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BACKGROUND: A comprehensive screening at delivery revealed that roughly 14% of pregnant women who tested positive for COVID-19 did not exhibit any symptoms. The SARS-CoV-2 antigen swab test is frequently utilized as a diagnostic technique. Inadequate implementation of health protocol compliance can enhance the vulnerability of a community to the COVID-19 virus, according to previous findings. This suggests that these health protocol compliance and the vaccination program are important for preventing and controlling the spread of the virus. AIM: This study aims to determine the relationship of vaccination history and health protocol compliance with positive antigen swab results among pregnant women at the Community Health Center in Medan. METHOD(S): This is a cross-sectional and observational study that was conducted in February 2022 at the Community Health Center in Medan, North Sumatra, Indonesia. Two hundred pregnant women who met the inclusion and exclusion criteria make up the sample population. Antigen sampling for SARS-CoV-2 was performed in the Pramita laboratory. Following the collection and processing of sample and antigen swab data, IBM SPSS version was utilized to conduct statistical analysis. RESULT(S): The result showed that four of the pregnant women were infected with COVID-19, and they accounted for 2% of the sample population. The health protocol carried out by pregnant women was not significantly related to the swab results. Therefore, vaccination history had no significant association with COVID-19 symptoms, but people who received vaccines had more negative swab test results compared to those who did not, where three out of four positive samples were unvaccinated. CONCLUSION(S): Based on the results, only 2% of pregnant women were infected with COVID-19 at the Community Health Centre in Medan, because this study was carried out when COVID-19 cases had decreased. The statistical analysis results showed that the history of vaccination was not significantly related to SARS-CoV-2 antigen swab results. However, there was a clinical tendency that vaccines can reduce the number of positive cases, where three out of four positive samples were not vaccinated.Copyright © 2023 Sarma Nursani Lumbanraja, Reni Hayati, Khairani Sukatendel, Johny Marpaung, Muhammad Rusda, Edy Ardiansyah.
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Intro: It is hypothesized that metagenomics could contribute to the effective sentinel surveillance of emerging infections to identify plausible cause of respiratory symptoms in the population. Method(s): This study forms part of a longitudinal household cohort study involving the collection of respiratory symptoms and vaccination history in Hong Kong. As a pilot, selected households were provided with swab collection kit for collecting nasopharyngeal and throat samples when there was an influenza-like illness (ILI) during a 4-month presumptive period of the year's winter influenza season. Sequence-Independent Single Primer Amplification (SISPA) and nanopore metagenomic sequencing were performed. After basecalling, demultiplexing, and quality filtering, taxonomic classification was done. Unclassified and host reads were removed and only taxon with over 0.1% abundance were included in the analysis. Finding(s): Between December 2021 and April 2022, of 101 collection kits delivered, 36 (36%) participants returned the samples. Two (6%) had previous COVID-19 diagnosis and almost all (97%) received at least one dose of COVID-19 vaccination. Metagenomics sequencing was performed on 13 samples collected from participants when ILI was present. Of the 1,592,219 reads obtained, 5308 taxa were identified and 136 had over 0.1% abundance, including 128 bacteria, 6 fungi, and 1 virus, which was a bacteriophage. The five most abundant genera of bacteria included Neisseria (19%), Streptococcus (10%), Haemophilus (9%), Veillonella (3%), and Rothia (3%). Haemophilus parainfluenzae was the most abundant species with 97,542 (6%) reads, followed by Neisseria meningitides (5%). Other bacteria identified included Rothia mucilaginosa, Acinetobacter baumannii, Lautropia mirabilis, Veillonella atypica, Streptococcus salivarius, and Streptococcus pneumonia. Inter-participant abundance profile was significantly different (p<0.001). Conclusion(s): The absence of viral infections identified echoed the extremely low proportion (3/21986, or 0.01%) of respiratory specimens testing positive for influenza virus by the government laboratory during the same period. The metagenomic profile could be useful for identifying the likely ILI-causing pathogen.Copyright © 2023
