioviruses will go on to be paralyzed.  Kimberly Thompson, a polio expert who is president of the nonprofit organization Kid Risk, said it’s not a surprise to see a vaccine-derived case pop up in this country, noting public health authorities in the United Kingdom recently discovered vaccine-derived polioviruses  in sewage in London, indicating some transmission there.  “With Covid having disrupted immunization (even in the U.S.) and travel now having resumed and much more type 2 poliovirus transmission happening … it’s been only a matter of time before we’d have some detection of polioviruses in sewage, as happened recently in the U.K, or more tragically, a case,” Thompson told STAT in an email. “There’s just a lot more polio going around than there should be.” The oral vaccine contains live but weakened polioviruses, which immunized children excrete in their stools. In places where hygiene is poor, these viruses can spread from child to child, immunizing others as they do. But as they spread, the vaccine viruses can regain the power to paralyze. Such cases are called vaccine-derived polio.  The United States uses injectable polio vaccine that contains killed viruses to teach the immune system to recognize and fight off polio. It cannot cause paralysis.

Mary Bassett, New York State’s health commissioner, said people who are vaccinated against polio do not face a risk from the newly discovered case. But children who are not immunized against the virus should receive the vaccine. “Based on what we know about this case, and polio in general, the Department of Health strongly recommends that unvaccinated individuals get vaccinated or boosted with the FDA-approved IPV polio vaccine as soon as possible,” Bassett said. Rockland County will host vaccine clinics on Friday and Monday, the department’s statement said. The United States used to have upwards of 20,000 paralytic polio cases a year in the early and mid-1950s, Orenstein said, recalling that as a 7-year-old in 1955 he was reluctant to be vaccinated when the Salk polio vaccine — the injected form — was released. “My mother said to me: ‘Better you should cry than I should cry,’’’ he said. With the advent of effective polio vaccines, the disease retreated in much of the developed world. The last recorded case of domestically acquired wild polio was in 1979, though there was an imported case in 1993. But over the years there have been rare imported cases of vaccine-derived polio, from countries where the oral vaccine is still in use. Orenstein said detecting where the virus in the New York case came from is critical. That work can be done by comparing the genetic sequence of the individual’s virus with others in a database the polio eradication program maintains. The world has been trying to eradicate polio for decades, with two of the original three types of polio — types 2 and 3 — having been driven out of existence. But the remaining version, type 1, has defied efforts to end its spread to date. Wild-type polio cases are at low numbers; the viruses are only endemic at this point in Afghanistan and Pakistan, which have recorded a total of 12 cases this year. But recently it was discovered that viruses from Pakistan had made their way to Malawi and Mozambique, a highly unwelcome development. Meanwhile, the numbers of vaccine-derived cases have exploded in Africa and some other parts of the world after the failure of an effort in 2016 to take type 2 viruses out of the oral vaccine. It was felt that given the fact that wild type 2 viruses no longer existed, it was not ethical to use oral vaccine containing type 2 viruses, because of the risk they would regain the power to paralyze.

In a coordinated move called “the switch,” countries around the world were told to stop using trivalent oral vaccine — vaccine that contained all three types of polioviruses — and begin to use a bivalent form that did not include type 2. In the years since, chains of transmission of type 2 vaccine-derived virus have spread to more than 40 countries around the world and the polio eradication program has struggled to contain the spread. So far this year 167 children in 12 countries have been paralyzed by type 2 vaccine viruses, not including the individual in New York. The Global Polio Eradication Program, which leads the effort to rid the world of polio, said in a statement that the discovery highlights the importance of countries continuing to be on the lookout for polio, noting “any form of poliovirus anywhere is a threat to children everywhere.” “It is vital that all countries, in particular those with a high volume of travel and contact with polio-affected countries and areas, strengthen surveillance in order to rapidly detect any new virus importation and to facilitate a rapid response,” the statement said. “Countries, territories, and areas should also maintain uniformly high routine immunization coverage … to protect children from polio and to minimize the consequences of any new virus being introduced.” The polio eradication program is a partnership involving the World Health Organization, the United Nations Children’s Fund, the service group Rotary International, the Centers for Disease Control and Prevention and the Bill and Melinda Gates Foundation.

