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1.
HERD ; : 19375867221128916, 2022 Sep 27.
Article in English | MEDLINE | ID: covidwho-2053791

ABSTRACT

OBJECTIVES: This study aimed to develop a better understanding of the unique needs of patients with highly infectious diseases and their perceptions of being placed in isolation. We explore the subjective experiences of patients treated for Ebola in a biocontainment unit (BCU) and the healthcare personnel who cared for them. BACKGROUND: The 2014 Ebola outbreak and the COVID-19 pandemic have brought to focus some major challenges of caring for patients with serious infectious diseases. Previous studies on BCU design have looked at ways to prevent self- and cross-contamination, but very few have examined how the built environment can support an improved patient experience. METHOD: A qualitative study was conducted with four patients treated for Ebola and two critical care nurses who provided direct care to them at a single BCU in the U.S. Data were collected through in-depth semi-structured interviews to capture the actual patients' perception and experience of isolation. The interviews were analyzed using the thematic analysis approach. RESULTS: The Ebola patients placed in source isolation perceived the BCU as an artificial environment where they lacked control, agency, autonomy, and independence. The physical separation from other patients, visitor restrictions, and staff wearing PPE contributed to feelings of social and emotional isolation, and loneliness. CONCLUSIONS: The isolation can take a toll on physiological and psychological well-being. A thoughtful design of isolation units may improve patients' experience by supporting human and social interactions, empowering patients through space flexibility and personalization of space, and supporting a more holistic approach to isolation care.

2.
JAMA ; 328(10): 935-940, 2022 09 13.
Article in English | MEDLINE | ID: covidwho-2047345

ABSTRACT

Importance: Despite the expansion of SARS-CoV-2 testing, available tests have not received Emergency Use Authorization for performance with self-collected anterior nares (nasal) swabs from children younger than 14 years because the effect of pediatric self-swabbing on SARS-CoV-2 test sensitivity is unknown. Objective: To characterize the ability of school-aged children to self-collect nasal swabs for SARS-CoV-2 testing compared with collection by health care workers. Design, Setting, and Participants: Cross-sectional study of 197 symptomatic children and adolescents aged 4 to 14 years old. Individuals were recruited based on results of testing in the Children's Healthcare of Atlanta system from July to August 2021. Exposures: Children and adolescents were given instructional material consisting of a short instructional video and a handout with written and visual steps for self-swab collection. Participants first provided a self-collected nasal swab. Health care workers then collected a second specimen. Main Outcomes and Measures: The primary outcome was SARS-CoV-2 detection and relative quantitation by cycle threshold (Ct) in self- vs health care worker-collected nasal swabs when tested with a real-time reverse transcriptase-polymerase chain reaction test with Emergency Use Authorization. Results: Among the study participants, 108 of 194 (55.7%) were male and the median age was 9 years (IQR, 6-11). Of the 196 participants, 87 (44.4%) tested positive for SARS-CoV-2 and 105 (53.6%) tested negative by both self- and health care worker-collected swabs. Two children tested positive by self- or health care worker-collected swab alone; 1 child had an invalid health care worker swab. Compared with health care worker-collected swabs, self-collected swabs had 97.8% (95% CI, 94.7%-100.0%) and 98.1% (95% CI, 95.6%-100.0%) positive and negative percent agreement, respectively, and SARS-CoV-2 Ct values did not differ significantly between groups (mean [SD] Ct, self-swab: 26.7 [5.4] vs health care worker swab: 26.3 [6.0]; P = .65). Conclusions and Relevance: After hearing and seeing simple instructional materials, children and adolescents aged 4 to 14 years self-collected nasal swabs that closely agreed on SARS-CoV-2 detection with swabs collected by health care workers.


Subject(s)
COVID-19 , SARS-CoV-2 , Adolescent , COVID-19/diagnosis , COVID-19 Testing , Child , Child, Preschool , Cross-Sectional Studies , Female , Health Personnel , Humans , Male , Specimen Handling/methods
3.
Virus Evol ; 8(1): veac011, 2022.
Article in English | MEDLINE | ID: covidwho-1816262

ABSTRACT

In early 2020, as diagnostic and surveillance responses for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ramped up, attention focused primarily on returning international travelers. Here, we build on existing studies characterizing early patterns of SARS-CoV-2 spread within the USA by analyzing detailed clinical, molecular, and viral genomic data from the state of Georgia through March 2020. We find evidence for multiple early introductions into Georgia, despite relatively sparse sampling. Most sampled sequences likely stemmed from a single or small number of introductions from Asia three weeks prior to the state's first detected infection. Our analysis of sequences from domestic travelers demonstrates widespread circulation of closely related viruses in multiple US states by the end of March 2020. Our findings indicate that the exclusive focus on identifying SARS-CoV-2 in returning international travelers early in the pandemic may have led to a failure to recognize locally circulating infections for several weeks and point toward a critical need for implementing rapid, broadly targeted surveillance efforts for future pandemics.

