Virus World

The cumulative hospitalization rate for flu in the U.S. is higher than it has been at this point for more than a decade. There are increasing signs that flu season is off to a very early start in parts of the United States, with the cumulative hospitalization rate higher than it has been at this point in the fall for more than a decade, the Centers for Disease Control and Prevention reported Friday.  In its weekly FluView report, the CDC estimated that there have already been 880,000 influenza illnesses, 6,900 flu hospitalizations, and 360 deaths caused by flu this season, which started at the beginning of October. It is unusual for the CDC to have enough data to issue estimates on the burden of flu this early in the season.  These figures are estimates, based on data from a flu hospitalization surveillance network of acute care hospitals in 14 states. Flu activity is currently highest in south-central and southeast parts of the country, and New York. It is also picking up along the Eastern Seaboard. The CDC also reported the death of a child, the first pediatric flu death of the new flu season. It occurred in the week ending Oct. 8. 

In the first two winters of the Covid-19 pandemic, the new coronavirus and the measures people took to protect themselves from it suppressed transmission of a number of respiratory pathogens that normally make the rounds. That hiatus has ended and those viruses are returning, though often at times when they didn’t normally circulate in the past. Hospitals around the country are seeing record numbers of cases of respiratory syncytial virus, or RSV, right now. In pre-Covid times, RSV didn’t typically emerge until the winter. Some people are interpreting the early start of flu activity as evidence we are in for a harsh flu season. But Lynnette Brammer, team lead for domestic surveillance in the CDC’s influenza division, said it’s impossible at this point to know how bad the season will be.  “What a lot of people are implying is because it’s early and levels are high for this time of year that it’s going to be a severe season. We don’t know that,” Brammer told STAT.  “Right now all we can say is we’re off to an early start.”  She noted that people who have been waiting to get a flu shot to try to time it to the start of flu circulation should not hold off any longer. “You need to get vaccinated now, if you haven’t already done that.” Ed Belongia, director of the Center for Clinical Epidemiology and Population Health at Wisconsin’s Marshfield Clinic Research Institute, said there is good reason to be worried that this could be a severe flu season. Most immune systems haven’t seen flu viruses for a couple of years, which means the pool of people susceptible to infection is large. And the measures society took to try to slow spread of Covid — mask-wearing, social distancing, school closures — have mostly been abandoned.  But Belongia has been studying flu for too long to guess how a flu season will unfold. The virus is maddeningly unpredictable. “Whether or not the whole season is going to be longer and more severe, we really just don’t know at this point. It’s too early to say,” he said.

Evidence from the Southern Hemisphere’s flu season — which sometimes provides hints of what’s in store for us — showed oddly timed and active flu seasons, but not necessarily bad ones. Australia had a lot of flu activity, mainly in children. But a report on its 2022 winter season issued earlier this month stated that the clinical severity of the season, based on the numbers of intensive care admissions and deaths, was actually low. It rated the overall impact of the flu season as low to moderate. Other hopeful news from the Southern Hemisphere was that the flu vaccine seems well-matched to the viruses that are circulating. A report this week from Chile in the CDC’s online journal Morbidity and Mortality Weekly Report estimated flu vaccine efficacy at 49% against H3N2 viruses, the subtype that caused most of the disease there. It is also the virus currently causing most disease in the U.S. Belongia said he was pleasantly surprised, adding  “49% is about as good as you can expect to see for H3N2. So I thought that was encouraging. While it’s impossible to guess how bad the flu season will be, there is one thing that does look reasonable to assume. If the current levels of circulation of influenza and RSV virus continue or increase, there could be a lot of respiratory illness around Thanksgiving. Much of the current illness is in young children, who typically get sick first in the cold and flu season and spread their bugs to siblings, parents, grandparents, and other adults with whom they are in contact.

Health care workers (HCW) are a high-risk population to acquire SARS-CoV-2 infection from patients or other fellow HCW. At the same time, they can be contagious to highly vulnerable individuals seeking health care. This study aims at estimating the seroprevalence of antibodies against SARS-CoV-2 and associated factors in HCW from a large referral hospital in Barcelona, Spain, one of the countries hardest hit by COVID-19 in the world.