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Intro: Uptake of SARS-CoV-2 rapid antigen tests (RATs) for self-testing has been high following authorisation by the Australian Therapeutic Goods Administration (TGA). However, there are no published Australian data assessing feasibility and compliance with home-based rapid antigen testing. The aim of this study was to determine the acceptability of daily rapid antigen self-testing. Method(s): We prospectively recruited a cohort of hospital employees and students from primary and secondary school to perform daily self-testing using RATs in the home over 14 consecutive days. Participants consenting to the study were supplied with 15 Roche SARS-CoV-2 Antigen Nasal Self Tests, 3 saliva swabs for self-collection for RT-PCR and were asked to record results and answer a daily survey using a smartphone application. Finding(s): 38% (26/68) of the cohort were compliant to 14 consecutive days of testing;this was significantly higher in students (71%) than hospital employees (28%). The median number of tests performed over 14 consecutive days was 11 and time to first missed test was a median 5.5 days. The most common reasons for missing days were "I forgot" (37.5%) and "too busy" (8.9%). Ease of self- nasal swabbing, self-nasal testing. performing the test and using the app were rated as comfortable/very comfortable in over 80% of the cohort. Discussion(s): Most study participants in this Australian cohort were compliant with frequent home-based RATs. By study end most participants (93.8%) found the testing process acceptable/very acceptable. There is need for further work on the cost-effectiveness and impact of self-tested RATs under a range of specific uses and conditions. Conclusion(s): This study provided valuable information on acceptability and feasibility of regular home-based testing which could be applied to other diseases. Ongoing community engagement with clear information on RATs including accuracy and use cases is important for decision-making and addressing concerns, particularly for linguistically diverse peoples.Copyright © 2023
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Background: The coronavirus disease 2019 (COVID-19) pandemic was a unique global challenge with a wide range of severity extending from an asymptomatic form to a serious intense respiratory syndrome. This study aimed to detect SARS-CoV-2 in the follicular and endocervical fluid of in vitro fertilization (IVF) candidate patients with a positive polymerase chain reaction (PCR) test for SARS-CoV-2. Method(s): All participants and their partners, who were a candidate to start assisted reproductive technology (ART) from April 2020 to October 2020, completed a triage questionnaire two weeks before starting the ART cycle. According to Avicenna center protocol, a diagnostic test for COVID-19 using real-time PCR of nasopharyngeal swabs was performed on all ART candidates, 48 hours before the day of the oocyte trigger. In the operating room, sterile swabs were used to provide cervicovaginal specimens to determine SARS-CoV-2 in cervicovaginal fluid. Moreover, the first aspirated follicular fluid was referred to the lab to assess the presence of SARS-CoV-2. Result(s): A positive PCR test for SARS-CoV-2 was verified in 32 participants. In this study, virus particles were not detected in the follicular and endocervical fluid of the women with positive PCR tests. Conclusion(s): We are still at the beginning of the road and need reliable data on the safety of ART at the time of the pandemic. The risk of infection during all processes of ART including oocyte retrieval needs attention. The fluid from mature follicles is a potential site to be infected and the human cumulus cells could not be a deterrent factor to the entrance of the virus in the oocyte. This process may lead to gametes infection. We did not detect virus RNA in the follicular and endocervical fluid of the patients with a positive PCR test. Although, more studies with a larger sample size are mandatory in this field.