Signaling its distrust of the Trump administration’s accelerated “Operation Warp Speed” initiative, California will conduct its own independent review of potential COVID-19 vaccines. To vet a vaccine before distribution to state residents, California Health and Human Services Secretary Dr. Mark Ghaly said Friday that the state will assemble a “review board” of leading scientists at academic institutions to assess the safety and effectiveness of any vaccine candidate. “We think it is an appropriate approach to take, especially because things are moving so quickly,” Ghaly said. “We want to make sure — despite the urge and interest in having a useful vaccine — that we do it with the utmost safety of Californians in mind.” The announcement came at a press conference in which Ghaly also expressed concern that California’s coronavirus numbers are beginning to move in the wrong direction after weeks of declines. Based on current trends, he projected an 89% increase in COVID-19 hospitalizations over the next month. That would still be far below hospital capacity and the worst rates in other states. On the vaccine testing issue, several other states, including New York, have signaled that they’ll also take the unusual step that Ghaly outlined. “Frankly, I’m not going to trust the federal government’s opinion, and I wouldn’t recommend to New Yorkers, based on the federal government’s opinion,”  New York Gov. Andrew M. Cuomo announced at a Thursday news briefing, according to the New York Times. President Trump has insisted a vaccine will be ready as early as next month, an assertion that other federal authorities say is unlikely.

California is already building a rollout plan for distribution of the vaccine, including whom to prioritize in the process, said Ghaly. Led by the state’s Department of Public Health, members of a new Vaccine Task Force include other state agencies, as well as academic experts, community groups and individuals. Once the state confirms the safety of the vaccine, this task force will advise distribution “in an equitable and smart way, to serve all the needs of Californians,” said Ghaly. “That absolutely is our plan.” Conflicting information about the timing of the vaccine and whether it will be safe and adequately tested has created growing concern that people are hesitant to take it, despite its importance in stopping the pandemic. The share of Americans who say they would get vaccinated for the coronavirus has declined sharply since earlier this year, according to a survey conducted this month by the Pew Research Center. About half of U.S. adults (51%) now say they would definitely or probably get a vaccine to prevent COVID-19 if it were available today, down from 72% in May. Only about 21% said they would definitely get a coronavirus vaccine, half as many as in May.

While it is the federal government’s role to approve a vaccine, states have authority for actual distribution — and could, in theory, reject a vaccine they think is unsafe. “Each state, indeed, has that sort of responsibility,” said Vanderbilt University’s Dr. William Schaffner, an internist and infectious disease specialist who formerly worked for the U.S. Public Health Service and the Centers for Disease Control and Prevention, at a Sept. 24 National Press Foundation program. “Some may be more ready to independently evaluate the data than others.” An FDA committee — called the Vaccines and Related Biological Products Advisory Committee comprising 15 authorities selected by the FDA commissioner — reviews the safety and effectiveness data at a public meeting. The FDA commissioner usually follows the committee’s recommendation, but not always. Typically, states follow the decision of the Advisory Committee on Immunization Practices, or ACIP, an independent committee that assesses data on FDA-approved vaccines and makes recommendations to the CDC. But there is growing worry that the federal regulators may feel pressure from the White House to activate “Emergency Use Authorization” of an unlicensed vaccine, which would not require completion of a full “Phase 3” trial, during which efficacy is tested in thousands of people...

States should look to New York’s strategies. It’s been six months since the United States reported its first coronavirus case, and getting a test can still take days. National labs are overwhelmed, leaving people to wait as much as two weeks for results. Every day that testing falls short is another day the virus can spread undetected, costing lives and delaying the reopening of our economy, schools and society. As states try to control the virus and as Congress considers the fourth Covid-19 relief bill, New York offers important lessons on how to fix the testing mess. Over the last 10 weeks, New York has used testing to not only flatten the curve, but actually reduce the rate of infection since our phased reopening started. We have kept our testing rates high through partnerships with federal and local governments. In February and early March, New York worked with the Food and Drug Administration to gain the necessary approvals to begin using our own coronavirus test and mobilize a network of hundreds of labs. In April, when our labs were struggling because of shortages of a necessary chemical ingredient, reagents, President Trump and I reached an agreement that helped double New York’s capacity.  Here’s what states should do to build a sustainable testing operation, and how Congress can help.

