Shiloh
Editor, Senior Moderator
Source: https://www.cidrap.umn.edu/news-perspective/2022/02/covid-19-scan-feb-22-2022
COVID-19 Scan for Feb 22, 2022
Omicron subvariant reinfection; SARS-CoV-2 variants in deer; COVID-19 severity by ZIP code
Filed Under:
COVID-19
Study highlights rare BA.2 subvariant reinfections after Omicron COVID-19
Infection with the SARS-CoV-2 Omicron BA.2 subvariant shortly after an initial infection with the Omicron BA.1 subvariant—the original Omicron strain—is rare, occurring mostly in young, unvaccinated people with mild symptoms, according to a non–peer-reviewed Danish study.
In the study, published today on the medRxiv preprint server, researchers at the Statens Serum Institut in Denmark analyzed the subgenomic and genomic RNA of viruses responsible for a randomly selected group of 263 paired samples from more than 1.8 million COVID-19 patients. The study period was Nov 22, 2021, when Omicron was first identified in that country, to Feb 11, 2022. The BA.2 variant now accounts for most COVID-19 cases in Denmark.
Of the 263 virus samples, 187 COVID-19 reinfections (71%) were identified, 47 (18%) of which were BA.2 cases after initial BA.1 infections. The severity of both types of infections was similarly mild, and no patients were hospitalized.
Median patient age was 15 years, none were older than 38, 89% were unvaccinated, 6% had received two COVID-19 vaccine doses, and 4% had received one dose.
Overall, viral load was significantly lower in patients with BA.2 reinfections than during the initial infection.
"This may indicate a more superficial and transient secondary infection that could be explained by T cell-mediated immunity obtained during the first infection," the researchers wrote.
Feb 22 medRxiv study
US researchers confirm SARS-CoV-2 Alpha, Delta variants in deer
A new preprint study describes detection of both Alpha and Delta SARS-CoV-2 variants in white-tailed deer in Pennsylvania—the first known detections of those strains in deer—with 18 of 93 nasal swab samples (19.3%) testing positive, adding to growing evidence that deer are a reservoir for the virus in the United States.
The study was published on medRxiv and has not been peer-reviewed.
All deer samples were collected in the fall and winter 2021, after Delta became the prominent variant in the United States but before Omicron emerged. The authors said samples collected from road-killed animals were significantly more likely to be positive than all other sample types (hunter harvested, 11 of 66; road-killed, 6/13; and other, 1/14 [P=0.002]).
Of the 18 positive nasal swabs, researchers performed whole-genome sequencing on seven, which were annotated as Alpha and Delta variants, the first reported observations of these lineages in deer, the authors said. This finding indicates at least four independent spillover events between humans and deer in the last year.
"Given that there are estimated to be 30 deer [per] square mile in PA, and over a million deer total, this suggests an enormous number of spillovers and infected deer in the state" the authors said.
Last year, research conducted in Iowa and Ohio showed that a significant proportion of white-tailed deer were SARS-CoV-2–positive.
Feb 21 medRxiv study
COVID-19 patient ZIP codes may affect disease severity
A pooled cross-sectional study in the Annals of Internal Medicine finds that COVID-19 patients' ZIP codes may affect clinical outcomes, with patients from high-vulnerability neighborhoods more likely to be hospitalized for infections.
The study is based on data from 2,309 patients hospitalized with COVID-19 at 38 Michigan hospitals. Medical history was compared with patients' social vulnerability index (SVI), which takes into account the local area's average income, education level, household density to percentage of households led by single parents, and homes in which English is the not the primary language.
Though once hospitalized, patients from high-vulnerability ZIP codes had similar outcomes to patients from low-vulnerability neighborhoods, they tended to present with more severe clinical symptoms, including lower pulse oximetry readings and higher respiratory rates.
When controlled for age, sex, and comorbidities, patients from high-vulnerability neighborhoods had more acute organ dysfunction (increase of 2.8 percentage points) and acute organ failure (increase of 2.8 percentage points) at hospitalization. But intensive care unit stay, mortality, and discharge disposition were similar across ZIP codes.
"What leads to the initial disparities in seriousness of illness that they arrive with?" said Renuka Tipirneni, MD, the lead study author, in a press release. "Are people not getting access to testing or treatment early in their illness? Are there other individual patient-level social risks such as ongoing difficulties with transportation, housing, or sick leave at work? Did they delay seeking care because of lack of access?"
The authors suggest SVIs will be a useful tool to predict trends in COVID-19 illness in the future.