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Introduction: In the current study we aimed to investigate the effects of Convalescent Plasma (CP) therapy on the health outcomes of patients aged 60 and older who have mild symptoms due to Covid-19 and do not need hospitalization. Materials and methods: A total of 84 patients detected to have acute respiratory syndrome coronavirus 2 by swab polymerase chain reaction who applied a single dose of 200 mL CP administered within 7 days after the onset of any Covid-19 symptoms constituted the CP group. Health outcomes including mortality within 15 days and 30 days, hospitalization into Covid-19 service or intensive care unit (ICU) within 30 days were compared with a control group of 3197 patients who did not applied CP. Results: In the CP group (48 female, 36 male) the mean age of the patients was 68.1 ± 7.1 (min= 60, max= 85). The groups were similar in terms of age and gender (p=0.454, p=0.373, respectively). The median time from onset of any Covid-19 symptoms to CP administration was 4.15 days (min=2, max=7 days). None of the CP group patient died within 15 days, while mortality within 30 days was 2.4% (2 patients, days 25 and 27). Hospitalization into Covid-19 service and ICU was 20.2% (17 patients) and 4.8% (4 patients), respectively. There was no significant differences in terms of health outcomes within groups albeit CP group has lower mortality and hospitalization rates (p=0.052, p=0.11, p=0.562, p=0.289, respectively). Conclusion: CP therapy administered in an early course remains an option for clinicians in the treatment of Covid-19 older adult patients who have mild disease on the other hand protecting them out of hospitalization.
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Aim: The Coronavirus disease (COVID-19) pandemic has strained healthcare systems worldwide. Some institutions have implemented additional precautionary measures such as pre-procedural swabbing (PPS) to reduce transmission in patients and healthcare workers. We evaluate our experience with universal pre-procedural screening for COVID-19 in low-risk pediatric patients. Method(s): We performed a retrospective review of patients aged 18 years and below who underwent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time reverse transcription-polymerase chain reaction (rRT-PCR) assay swabs in our center over two waves (1st May 2020 to 31st July 2020 and 1st April 2021 to 30th June 2021). We included patients who underwent rRT-PCR for SARS-CoV-2 prior to any procedures requiring general anesthesia and were deemed low risk for COVID-19 according to our institutional screening criteria. All study patients were followed up for 14 days post-procedure. Result(s): Of 2065 swabs done for patients aged 18 years and below during the study period, 645 (31.2%) were pre-procedural swabs. Patients were aged 4.2 years (median, interquartile range: 1.6 years-9.8 years). Two patients (0.3%) tested positive for COVID-19 by PPS, detected during Period 2 - both had risk criteria which were overlooked by healthcare workers. Within 14 days post-procedure, 10 patients had unscheduled readmissions and 15 required repeat rRT-PCR, all of which were negative. Conclusion(s): In patients deemed low risk for COVID-19 infection according to our screening criteria, routine pre-procedural swabbing returns a low positive rate. Our findings can guide screening protocols at institutions that provide surgical services during the COVID-19 pandemic. Copyright © The Author(s) 2022.
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Background. Characterizing SARS-CoV-2 outbreaks on university campuses is critical for informed public health measures and understanding transmission dynamics. Figure 1. Dropbox and Kiosk Samples Collected September 10, 2021 to April 23, 2022. Methods. Faculty, staff, and students at a major public university in Seattle, WA, USA were enrolled in a COVID-19 testing study. Individuals could test using observed self-swabs at on-campus kiosks or unobserved self-swabs using a kit and returning it to a dropbox on campus. Sample collection volume for observed self-swabs was limited by staffing and space. All samples were returned to the laboratory and tested for SARS-CoV-2 by qRT-PCR. Results. From September 10, 2021 to April 23, 2022, 38,400 individuals were enrolled in the study. Of these individuals, 5,089 used dropboxes only, 14,421 used kiosks only, and 5,820 used both. A total of 21,653 dropbox swabs and 75,493 observed self-swabs were collected. Median age was similar between individuals using dropboxes and observed self-swabs (20 vs. 22 years). A greater proportion of dropbox users were students compared to faculty and staff (students made up 83% of dropbox only population, 75% of kiosk only, and 86% of both, chi2 p-value< 0.0001). Symptom data was reported for 65,349 swabs. Dropbox users were less likely to have symptoms compared to observed self-swab users (24% of swabs vs. 54%, chi2 p-value< 0.0001). SARS-CoV-2 positivity was slightly lower for dropboxes compared to kiosks (4% vs. 5%;p=0.001). Dropboxes were highly utilized during periods of increased testing demand, including after academic breaks and variant emergence (Figure 1). Of the total tests distributed for use, a greater proportion of dropbox kits were unable to be resulted (6%) compared to observed self-swab kits (0.02%). Conclusion. Dropboxes provided a flexible, high-volume collection method at times of increased testing demand. Individuals who used dropboxes were less likely to report symptoms and slightly less likely to test positive, suggesting a role for dropbox utilization in high-risk asymptomatic individuals during periods of high community transmission on a university campus.
