Genomic epidemiology reveals the dominance of Hennepin County in the transmission of SARS-CoV-2 in Minnesota from 2020 to 2022

IMPORTANCE

We analyzed over 22,000 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes of patient samples tested at Mayo Clinic Laboratories during a 2-year period in the COVID-19 pandemic, which included Alpha, Delta, and Omicron variants of concern to examine the roles and relationships of Minnesota virus transmission. We found that Hennepin County, the most populous county, drove the transmission of SARS-CoV-2 viruses in the state after including the formation of earlier clades including 20A, 20C, and 20G, as well as variants of concern Alpha and Delta. We also found that Hennepin County was the source for most of the county-to-county introductions after an initial predicted introduction with the virus in early 2020 from an international source, while other counties acted as transmission "sinks." In addition, major policies, such as the end of the lockdown period in 2020 or the end of all restrictions in 2021, did not appear to have an impact on virus diversity across individual counties.

Genomic epidemiology reveals the dominance of Hennepin County in transmission of SARS-CoV-2 in Minnesota from 2020-2022

SARS-CoV-2 has had an unprecedented impact on human health and highlights the need for genomic epidemiology studies to increase our understanding of virus evolution and spread, and to inform policy decisions. We sequenced viral genomes from over 22,000 patient samples tested at Mayo Clinic Laboratories between 2020-2022 and use Bayesian phylodynamics to describe county and regional spread in Minnesota. The earliest introduction into Minnesota was to Hennepin County from a domestic source around January 22, 2020; six weeks before the first confirmed case in the state. This led to the virus spreading to Northern Minnesota, and eventually, the rest of the state. International introductions were most abundant in Hennepin (home to the Minneapolis/St. Paul International (MSP) airport) totaling 45 (out of 107) over the two-year period. Southern Minnesota counties were most common for domestic introductions with 19 (out of 64), potentially driven by bordering states such as Iowa and Wisconsin as well as Illinois which is nearby. Hennepin also was, by far, the most dominant source of in-state transmissions to other Minnesota locations (n=772) over the two-year period. We also analyzed the diversity of the location source of SARS-CoV-2 viruses in each county and noted the timing of state-wide policies as well as trends in clinical cases. Neither the number of clinical cases or major policy decisions, such as the end of the lockdown period in 2020 or the end of all restrictions in 2021, appeared to have impact on virus diversity across each individual county.

Viral detection using a multiplex polymerase chain reaction-based assay in outpatients with upper respiratory infection

We evaluated a commercial multiplex polymerase chain reaction (PCR) assay in a cross-sectional study among 81 adult and pediatric outpatients—40 cases with upper respiratory infection symptoms and 41 asymptomatic controls—from February to April 2008. Two specimens (throat swab and nasal swab) from each participant were tested using the EraGen MultiCode-PLx Respiratory Virus Panel that detects 17 viral targets. Throat swabs were also tested for Group A Streptococcus (GAS) by PCR. Respiratory viruses were detected in 22/40 (55%) cases and in 3/41 (7%) controls (P < 0.001). GAS was detected in 10 (25%) cases; GAS and respiratory virus co-infection was found in 4 (10%). Agreement between nasal and throat swabs for viral detection was 69% in cases and 95% in controls. Of 22 cases with a detectable virus, 12 (54%) were picked up by only 1 (throat or nasal) specimen, and the detection rate was increased by combining results of nasal and throat swab testing.

Real-time PCR method for detection of Encephalitozoon intestinalis from stool specimens

The prevalence of microsporidiosis is likely underestimated due to the labor-intensive, insensitive, and nonspecific clinical laboratory methods used for the diagnosis of this disease. A real-time PCR assay was designed to assess DNA extraction methods and to detect three Encephalitozoon species in feces. Modifications of the MagNA Pure LC DNA isolation kit protocol (Roche Applied Sciences, Indianapolis, Ind.) were compared by using the automated MagNA Pure LC instrument (Roche) and fecal specimens spiked with Encephalitozoon intestinalis spores. Extracted DNA was amplified by the LightCycler (Roche) PCR assay. Assay sensitivity, reproducibility, and efficiency were assessed by comparing threshold crossover values achieved with different extraction and storage conditions (fresh, refrigerated, frozen, and preserved specimens). Optimal extraction conditions were achieved by using a commercial buffer, tissue lysis buffer (Roche), as the specimen diluent. LightCycler PCR results were compared to those obtained from routine stool microscopy with trichrome blue stain. The lower limit of detection for the LightCycler PCR assay varied by storage conditions from 10(2) to 10(4) spores/ml of feces, a value which represented a significant improvement over that achieved by staining (> or =1.0 x 10(6) spores/ml). Melting temperature analysis of the amplicons allowed for the differentiation of three Encephalitozoon species (E. intestinalis, E. cuniculi, and E. hellem). The assay is readily adaptable to the clinical laboratory and represents the first real-time PCR assay designed to detect Encephalitozoon species.

