News Scan for Nov 05, 2020

News brief

H1N2v flu case reported in Canada

Health Canada yesterday announced that a rare variant H1N2 (H1N2v) influenza case has been confirmed in Alberta, marking the province's only flu case reported so far this season.

The virus was detected in the middle of October after the patient sought care for mild flulike symptoms and quickly recovered, the agency said in a statement. So far there's no evidence that the virus has spread, and agriculture officials are working with health investigators to identify the source of the virus and the possibility of further spread. At a news conference yesterday, officials said the virus is a swine variant and so far no links have been found to swine slaughterhouses, the CBC reported.

Health Canada noted that sporadic H1N2v cases have been reported in North America over the past decade, with 27 cases reported globally since 2005. The case is Canada's first, however. The last known case was reported by Brazil in July, which involved a slaughterhouse worker.
Nov 4 Health Canada statement
Jul 10 CIDRAP News scan

Avian flu outbreaks strike again in 4 countries

Four countries—Israel, Japan, the Netherlands, and Germany--reported more highly pathogenic avian flu outbreaks in poultry, according to official and media reports.

Israel, which has recently reported sporadic H5N8 outbreaks in poultry, reported one more, which struck a turkey farm in Hazafon, according to a notification from the World Organization for Animal Health (OIE). The event began on Nov 3, killing 500 of 28,000 birds. The survivors were slated for culling, and officials said the source of the virus is probably migratory wild birds.

In Japan, animal health officials reported an outbreak at a poultry farm in Kagawa prefecture in the western part of the country, with the preliminary investigation indicating avian influenza, though the subtype and pathogenicity haven't been determined, Reuters reported yesterday. Culling is under way on 330,000 chickens. Japan reported its last avian flu outbreak in early 2018.

The Netherlands, meanwhile, reported a second suspected highly pathogenic H5 outbreak at a poultry farm, which occurred at a layer facility in Puiflijk, according to a government statement today translated and posted by Avian Flu Diary (AFD), an infectious disease news blog. The farm, located not far from the site of an earlier farm outbreak, has 100,000 layers and 115,000 breeders, and culling is under way.

And following recent detections in wild birds, Germany reported its first avian flu outbreak this year in poultry, which involved H5N8 at a farm in North Friesland district in Schleswig-Holstein state. A state government announcement translated by AFD said 27 detections were also noted in the area's wild bird population.
Nov 5 OIE report on H5N8 in Israel
Nov 4 Reuters report on avian flu in Japan
Nov 5 AFD post on Netherlands and German outbreaks

COVID-19 Scan for Nov 05, 2020

News brief

COVID-19 jail outbreak curbed using network-informed steps, CDC says

Researchers from the Centers for Disease Control and Prevention (CDC) and the Chicago area analyzed movement networks during a COVID-19 outbreak at the Cook County Jail in Chicago, finding that medical isolation and contact interventions were effective at reducing transmission.

From Mar 1 through Apr 30, 472 (12.3%) of 3,843 inmates and 198 (9.7%) of 2,041 staff members across 13 separate buildings had COVID-19, according to a report in the Morbidity and Mortality Weekly Report (MMWR). Network analysis looked at both person-division networks (by building) and person-person networks (same location, same time). The findings reflect staff and inmates as two separate groups, as no strong patterns emerged when combining them, although the researchers acknowledge intergroup transmissions would have most likely occurred.

Staff members did not show a clear pattern of transmissions during person-division networks, but a person-person lens indicated that 1.4% of the 103,701 shared shift connections were between staff members with COVID-19, exceeding the expected percentage of 0.9%. Because of this, as well as the positive linear relationship between infected staff and connections by division and the uncalculated community transmissions, the researchers advocate for staff cohorts, consistent shift locations, and mask use.

Inmates with COVID-19 had the highest location rates at the buildings used for medical isolation and offsite locations, such as hospitals. Person-person networks showed that 3.2% of the 1,214,462 connections were between two people with COVID-19, compared with the expected 1.5%. Notably, this rate decreased to 1.0% when medical isolation occurred, helping support the researchers' recommendations for testing, quarantine, and restricted division movements during potential outbreaks.