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Introduction/ Background: The COVID pandemic continues to devastate the world population since January 2020. RDTs are a key tool for COVID-19 response. We evaluated the performance of a commercially available SARSCoV- 2 antigen RDT for the screening of suspect cases of COVID-19 in two West African countries, Burkina Faso and The Gambia. Methods: The study was implemented between September 2020 and September 2021 in Burkina Faso (Bobo- Dioulasso) and The Gambia (West Coast division). Patients presenting with COVID-19 symptoms (WHO case definition, August 2020) were systematically screened for COVID-19 by RDT and diagnostic PCR and enrolled in a 6-month prospective follow-up study. Oro- and nasopharyngeal (OP/NP) swabs were collected from suspected case and the RDT performed within <8h of collection. The sensitivity and specificity of the RDT- with and without universal transport medium (UTM), were analyzed against COVID-19 diagnostic PCR and the positiveand negative predictive values were also estimated. Results: Between September 2020 and March 2021, a total of 478 patients were screened with 263 from Burkina Faso and 215 from The Gambia. From these, 118 COVID-19 positive by PCR were enrolled in the cohort (Burkina Faso: 92;The Gambia: 26). Specificity was 100% for samples from UTM, but sensitivity was 24%. When stratifying the analysis to patients with Ct values ≤ 30 and ≤ 25, the sensitivity was 44% and 65%, respectively. Sensitivity on samples with buffer only was 71% and specificity 100%. On samples with buffer only and Ct values ≤ 34, RDT sensitivity and specificity were 100%. Impact: The COVID-19 Ag Respi Strip represents a rapid, reliable, and affordable triage tool for clinically suspect COVID-19 cases in Africa allowing for the timely isolation and management of COVID-19 patients before PCR confirmation. Conclusion: The RDT performs much better as a point of care test without UTM using the direct swab method. A newer version of the RD (COVID-19 Ag K-Set) with improved sensitivity could be assessed in the future.
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Introduction/ Background: The COVID-19 pandemic has impacted public health laboratories with shortages and an increase in the cost of RNA extraction kits. The aim of this project was to develop and validate an RNA extraction kit for use in the diagnosis of SARS-CoV-2 infection to improve COVID-19 testing and surveillance in Nigeria. Methods: The developed kit is based on the spin-column method and named the NIMR Biotech Total RNA Extraction Kit. The kit is intended for RNA extraction from different specimens, including blood, animal tissues, cell lines, bacteria, viruses, and swabs. Analytical validation of the kit for COVID-19 diagnosis was done at six different COVID-19 testing sites on 20 different nasopharyngeal and oropharyngeal specimens, with the results compared using NIMR Biotech. Kit and another commercial RNA extraction kit (spin-column and magnetic-bead based). Results: Validation results showed an average correlation of 93% when compared to other spin-column based kits. When compared with the Qiagen RNA extraction kit, the performance indices of the kit were sensitivity of 94%, specificity of 100%, positive predictive value of 100%, negative predictive values of 94.7%, and accuracy of 95%. The NIMR Biotech total RNA kit showed a good correlation with the DaanGene and the Geneaid extraction kits. In both instances, there was only one disparity between the NIMR Biotech kit and these two kits. Impact: The developed RNA extraction kit from this study provides a suitable and cheaper alternative to high-end, commercially available RNA extraction kits. The adoption of this kit in all COVID-19 testing laboratories in Nigeria, and Africa, will help scale-up COVID-19 testing in Africa. Conclusion: NIMR Biotech's Total RNA extraction kit is sufficiently robust for the extraction of viral and human RNA from oropharyngeal and nasopharyngeal samples. The kit correlates better with the spin-columnbased RNA extraction method when compared to the magnetic-bead-based method and will be useful for monitoring SARS-CoV-2 infection and other RNA viruses.
