COVID-19 Scan for Mar 03, 2021

News brief

COVID-19 P1 variant may be more transmissible, infectious

The P1 variant that caused a second wave of COVID-19 infections in Manaus, Brazil, is more transmissible and from 25% to 61% of previously infected people may be susceptible to reinfection, according to a preprint, non–peer-reviewed study from researchers at the University of Sao Paulo, Imperial College London, and the University of Oxford.

Despite fall 2020 serosurveys suggesting that Manaus' population had almost reached herd immunity for COVID-19 and had an attack rate above 67%, another COVID-19 surge hit the city late in the year. For the new study, researchers examined 184 viral genomic samples collected from residents in November and December 2020 and found that the dominant strain, now called P1, was a variant with 17 amino acid changes from its most similar strain, B1128. Of note, the variant had three mutations in the spike protein associated with the virus' binding to the host's angiotensin-converting enzyme-2 receptor.

P1 may have gone from 0% to 87% of COVID-19 cases in 7 weeks, according to 147 positive reverse-transcription polymerase chain reaction (RT-PCR) samples dating from May 2020. The researchers estimate that P1 could be 1.4 to 2.2 times more transmissible than other local strains, given that it had to overcome partial immunity to cause a second surge.

The researchers also found a correlation between P1 and lower threshold cycle (Ct) values, indicating a higher viral load, but the finding was not statistically significant. Similarly, while the researchers noticed a possible relationship between P1 infection and higher mortality rates, they noted that Manaus's overloaded health system could have been the cause.

"Global collaborative efforts on rapid virus genome sequencing are allowing us to identify SARS-CoV-2 lineages of concerns in near real-time," said one of the study's authors, Ester Sabino, MD, in an Imperial College London news release. "Yet, uncertainty in the ways SARS-CoV-2 is changing and implications for vaccine design calls for much more sequencing and analysis of virus genomes globally."

The researchers believe that the first case of P1 occurred in Manaus around Nov 6, 2020. Since then, it has been found in more than 20 countries, including the United States. Today's Morbidity & Mortality Weekly Report covers the first two US cases, found in travelers who returned to Minnesota after going to Brazil early January. As of Feb 28, 10 P1 cases have been reported in the country.
Feb 25 CADDE Centre study
Mar 2 Imperial College London news release

Hotels found effective for COVID isolation, quarantine for homeless people

The use of five isolation/quarantine (I/Q) hotels in San Francisco County may have contributed to better public health outcomes among people experiencing homelessness, according to a JAMA Open Network study published yesterday.

The I/Q hotels were created so that people who were experiencing homelessness and who had suspected or confirmed COVID-19 could have a place to recover and physically distance. Staff and provided resources took care of residents' general health, dietary, hygiene, and child (eg, diapers, formula) needs, and those who had substance use disorders had access to methods for reducing harm.

Almost half (45.9%) of the 1,009 hotel residents from Mar 19 to May 31, 2020, were diagnosed as having COVID-19. Most were men (74.9%) or Latino (45.0%), and of those with Coordinated Care Management System records, 33.4% had comorbidities, 24.8% had mental health disorders, and 26.0% had substance use disorders. Of the total 1,065 referrals, more than 70% came from emergency departments, urgent care, and ambulatory care clinics. Only 3.8% of the 346 transferred from a county hospital had to be readmitted.

The median length of stay was 10 days, but almost 1 in 5 participants discontinued their stay prematurely. The researchers suggest this could be due to misunderstandings about the program's purpose, but they also note that women, those younger than 40, those who experienced unsheltered homelessness, and Black people were 1.8, 2.5, 4.5, and 1.7 times more likely to discontinue. (The last factor was not statistically significant after a further sensitivity analysis.)

The researchers also suggest these hotels may have lightened the burden on hospitals stressed with severe COVID-19 but say more study is needed.

"Overall, this study suggests that both individual and public health outcomes are improved when people have access to resources that meet a broad variety of needs, recognizes them as whole people, and provides support to address social determinants of health," write Joshua Barocas, MD, and Esther Choo, MD, MPH, in a related commentary.
Mar 2 JAMA Netw Open study
Mar 2 JAMA Netw Open commentary

News Scan for Mar 03, 2021

News brief

Studies examine dental antibiotic prescribing in VA patients

Two studies yesterday in Infection Control & Hospital Epidemiology provide a snapshot of dental antibiotic prescribing among Veterans Affairs (VA) dental patients.

In one study, to establish a baseline for national antibiotic prescribing for acute oral infections prior to the release of the American Dental Association (ADA) 2019 guidelines, a team of VA researchers analyzed national VA data for 2017. They identified cases of three common acute oral infections—irreversible pulpitis (IP), apical periodontitis (AP), and acute apical abscess (AAP)—for which antibiotics are not recommended under the 2019 ADA guidelines, and included any antibiotics prescribed within 7 days of a dental clinic visit.

Of the 470,039 dental clinic visits in 2017, 12% of patients with IP, 17% with AP, and 28% with AAP received antibiotics. Although the median days' supply of antibiotics for patients with a prescription was 7, prolonged antibiotic use was frequent: 42.5% of IP visits, 44.9% of AP visits, and 49.4% of AAP visits received antibiotics for more than 8 days. Multivariable logistics regression identified patients with high-risk cardiac conditions, prosthetic joints, and endodontic, implant, and oral and maxillofacial surgical procedures as more likely to receive antibiotics.

The study authors say that while guideline-discordant treatment was low, the findings may serve as a benchmark for future antibiotic stewardship efforts within the dental setting.

"The guideline-discordant antibiotic prescribing observed within the study may represent unnecessary antibiotic prescribing placing patients at increased risk of adverse events without providing any meaningful benefit," they wrote.
Mar 2 Infect Control Hosp Epidemiol abstract

In the other study, some of the same researchers found that the rate of infection after getting teeth pulled was no different among VA patients who received antibiotics and those who did not.

Of 69,610 patients with dental extractions identified from 2017 national VA data, 404 were randomly selected for inclusion, and 154 (38.1%) received adjunctive antibiotics. An analysis of electronic health records found no difference in the frequency of post-extraction oral infection among those who did and did not receive antibiotics (4.5% versus 3.2%).

"These results suggest that antibiotics have a limited role in preventing postprocedural infection," the authors wrote.
Mar 2 Infect Control Hosp Epidemiol abstract

H9N2 avian flu infects 3 children in China

China has reported three more H9N2 avian flu cases, all in young girls, the World Health Organization (WHO) Western Pacific regional office said in its most recent weekly update on avian flu.

The children are from three different provinces, one had known exposure to poultry, and all had mild infections, a pattern common to H9N2 infections. The first is a 1-year-old girl from Sichuan province, the second is a 5-year-old girl from Anhui province, and the third is a 2-year-old girl from Jiangxi province.

Their symptoms began between Nov 30 and Jan 18. All have recovered, and so far, no other infections have been found among their contacts.

China has reported 5 H9N2 cases this year, and so far, the country has reported 43 cases since December 2015. Sporadic H9N2 cases have been reported in China and other countries where the virus is endemic in poultry.
Feb 26 WHO Western Pacific regional office avian flu report