Evaluation of ColorPAC Giardia/Cryptosporidium rapid assay and ProSpecT Giardia/Cryptosporidium microplate assay for detection of Giardia and Cryptosporidium in fecal specimens

Detection of Giardia and Cryptosporidium in clinical stool specimens using the ColorPAC and ProSpecT enzyme immunoassays revealed 98.7% agreement for Giardia detection and 98.1% agreement for Cryptosporidium detection. Sensitivities were uniformly 100%. The specificities of the ColorPAC immunoassay for Giardia and Cryptosporidium detection were 100 and 99.5%, respectively, and those for the ProSpecT assay were 98.4 and 98.6%, respectively. The false-positive reactions with the ProSpecT assay occurred with specimens that were grossly bloody.

Evaluation of a social norms marketing campaign to reduce high-risk drinking at The University of Mississippi

A social marketing campaign to change perceptions of peer drinking norms was conducted by the National Golden Key Honor Society at the University of Mississippi during the 1995-1996 school year. To assess the campaign's impact on perceptions of student drinking norms and alcohol consumption, Golden Key's national office administered a survey three times during the school year to all students enrolled in a random sample of required freshmen English courses. Regression analyses suggest that exposure to the marketing campaign may be associated with lower (and more accurate) estimates of student drinking norms. While offering promising results, this study was limited due to shortcomings in the research design. Future evaluations of social norms marketing campaigns should adhere to basic evaluation principles, such as using comparison groups, collecting contextual data, using a valid and reliable survey instrument, and ensuring proper survey administration techniques.

Diagnostic value of a miracidium in urinary sediment

Although rarely encountered in the United States, urinary tract schistosomiasis occurs commonly in many countries in the eastern hemisphere. Travel and immigration may contribute to imported cases of schistosomiasis. Excessive morbidity and increased mortality, including the development of urinary-tract squamous-cell carcinoma, are associated with untreated Schistosoma haematobium infection. Therefore, in the appropriate clinical context, all efforts should be made to rule out infectious and readily treatable causes of chronic hematuria. The presence of characteristic eggs in the urinary sediment is the usual means of diagnosing a S. haematobium infection. Additionally, the small and less commonly encountered miracidium stage of S. haematobium may also be present in the urine, which is another means of diagnosing urinary tract schistosomiasis. The present report describes a case in which a miracidium was detected in a fresh, unstained urine specimen. As detection of miracidia can be made in specimens also processed by routine cytologic methods, it behooves cytologists to be aware of this entity for the diagnosis of schistosomiasis.

Evaluation of an enzyme-linked immunosorbent assay for the detection of Giardia lamblia in stool specimens

A commercially available enzyme-linked immunosorbent assay (ELISA) for the detection of Giardia lamblia in stool specimens was evaluated on 342 specimens submitted to the Mayo Clinic Parasitology Laboratory for routine examination. The stools were either fresh or fresh/frozen at -65 degrees C (139 specimens) or were preserved in formalin (203 specimens). ELISA results were compared with those obtained by conventional microscopic examination: 143 stools were positive by both methods and 186 were negative. Sixty-six of the negative specimens contained 96 parasites belonging to 16 species other than Giardia, indicating a low rate of cross-reactivity. There were eight "false positive" ELISA results, which included specimens from one patient who had previously had a "true positive" and another patient with multiple family members infected with Giardia. Five stools that were "falsely negative" by ELISA contained only rare G. lamblia. The ELISA sensitivity was 97%, the specificity was 96%, and the positive predictive value was 95%. Results were evenly distributed between frozen and formalinized stools. The LMD/Seradyn ELISA appears to be a simple, rapid, and accurate method for the detection of G. lamblia in unprocessed stool samples.

Do callosal projection neurons reflect sex differences in axon number?

We have reported that female rats have more axons in the splenium of the corpus callosum than do male rats (12). To determine if the greater number of axons found in female rats might be reflected in a larger distribution of callosal projection neurons, horseradish peroxidase (HRP) was injected into the visual cortex of 55-65-day-old rats of both sexes that had been housed in a complex environment since weaning. The pattern of labeled neurons was examined in tangential sections in the cortex contralateral to the injection site, and three-dimensional reconstructions were quantified at the area 17/18a border and in area 18b. Male and female rats were found to have indistinguishable distributions of labeled callosal projection neurons. The present study failed to find an obvious difference in the distribution of projection neurons as the basis for the sex differences in axon number, but because of the limitations of tracing techniques, subtle differences cannot be excluded.