From 28 March to 9 April 2020, we recruited a random sample of 578 HCW from the human resources database of Hospital Clínic in Barcelona. We collected a nasopharyngeal swab for direct SARS-CoV-2 detection through real time reverse-transcriptase polymerase chain reaction (rRT-PCR), as well as blood for plasma antibody quantification. IgM, IgG and IgA antibodies to the receptor-binding domain of the spike protein were measured by Luminex. The cumulative prevalence of infection (past or current) was defined by a positive SARS-CoV-2 rRT-PCR and/or antibody seropositivity. 

Of the 578 total participants, 39 (6.7%, 95% CI: 4.8-9.1) had been previously diagnosed with COVID-19 by rRT-PCR, 14 (2.4%, 95% CI: 1.4-4.3) had a positive rRT-PCR at recruitment, and 54 (9.3%, 95% CI: 7.2-12.0) were seropositive for IgM and/or IgG and/or IgA against SARSCoV-2. Of the 54 seropositive HCW, 21 (38.9%) had not been previously diagnosed with COVID-19, although 10 of them (47.6%) reported past COVID-19-compatible symptoms. The cumulative prevalence of SARS-CoV-2 infection was 11.2% (65/578, 95% CI: 8.9-14.1). Among those with evidence of past or current infection, 40.0% (26/65) had not been previously diagnosed with COVID-19, of which 46.2% (12/26) had history of COVID-19-compatible symptoms. The odds of being seropositive was higher in participants who reported any COVID19 symptom (OR: 8.84, 95% CI: 4.41-17.73). IgM levels positively correlated with age (rho=0.36, p-value=0.031) and were higher in participants with more than 10 days since onset of symptoms (p-value=0.022), and IgA levels were higher in symptomatic than asymptomatic subjects (p-value=0.041).  

The seroprevalence of antibodies against SARS-CoV-2 among HCW was lower than expected. Thus, being a high-risk population, we anticipate these estimates to be an upper limit to the seroprevalence of the general population. Forty per cent of those with past or present infection had not been previously diagnosed with COVID-19, which calls for active periodic rRT-PCR testing among all HCW to minimize potential risk of hospital-acquired SARS-CoV-2 infections.  In summary, we found that 9.3% (95% CI: 7.2-12.0) of HCW from a large Spanish referral hospital (recruited from March 28th to April 9th, 2020) developed detectable IgA, IgG and/or IgM antibodies. Given that HCW are a high risk population for SARS-CoV-2, it is likely that the community seroprevalence is lower than this figure, showing that we are still very far from reaching the 67% herd immunity level that is estimated to be needed to protect the susceptible population,23 assuming that this immunity prevents from reinfection.

There currently is substantial controversy about the role played by SARS-CoV-2 in aerosols in disease transmission, due in part to detections of viral RNA but failures to isolate viable virus from clinically generated aerosols. Methods - Air samples were collected in the room of two COVID-19 patients, one of whom had an active respiratory infection with a nasopharyngeal (NP) swab positive for SARS-CoV-2 by RT-qPCR. By using VIVAS air samplers that operate on a gentle water-vapor condensation principle, material was collected from room air and subjected to RT-qPCR and virus culture. The genomes of the SARS-CoV-2 collected from the air and of virus isolated in cell culture from air sampling and from a NP swab from a newly admitted patient in the room were sequenced.

Viable virus was isolated from air samples collected 2 to 4.8m away from the patients. The genome sequence of the SARS-CoV-2 strain isolated from the material collected by the air samplers was identical to that isolated from the NP swab from the patient with an active infection. Estimates of viable viral concentrations ranged from 6 to 74 TCID50 units/L of air. Patients with respiratory manifestations of COVID-19 produce aerosols in the absence of aerosol-generating procedures that contain viable SARS-CoV-2, and these aerosols may serve as a source of transmission of the virus.

As reported in air sampling tests performed by others and in our previous report, airborne SARS-CoV-2 was present in a location with COVID-19 patients. The distance from the air-samplers to the patients (≥ 2 m) suggests that the virus was present in aerosols. Unlike previous studies, we have demonstrated the virus in aerosols can be viable, and this suggests that there is an inhalation risk for acquiring COVID-19 within the vicinity of people who emit the virus through expirations including coughs, sneezes, and speaking.

Preprint available at medRXiv (August 4, 2020):

https://doi.org/10.1101/2020.08.03.20167395

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.