Mobilize smaller local labs. Almost all states are now using a handful of national testing companies, and they are overwhelmed. New York has managed to avoid the delays because more than 80 percent of our testing does not depend on the national laboratories experiencing long turnaround times for results. In the early days of the pandemic, New York organized hundreds of local labs to conduct as many tests as possible. We moved equipment sitting idle to labs that could run them around the clock. Today, more than 250 labs in the state report results each day — some conducting 10 tests daily, some thousands. All together, New York can now conduct on average 65,000 tests a day...

Streamline the supply chain. In New York and other states, there are high-capacity labs running at partial capacity because they don’t have enough supplies. How can it be, six months after America’s first case was reported, that the United States still doesn’t have an adequate supply chain? What labs need — reagents and plastic pipette tips — are not complicated to manufacture. They can, and should, be made in mass quantity, immediately, and here at home. New York invested $750,000 in Rheonix, an Ithaca-based manufacturer, to build lab instruments and make reagent kits, which are now being used for thousands of tests daily. States should tap their local manufacturing companies to compensate for international shortages, and Congress should allocate funding for businesses that fill these needs...

Invest in innovative solutions. The Food and Drug Administration recently approved pooled testing, where multiple samples are run at once, increasing capacity and saving lab supplies. But for one national lab, the approved pool size is just four samples. In Wuhan, China, up to 10 specimens were pooled, allowing the city to increase its capacity to 1.5 million tests daily, up from 46,000 tests daily.

Fund all necessary testing. Currently, under federal rules, “medically necessary” testing is free for those with Covid-19 symptoms, as well as asymptomatic people who have been exposed to the virus. But states should be able to conduct broad community screening — 40 percent of infected people are asymptomatic — to detect the virus and control its spread. For example, Congress should ensure testing is free for individuals who attend mass gatherings, regularly ride public transportation or interact with members of the public at work. New York is proof that a real testing strategy can control Covid-19. But our future success depends on other states to do the same — a virus anywhere is a virus everywhere.

New research indicates that the coronavirus began to circulate in the New York area by mid-February, weeks before the first confirmed case, and that travelers brought in the virus mainly from Europe, not Asia. “The majority is clearly European,” said Harm van Bakel, a geneticist at Icahn School of Medicine at Mount Sinai, who co-wrote a study awaiting peer review.

A separate team at N.Y.U. Grossman School of Medicine came to strikingly similar conclusions, despite studying a different group of cases. Both teams analyzed genomes from coronaviruses taken from New Yorkers starting in mid-March. The research revealed a previously hidden spread of the virus that might have been detected if aggressive testing programs had been put in place.

Hoping to stem the toll of the state’s surging coronavirus outbreak, New York health officials plan to begin collecting plasma from people who have recovered and injecting the antibody-rich fluid into patients still fighting the virus. Gov. Andrew Cuomo announced the plans during a news briefing Monday. The treatment, known as convalescent plasma, dates back centuries and was used during the flu epidemic of 1918 — in an era before modern vaccines and antiviral drugs.

Some experts say the treatment, although somewhat primitive, might be the best hope for combating the coronavirus until more sophisticated therapies can be developed, which could take several months.  "There have been tests that show when a person is injected with the antibodies, that then stimulates and promotes their immune system against that disease," Cuomo said. "It's only a trial. It's a trial for people who are in serious condition, but the New York State Department of Health has been working on this with some of New York's best health care agencies, and we think it shows promise, and we're going to be starting that this week."

New York has seen a dramatic rise in coronavirus cases in recent days, with about 20,000 confirmed cases and more than 150 deaths as of Monday afternoon, more than in any other state. 

State health officials said they expect to get approval from the Food and Drug Administration to begin the plasma trial in the coming days. A spokesman for the FDA confirmed to NBC News that the agency is "working expeditiously to facilitate the development and availability" of convalescent plasma. And at a White House briefing last week, FDA Commissioner Stephen Hahn singled out the treatment as a promising option to fight the disease in the near term.

