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