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Background and objectives: Healthcare workers (HCWs) are at significant risk of exposure to COVID-19 virus during this pandemic period. As part of healthcare protocol and staff risk assessment in Brunei Darussalam, all emergency department (ED) staff underwent periodical COVID-19 surveillance nasopharyngeal (NP) swabbing. This study was performed to evaluate the experience and comfort level of HCWs toward COVID-19 NP swab. Methodology: All HCWs (n=151) based in the ED, Raja Isteri Pengiran Anak Saleha (RIPAS) Hospital, Brunei Darussalam, underwent COVID-19 surveillance NP swabbing followed by voluntary basis of completing an anonymous perception questionnaire form. The perception scale used in this study was adopted from numeric pain scale (0-10) with additional input of comfort level description. Data were analyzed using Excel software for demography profile, median perception scale, perception of comfort level, and correlation between the variables. Result: The HCWs (n=138) who completed the form consisted of nurses (52%), doctors (27%), support staffs (14%), and cleaners (7%);56% were male gender;61% were in the 20-to 40-year-old age group, and only 11% were in the >51-year-old age group. For the majority of the participants, this was their first time undergoing an NP swab (86%), and those who had previous swab experience accounted for 14%. The overall median perception scale was 3 (scale 0-10). In all, 26% reported that they were comfortable with the procedure, 29% were mild uncomfortable, 33% moderate uncomfortable, 10% severe uncomfortable, and 2% reported this was their worst ever experience. Some participants reported tearing eyes (n=4), runny nose (n=2), pain (n=3), and mild bleeding (n=1) as side effects. There was no correlation between gender, age, profession, or previous swab experience and the perception scale of NP swab. Conclusion: NP swab test procedure is well tolerated by the majority of HCWs. The perception scale could be affected by type of specimen, type and size of swab kit, and sampling procedure technique. Further comparison study is needed to determine the factors that may contributes to the level of comfort perception.
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Using retrospective data from 6 breedto- wean herds over 4 years, porcine reproductive and respiratory syndrome virus (PRRSV) statuses were assigned by week according to the 2021 American Association of Swine Veterinarians PRRSV classification. Productivity changes were characterized as herds transitioned through status categories. Overall, productivity improved as farm status improved.
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Background and Aim: The diagnosis of Covid 19 is made by the detection of viral RNA by PCR on nasopharyngeal swabs. In some patients the test is falsely negative, while other biological samples are positive. The aim of the study is to identify characteristics and prognostic factors for swab negativity in COVID-19 patients with BA-confirmed disease. Materials and Methods: Multicentre retrospective case-control study of patients admitted for COVID-19 between March and November 2020 in two internal medicine units of the AOU Careggi and in the Internal Medicine of the Hospital of Varese. Enrolled patients aged ≥18 years hospitalized for Covid with viral RNA isolation on biological specimen, considering as cases the patients negative to swab but positive to BA. For each case, four swab-positive controls at admission. Results: Included 95 patients, 19 cases and 76 controls. Advanced mean age, male predominance. The mean time between symptoms onset and swab was 2.65±1.9 days in cases, with a statistically significant difference compared to controls (5.53±3.0 days). Longer mean length of stay and more frequent adverse outcome in patients with negative swab than in controls. Conclusions: Swabbing within a short time of symptoms onset is a predictor for false negative. Patients with repeated negative swabs have a worse clinical picture with longer hospital stay, greater need for non-invasive ventilation and higher frequency of adverse outcome.