In the recent Morbidity and Mortality Weekly Report (MMWR) published by the Centers for Disease Control and Prevention (CDC), researchers reported on JYNNEOS vaccine effectiveness (VE) against Mpox infections among New York (NY) residents in 2022. Bavarian Nordic’s JYNNEOS (Modified Vaccinia Ankara) vaccine was used in the state- and nation-wide vaccination campaigns during the 2022 Mpox outbreak, which primarily affected gays, bisexuals, and males who had sex with males (MSM). As a result, health authorities prioritized postexposure prophylaxis (PEP) and vaccinating high-risk individuals (mainly MSM). However, data on JYNNEOS VE from controlled trials are limited.

About the report

In the present report, researchers presented JYNNEOS VE in preventing Mpox infections among NY residents during 2022. The team compared JYNNEOS vaccination results among adult males with laboratory-verified Mpox (case-patients) diagnosed between 24 July and 31 October 2022, in New York, to those among control individuals diagnosed with primary syphilis or rectal gonorrhea and prior history of sexual intercourse with males without Mpox infection. Surveillance data were systematically obtained for the analysis. The team matched cases and controls to the vaccination system records of the state. Logistic regression modeling was performed to calculate the odds ratios (OR), which were used along with the number of JYNNEOS vaccination doses received to estimate VE. The data were adjusted for age, ethnicity, race, a residential region within New York but outside of New York City, and the Mpox diagnosis week. The status of JYNNEOS vaccination was classified into the following groups: an unvaccinated group (zero JYNNEOS vaccine doses received); vaccinated for Mpox or sexually transmitted infections (STIs) with specimens obtained within two weeks of initial vaccine administration; vaccinated with STI specimens obtained after two or more weeks of the initial vaccination; and vaccinated with STI specimens obtained following the subsequent vaccination. Reports were assessed by population health staff members and entered into the Communicable Disease Electronic Surveillance System (CDESS). One-dose, two-dose, and combined estimates of JYNNEOS vaccine effectiveness were obtained.

Results

Between 2 June and 31 December 2022, the NYSDOH recorded 375 Mpox cases, and the NYSIIS recorded 27,385.0 vaccine doses administered, of which 61% (n=16,769) and 39% (n=10,616) were the first and second doses, respectively. The case counts were highest in the middle of August, five weeks following the JYNNEOS immunization campaign launch. Between 24 July and 31 October, 252 cases and 255 controls (80 and 175 with primary-type syphilis and rectal gonorrhea, respectively) satisfied the eligibility criteria and had similar ages. Hispanics were more common among cases than controls (44% versus 19%, respectively), and more cases  (69%) than controls (36%) resided in urban areas outside New York City. The majority (91%) of participants (n=220) were unvaccinated, and 9.0% of cases (n=22) were JYNNEOS vaccinees, among whom 10 individuals (4.0%), 10 individuals (4.0%), and two individuals (1.0%) had received one dose <2.0 weeks prior, one dose ≥2.0 weeks prior, and two doses, respectively. Among controls, 51 (20%) were JYNNEOS vaccinees, including 42 individuals (17%) who were diagnosed with an STI ≥2.0 weeks after receiving the initial dose (9.0%, 23 individuals) or both doses (7.5%, 19 individuals). The adjusted one-dose, two-dose, and combined JYNNEOS VE estimates were 68%, 89%, and 76%, respectively. JYNEEOS VE observed in less than two weeks of receiving the initial dose was non-significant, probably due to the inclusion of PEP recipients and individuals with Mpox exposure after vaccination but before developing protective immunity.