As the outbreak continued, more interventions were put in place, as well. Guest visits stopped Mar 15, program activities were suspended Mar 23, cells were converted into single occupancies and staff wore masks on Apr 2, and detained persons all wore masks on Apr 13.

The authors conclude, "A network-informed approach can identify likely points of high transmission, enabling targeted interventions to reduce transmission."
Nov 6 MMWR report

Report details 70-day SARS-CoV-2 shedding in asymptomatic leukemia patient

A Cell case report yesterday details a 105-day infection (as determined by the presence of viral RNA) and 70-day infectious period (live virus detected) in a 71-year old woman with leukemia, suggesting that immunocompromised patients may shed virus for longer than previously recognized.

Researchers detailed the case of a Washington state woman with chronic lymphocytic leukemia and low antibody count who was admitted to a Seattle-area hospital for severe anemia, tested positive for SARS-CoV-2, the virus that causes COVID-19, for the first time on Mar 2 via reverse-transcriptase polymerase chain reaction (RT-PCR), and continued to test positive through Jun 15 while remaining asymptomatic. The authors suggest this is the longest known case of anyone being actively infected with SARS-CoV-2 while remaining asymptomatic.

Duration of viral shedding has important implications for disease transmission, and although wide variability has been observed, most people appear to shed active virus for 8 to 20 days after an initial positive test result, the researchers say. Similar duration and viral loads have been observed for both symptomatic and asymptomatic patients, but differences between populations, including the immunocompromised, have not yet been fully explored.

The patient was given two transfusions of SARS-CoV-2 convalescent plasma on May 12 and 23, but subsequent positive RT-PCR tests suggest that the therapy was not successful in rapidly clearing the infection. The researchers speculate that the patient's compromised immune system did not allow her to mount a response to the virus, and blood tests showed that her body was never able to make antibodies against SARS-CoV-2.

"Although it is difficult to extrapolate from a single patient, our data suggest that long-term shedding of infectious virus may be a concern in certain immunocompromised patients," the study authors wrote. "Given that immunocompromised patients could have prolonged shedding and may not have typical symptoms of COVID-19, symptom-based strategies for testing patients and discontinuing transmission-based precautions, as recommended by the CDC, may fail to detect whether certain patients are shedding infectious virus."
Nov 4 Cell study
Nov 4 Cell Press news release

Study finds 6.3% lack antibodies after COVID-19 infection

A serologic study of 2,547 people with previously confirmed SARS-CoV-2 infections showed that 6.3% lacked detectable antibodies. The study in Clinical Infectious Diseases yesterday suggested that a sizeable proportion of people do not have immunoglobulin (Ig) G antibodies following infection, and identified race, weight status, and illness severity as independent predictors of IgG antibody presence.

Researchers analyzed blood serum collected from healthcare workers and first responders in New York City (May 18 to Jun 19) and the Detroit metropolitan area (May 18 to Jun 13) with a history of RT-PCR–confirmed infection and with symptom onset at least 2 weeks prior. Serum samples were tested with an assay that detects IgG antibodies against the SARS-CoV-2 S1 protein domain that is implicated in target cell receptor binding.

Of 2,547 persons with previously confirmed SARS-CoV-2 infection, 160 (6.3%) were seronegative—showed no detectable IgG antibodies. Of 2,112 previously symptomatic persons, the seronegative proportion slightly increased from 14 to 90 days post–symptom onset (P = 0.06). The seronegative rate ranged from 0% among 79 persons previously hospitalized to 11.0% among 308 persons with asymptomatic infections, with the seronegative proportion remaining relatively stable in people tested up to 90 days post–symptom onset.

Those taking immunosuppressive medications were more likely to be seronegative (31.9%, 95% confidence interval [CI], 10.7% to 64.7%), while blacks, the severely obese, and people with more symptoms were less likely to be seronegative. The results demonstrate that such factors are useful predictors of IgG antibody presence after infection and point to the importance of using similar populations when comparing serologic data, the authors suggest.

Repeat COVID-19 is rare, despite an apparent lack of demonstrable antibody in a sizeable proportion of previously infected people, providing reassurance for the interpretation of population seroprevalence studies. "While certainly not definitive, this observation suggests short-term immunity from clinically apparent reinfection despite lack of demonstrable antibody in some persons," the study authors note.
Nov 4 Clin Infect Dis study