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Introduction: Contact tracing is an integral component of the overall public health strategy for controlling the outbreak of infectious diseases such as COVID-19. In addition to the conventional contact tracing, Qatar has implemented Ehteraz, a proximity-tracing mobile phone App using global positioning system and Bluetooth technologies. In this paper, we aim to evaluate the accuracy of Ehteraz as a contact tracing App based on the WHO contact tracing criteria and compare its effectiveness to the traditional human led case investigation. Methods: A cross-sectional study was conducted using two databases, including Ehteraz proximity data and swab collection and case investigations reports for the same period. Results: 46.9% of contacts identified by the Ehteraz app did not meet WHO duration and distance criteria. Among the 5650 contacts flagged by Ehteraz during the period, 4973 (88.0%) of contacts did not share any known relation with the index case they are linked to. Conclusion: The study highlighted the inaccuracy of the Ehteraz tool as its technology enables signals passing through walls, so people in different rooms could be unnecessarily flagged as having had contact. Big segments of the population (eg, Children) do not necessarily use smartphones and are not, therefore, flagged by Ehteraz digital contact tracing App. Similarly, Ehteraz rarely flags close contacts identified by human investigation as Bluetooth is usually turned off in a household or at a workplace. These findings highlight that digital contact tracing would be an efficient public health strategy when integrated to and complementing human investigation.
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Introduction: Until sufficient herd immunity is generated in the population, contact tracing, testing, and quarantining should be continued as key interventions in breaking the chain of transmission of Coronavirus Disease 2019 (COVID-19). Aim: To identify appropriate strategies for testing of the travellers, who were coming from high-risk areas by analysing patterns of testing among COVID-19 positive returnees. Materials and Methods: A retrospective cohort study was conducted in Community Medicine Department, Government Medical College, Palakkad, Kerala, India, during 25th Sepetember 2020 to 15th October 2020, using the secondary data available from the database of COVID-19 Contact Tracing Cell (CCTC) to determine the testing pattern among the laboratory confirmed cases of COVID-19 positive returnees in Palakkad district. Only COVID-19 positive travellers returning to Palakkad district in May 2020 were included in the study, thus the sample size obtained was 122. Data regarding age, gender, co-morbidity, presence of symptom and time of its onset, time of swab collection and reporting of results which were collected by CCTC were analysed. The Statistical Package for the Social Sciences (SPSS) version 20.0 was used to analyse the data collected by CCTC. Quantitative variables were summarised as means with standard deviations and median with interquartile ranges. Qualitative variables were summarised as percentages. Results: Between arrival and swab collection there was mean duration of 6.9±3.8 days and a median duration of 7 days among the total positive returnees. Among the asymptomatic cases the mean duration was found to be 7.4±3.6 days for the same. Between day 10 and day 12 of quarantine 79%-91% of the cases have given swabs for Reverse Transcription Polymerase Chain Reaction (RT-PCR) testing. This had yielded 90% positive reporting within 14 days of quarantining. Total 10 cases were diagnosed after 14 days of quarantine due to late swab collection while in quarantine. Mean duration between symptom onset and swab collection among 22 symptomatic cases was 1.9±1.6 days (median= 2 days). Conclusion: Testing of asymptomatic returnees from high risk area may be initiated (swab collection) by day 10 as swabs collected around 10th day of quarantine capture maximum number of positive cases. A delayed initiation for testing may prolong the time taken for diagnosis. Those who have tested negative during 14 days of quarantine should self-monitor for symptoms and reduce contact with high risk persons for one more week.