Multiple sensitivity analyses were performed to assess the robustness of the study findings. The initial analyses, excluding males aged ≥50.0 years who may have been administered smallpox vaccines before the termination of regular non-military US vaccinations in 1972, yielded similar results. The second analysis comprised 71.0 control individuals diagnosed with secondary syphilis and yielded a single-dose or double-dose VE of 65.0%. Among controls, 84% (n=213) underwent testing due to the presence of symptoms (41%, 88 individuals), partner referrals (9.0%, 19 individuals), screening purposes (48%, 103 individuals), or other reasons (1.40%, three individuals). The third sensitivity analysis, including only control individuals undergoing testing due to referrals or symptoms, yielded a one-dose or two-dose VE estimate of 64.0%. The fourth sensitivity analysis included the findings of only individuals with known ethnicity and race estimates, yielded single-dose or double-dose VE estimates of 81.0%. The lower estimated VE obtained by analyzing secondary syphilis patients may reflect control individuals with different clinical presentations or more remote risk behaviors. Lower VE obtained by limiting the control group to individuals undergoing testing due to symptoms or referrals may reflect the intended elimination of low-risk individuals seeking care or the inadvertent elimination of high-risk individuals accessing Mpox screening frequently. Based on the findings, the adjusted combined one-dose (administered ≥2.0 weeks prior) or two-dose JYNNEOS vaccine effectiveness was 76%. The findings underpin the advocacy of two-dose JYNNEOS vaccination regimens to prevent Mpox, following CDC and NY State Department of Health (NYSDOH) recommendations. The vaccine may be incorporated into broader sexual health programs.

Cited study published (May 19, 2023) in MMWR:

http://dx.doi.org/10.15585/mmwr.mm7220a4

Significance

Two human cases of West Nile virus have been reported in New York as the virus has been detected in a record number of mosquitoes in the city, health officials said Tuesday.  Across the city's five boroughs, 1,068 mosquito pools have tested positive for the virus, according to the New York City Department of Health and Mental Hygiene. The city recorded 779 positive pools at the same time last year. The two human cases were reported in Brooklyn and Queens, the health department said in a statement. The West Nile virus is most commonly spread to people through the bite of an infected mosquito, according to the US Centers for Diseases Control and Prevention. Those cases happen during mosquito season, which starts in the summer and continues through fall, the CDC said.  "We are in the height of West Nile virus season, but there are things you can do to decrease your risk of being bitten," New York City Health Commissioner Dr. Ashwin Vasan said. Using an insect repellent and wearing long sleeves and pants, especially when outside during late and early hours, may help prevent the risk of getting bit, Vasan explained. 

There is no vaccine for the virus, so preventative measures are the most effective way to avoid infection. Symptoms of West Nile infection include fatigue, fever, headache, body aches and rash. However, 80% of infected people do not display any symptoms, according to the CDC. In rare cases, the virus can also be spread through blood transfusions, organ transplants, exposure in a lab setting or from mother to infant. Less than 1% of infected people develop a serious neuroinvasive illness, such as encephalitis (inflammation of the brain) or meningitis (inflammation of the protective membranes covering the brain and spinal cord), according to the CDC. As of August 9, a total of 54 human cases of the virus disease have been reported to the CDC this year. Last year, 2,695 human cases were reported to the agency.

CNN's Aya Elamroussi contributed to this report.

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.

Two separate teams of researchers have found a worrying new coronavirus variant in New York City that carries mutations that help it evade the body's natural immune response -- as well as the effects of monoclonal antibody treatments.  Genomics researchers have named the variant B.1.526. It appears in people affected in diverse neighborhoods of New York City, they said, and is "scattered in the Northeast." One of the mutations in this variant is the same concerning change found in the variant first seen in South Africa and known as B.1.351. It appears to evade, somewhat, the body's response to vaccines, as well. And it's becoming more common. "We observed a steady increase in the detection rate from late December to mid-February, with an alarming rise to 12.7% in the past two weeks," one team, at Columbia University Medical Center, write in a report that has yet to be published, although it is scheduled to appear in pre-print version this week.  It's the latest of a growing number of viral variants that have arisen in the US, which has had more coronavirus cases -- 28 million -- than any other country and where spread is still intense. It's "home grown, presumably in New York," Dr. David Ho, Director of the Aaron Diamond AIDS Research Center at Columbia, who led the study team, said by email.  Viruses mutate all the time. The more people who are infected, and the longer they are infected, the more chance the viruses have to change. A patient's body will be loaded with billions of copies of a virus, and may will be slightly changed, or mutated. Most will come and go. But sometimes a mutation or pattern of mutations takes hold and gets passed along. If viruses with such patterns become more common, they're called variants. Again, it's not unusual for variants to arise but if they give the virus worrying properties, such as better transmissibility or the ability to evade treatments and vaccines, that's when doctors start to worry.

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

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....

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.