Feb 21 Ann Intern Med study
Feb 21 University of Michigan press release
COVID-19 Scan for Feb 22, 2022
Omicron subvariant reinfection; SARS-CoV-2 variants in deer; COVID-19 severity by ZIP code
Filed Under:
COVID-19
Study highlights rare BA.2 subvariant reinfections after Omicron COVID-19
Infection with the SARS-CoV-2 Omicron BA.2 subvariant shortly after an initial infection with the Omicron BA.1 subvariant—the original Omicron strain—is rare, occurring mostly in young, unvaccinated people with mild symptoms, according to a non–peer-reviewed Danish study.
In the study, published today on the medRxiv preprint server, researchers at the Statens Serum Institut in Denmark analyzed the subgenomic and genomic RNA of viruses responsible for a randomly selected group of 263 paired samples from more than 1.8 million COVID-19 patients. The study period was Nov 22, 2021, when Omicron was first identified in that country, to Feb 11, 2022. The BA.2 variant now accounts for most COVID-19 cases in Denmark.
Of the 263 virus samples, 187 COVID-19 reinfections (71%) were identified, 47 (18%) of which were BA.2 cases after initial BA.1 infections. The severity of both types of infections was similarly mild, and no patients were hospitalized.
Median patient age was 15 years, none were older than 38, 89% were unvaccinated, 6% had received two COVID-19 vaccine doses, and 4% had received one dose.
Overall, viral load was significantly lower in patients with BA.2 reinfections than during the initial infection.
"This may indicate a more superficial and transient secondary infection that could be explained by T cell-mediated immunity obtained during the first infection," the researchers wrote.
Feb 22 medRxiv study
US researchers confirm SARS-CoV-2 Alpha, Delta variants in deer
A new preprint study describes detection of both Alpha and Delta SARS-CoV-2 variants in white-tailed deer in Pennsylvania—the first known detections of those strains in deer—with 18 of 93 nasal swab samples (19.3%) testing positive, adding to growing evidence that deer are a reservoir for the virus in the United States.
The study was published on medRxiv and has not been peer-reviewed.
All deer samples were collected in the fall and winter 2021, after Delta became the prominent variant in the United States but before Omicron emerged. The authors said samples collected from road-killed animals were significantly more likely to be positive than all other sample types (hunter harvested, 11 of 66; road-killed, 6/13; and other, 1/14 [P=0.002]).
Of the 18 positive nasal swabs, researchers performed whole-genome sequencing on seven, which were annotated as Alpha and Delta variants, the first reported observations of these lineages in deer, the authors said. This finding indicates at least four independent spillover events between humans and deer in the last year.
"Given that there are estimated to be 30 deer [per] square mile in PA, and over a million deer total, this suggests an enormous number of spillovers and infected deer in the state" the authors said.
Last year, research conducted in Iowa and Ohio showed that a significant proportion of white-tailed deer were SARS-CoV-2–positive.
Feb 21 medRxiv study
COVID-19 patient ZIP codes may affect disease severity
A pooled cross-sectional study in the Annals of Internal Medicine finds that COVID-19 patients' ZIP codes may affect clinical outcomes, with patients from high-vulnerability neighborhoods more likely to be hospitalized for infections.
The study is based on data from 2,309 patients hospitalized with COVID-19 at 38 Michigan hospitals. Medical history was compared with patients' social vulnerability index (SVI), which takes into account the local area's average income, education level, household density to percentage of households led by single parents, and homes in which English is the not the primary language.
Though once hospitalized, patients from high-vulnerability ZIP codes had similar outcomes to patients from low-vulnerability neighborhoods, they tended to present with more severe clinical symptoms, including lower pulse oximetry readings and higher respiratory rates.
When controlled for age, sex, and comorbidities, patients from high-vulnerability neighborhoods had more acute organ dysfunction (increase of 2.8 percentage points) and acute organ failure (increase of 2.8 percentage points) at hospitalization. But intensive care unit stay, mortality, and discharge disposition were similar across ZIP codes.
"What leads to the initial disparities in seriousness of illness that they arrive with?" said Renuka Tipirneni, MD, the lead study author, in a press release. "Are people not getting access to testing or treatment early in their illness? Are there other individual patient-level social risks such as ongoing difficulties with transportation, housing, or sick leave at work? Did they delay seeking care because of lack of access?"
The authors suggest SVIs will be a useful tool to predict trends in COVID-19 illness in the future.
Feb 21 Ann Intern Med study
Feb 21 University of Michigan press release