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Objective : In this study, we have assessed the hematological characteristics of the patients. This study aimed to evaluate the accuracy of laboratory parameters in predicting cases with positive RT-PCR for COVID19. Methodology: This was a cross-sectional study that included 32 RTPCR +ve and 64 RTPCR -ve cases over a period of 5 weeks. The blood samples were collected from symptomatic patients who presented to cough OPD. On the day of swab sampling, blood sampling was done for each participant. All tests were performed in an appropriate autoanalyzer after complying with internal quality control. Results: The mean CT value of RT-PCR test was found to be 22.7, while mean PCT value was 0.3 ng/ml. The mean ferritin value came out to be 133.5 ng/ml and mean D-dimer values calculated to be just 1.3 mg/L. The mean LDH and CRP levels were 340.4 IU/L and 12.6 mg/L respectively. The sensitivity and specificity for procalcitonin analysis among these patients were 97% with CI (93.8-100) followed by serum ferritin with 82%, CI (70-94) and CRP levels were having just 77.3%, CI (61.2-93.4). Conclusion: In the current study, the AUC of procalcitonin and serum ferritin were above 0.80;thus, they are effective and have very good predictive value for predicting COVID-19. It seems that these blood laboratory parameters could be used in screening cases with positive RT-PCR for COVID-19. However, serum LDH, D Dimer, and vitamin D levels or liver function tests, renal function tests remain insignificantly linked with covid positivity rate in this study.
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Background. SARS-CoV-2 variants of concern (VOC) have challenged real-time reverse transcriptase polymerase chain reaction (RT-PCR) methods for the diagnosis of COVID-19. Methods. The CDC 2019-Novel Coronavirus real-time RT-PCR panel was modified to create a single-plex extraction-free proxy RT-PCR assay, VOCFast™. This assay uses the nucleocapsid N1 as well as novel primer/probe pairs to target VOC mutations in the Orf1a and spike (S) genes. For analytical validation of VOCFast, synthetic controls for the Wuhan, alpha/B.1.1.7, beta/B.1.351, and gamma/P.1 strains were tested at various concentrations. Clinical validation was performed using patient anterior nares swab and saliva specimens collected in the Denver, CO area between Nov 2020 and Feb 2021 or in March 2021. Orthogonal next-generation sequencing (NGS) was also performed. Results. Similar N1 quantification cycle (Cq) values corresponding to viral load were observed for all strains, suggesting that VOC mutations do not affect performance of the N1 primer/probe. Orf1a-mut and S1-mut primer/probes generated a stable high Cq value for the Wuhan strain. Conversely, Orf1a-mut Cq values were inversely correlated with viral load for all VOC. The S1-mut Cq was inversely correlated with viral load of the alpha strain, but did not reliably amplify beta/gamma VOC. The limit of detection was 8 copies/uL. The first set of COVID-19 patient specimens revealed no amplification using Orf1amut whereas 53% of specimens collected in Mar 2021 demonstrated amplification by Orf-1a. Orthogonal testing by the SARS-CoV-2 NGS Assay and COVID-DX software demonstrated that 12/12 alpha strains, 2/2 beta/gamma strains, and 33/33 Wuhan strains were correctly identified by VOCFast. Conclusion. The combination of the N1, Orf1a-mut, and S1-mut primers/probes in VOCFast can distinguish the Wuhan, alpha, and beta/gamma strains and it consistent with NGS results. Testing of clinical samples revealed that VOC emerged in Denver, CO in March 2021. Future work to discriminate beta, gamma, and emerging VOC is ongoing. In summary, VOCFast is an extraction-free RT-PCR assay for nasal swab and saliva specimens that can identify VOC with a turnaround time suitable for clinical testing.
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Background. The risk factors of venous thromboembolism (VTE) in COVID-19 warrant further study. We leveraged a cohort in the Military Health System (MHS) to identify clinical and virological predictors of incident deep venous thrombosis (DVT), pulmonary embolism (PE), and other VTE within 90-days after COVID-19 onset. Methods. PCR or serologically-confirmed SARS-CoV-2 infected MHS beneficiaries were enrolled via nine military treatment facilities (MTF) through April 2021. Case characteristics were derived from interview and review of the electronic medical record (EMR) through one-year follow-up in outpatients and inpatients. qPCR was performed on upper respiratory swab specimens collected post-enrollment to estimate SARS-CoV-2 viral load. The frequency of incident DVT, PE, or other VTE by 90-days post-COVID-19 onset were ascertained by ICD-10 code. Correlates of 90-day VTE were determined through multivariate logistic regression, including age and sampling-time-adjusted log10-SARS-CoV-2 GE/reaction as a priori predictors in addition to other demographic and clinical covariates which were selected through stepwise regression. Results. 1473 participants with SARS-CoV-2 infection were enrolled through April 2021. 21% of study participants were inpatients;the mean age was 41 years (SD = 17.0 years). The median Charlson Comorbidity Index score was 0 (IQR = 0 -1, range = 0 - 13). 27 (1.8%) had a prior history of VTE. Mean maximum viral load observed was 1.65 x 107 genome equivalents/reaction. 36 (2.4%) of all SARS-CoV-2 cases (including inpatients and outpatients), 29 (9.5%) of COVID-19 inpatients, and 7 (0.6%) of outpatients received an ICD-10 diagnosis of any VTE within 90 days after COVID-19 onset. Logistic regression identified hospitalization (aOR = 11.1, p = 0.003) and prior VTE (aOR = 6.2 , p = 0.009) as independent predictors of VTE within 90 days of symptom onset. Neither age (aOR = 1.0, p = 0.50), other demographic covariates, other comorbidities, nor SARS-CoV-2 viral load (aOR = 1.1, p = 0.60) were associated with 90-day VTE. Conclusion. VTE was relatively frequent in this MHS cohort. SARS-CoV-2 viral load did not increase the odds of 90-day VTE. Rather, being hospitalized for SARS-CoV-2 and prior VTE history remained the strongest predictors of this complication.
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Background. The COVID-19 pandemic has disproportionately affected nursing home (NH) patients, accounting for 5% of all cases and 32% of all COVID-19 deaths nationwide. Little is known about the frequency and persistence of SARSCoV-2 environmental contamination in NHs. We characterize SARS-CoV-2 contamination in the rooms of COVID-19 patients and common areas in and around COVID-19 units. Methods. A prospective cohort study was conducted at four NHs in Michigan between October 2020 and January 2021. Clinical research personnel obtained swab specimens from high-touch room surfaces of COVID-19 infected patients, up to three times per patient. Weekly swab specimens from six high-touch surfaces in common areas were also obtained. Demographic and clinical data were collected from patient clinical records. Our primary outcome of interest was the probability of SARS-CoV-2 detection from specific environmental surfaces in COVID-19 patient rooms. Results. One hundred four patients with COVID-19 were enrolled and followed for 241 visits. Patient characteristics included: 61.5% over the age of 80;67.3% female;89.4% non-Hispanic white;50.1% short-stay. The study population had significant disabilities in activities of daily living (ADL;81.7% dependent in four or more ADLs) and comorbidities including dementia (55.8%), diabetes (40.4%) and heart failure (32.7) (Table 1). Over the 3-month study period, 2087 swab specimens were collected (1896 COVID-19 patient room surfaces, 191 common area swabs). Figure 1 shows contamination rates at sites proximate and distant to the patient bed. SARS-CoV-2 positivity was 28.4% (538/1896 swabs) on patient room surfaces and 3.7% (7/191 swabs) on common area surfaces. Over the course of follow-up, 89.4% (93/104) of patients had SARS-CoV-2 contamination in their room at least once (Figure 2). Environmental contamination detected on enrollment correlated with contamination of the same site during follow-up. Functional independence increased the odds of proximate contamination. Conclusion. We conclude that environmental contamination of surfaces in the rooms of COVID-19 patients is nearly universal and persistent. Patients with greater independence are more likely than fully dependent patients to contaminate their immediate environment.