4.
Sci Total Environ ; 821: 153291, 2022 May 15.
Article in English | MEDLINE | ID: covidwho-1649057

ABSTRACT

As COVID-19 continues to spread globally, monitoring the disease at different scales is critical to support public health decision making. Surveillance for SARS-CoV-2 RNA in wastewater can supplement surveillance based on diagnostic testing. In this paper, we report the results of wastewater-based COVID-19 surveillance on Emory University campus that included routine sampling of sewage from a hospital building, an isolation/quarantine building, and 21 student residence halls between July 13th, 2020 and March 14th, 2021. We examined the sensitivity of wastewater surveillance for detecting COVID-19 cases at building level and the relation between Ct values from RT-qPCR results of wastewater samples and the number of COVID-19 patients residing in the building. Our results show that weekly wastewater surveillance using Moore swab samples was not sensitive enough (6 of 63 times) to reliably detect one or two sporadic cases in a residence building. The Ct values of the wastewater samples over time from the same sampling location reflected the temporal trend in the number of COVID-19 patients in the isolation/quarantine building and hospital (Pearson's r < -0.8), but there is too much uncertainty to directly estimate the number of COVID-19 cases using Ct values. After students returned for the spring 2021 semester, SARS-CoV-2 RNA was detected in the wastewater samples from most of the student residence hall monitoring sites one to two weeks before COVID-19 cases surged on campus. This finding suggests that wastewater-based surveillance can be used to provide early warning of COVID-19 outbreaks at institutions.


Subject(s)
COVID-19 , Waste Water , COVID-19/epidemiology , Humans , RNA, Viral , SARS-CoV-2 , Universities , Wastewater-Based Epidemiological Monitoring
5.
N Engl J Med ; 386(3): 220-229, 2022 01 20.
Article in English | MEDLINE | ID: covidwho-1632249

ABSTRACT

BACKGROUND: Current therapies for recurrent Clostridioides difficile infection do not address the disrupted microbiome, which supports C. difficile spore germination into toxin-producing bacteria. SER-109 is an investigational microbiome therapeutic composed of purified Firmicutes spores for the treatment of recurrent C. difficile infection. METHODS: We conducted a phase 3, double-blind, randomized, placebo-controlled trial in which patients who had had three or more episodes of C. difficile infection (inclusive of the qualifying acute episode) received SER-109 or placebo (four capsules daily for 3 days) after standard-of-care antibiotic treatment. The primary efficacy objective was to show superiority of SER-109 as compared with placebo in reducing the risk of C. difficile infection recurrence up to 8 weeks after treatment. Diagnosis by toxin testing was performed at trial entry, and randomization was stratified according to age and antibiotic agent received. Analyses of safety, microbiome engraftment, and metabolites were also performed. RESULTS: Among the 281 patients screened, 182 were enrolled. The percentage of patients with recurrence of C. difficile infection was 12% in the SER-109 group and 40% in the placebo group (relative risk, 0.32; 95% confidence interval [CI], 0.18 to 0.58; P<0.001 for a relative risk of <1.0; P<0.001 for a relative risk of <0.833). SER-109 led to less frequent recurrence than placebo in analyses stratified according to age stratum (relative risk, 0.24 [95% CI, 0.07 to 0.78] for patients <65 years of age and 0.36 [95% CI, 0.18 to 0.72] for those ≥65 years) and antibiotic received (relative risk, 0.41 [95% CI, 0.22 to 0.79] with vancomycin and 0.09 [95% CI, 0.01 to 0.63] with fidaxomicin). Most adverse events were mild to moderate and were gastrointestinal in nature, with similar numbers in the two groups. SER-109 dose species were detected as early as week 1 and were associated with bile-acid profiles that are known to inhibit C. difficile spore germination. CONCLUSIONS: In patients with symptom resolution of C. difficile infection after treatment with standard-of-care antibiotics, oral administration of SER-109 was superior to placebo in reducing the risk of recurrent infection. The observed safety profile of SER-109 was similar to that of placebo. (Funded by Seres Therapeutics; ECOSPOR III ClinicalTrials.gov number, NCT03183128.).


Subject(s)
Clostridioides difficile , Clostridium Infections/therapy , Firmicutes , Aged , Anti-Bacterial Agents/adverse effects , Double-Blind Method , Feces/microbiology , Female , Gastrointestinal Tract/microbiology , Humans , Intention to Treat Analysis , Male , Microbiota/drug effects , Middle Aged , Recurrence , Secondary Prevention , Spores, Bacterial
7.
Open forum infectious diseases ; 8(Suppl 1):S89-S89, 2021.
Article in English | EuropePMC | ID: covidwho-1564872

ABSTRACT

Background Detection and surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants is of great public health importance. Broadly accessible and inexpensive assays are needed to enhance variant surveillance and detection globally. We developed and validated a single-reaction multiplex real-time RT-PCR (the Spike SNP assay) to detect specific mutations associated with variants of concern (VOC). Methods A single primer pair was designed to amplify a 348 bp region of spike. Probes were initially designed with locked nucleic acids (LNAs) to increase probe melting temperature, shorten probe length, and specifically detect 417K, E484K, and N501Y (Figure). The assay was optimized and evaluated using characterized variant sample pools. Clinical evaluation was performed on a convenience set of residual nasopharyngeal swabs, and variant calls were confirmed by SARS-CoV-2 genomic sequencing in a subset of samples. Following the initial evaluation, unmodified probes (without LNAs) were designed to detect L452R, L452Q, and E484Q. Figure. Spike SNP distinguishes mutations occurring in different lineages (A-C). Representative results of variant detection a single Spike SNP run are shown for mutations in the codons for 4177K (A) and mutations that encode 484K (B) and 501Y (C). Curves show dilutions of the following variants: blue, BEI 52286 (wild type);pink B.1.1.7;purple, B1.525;and green, P.1. Variant pools were used for B.1.17, B.1.525, and P.1 strains. Curves are displayed for a given dilution in each channel and result interpretation is shown (D). Results The lower limit of 95% detection was 2.46 to 2.48 log10 GE/mL for the three targets (~1-2 GE/reaction). Among 253 nasopharyngeal swabs with detectable SARS-CoV-2 RNA, the Spike SNP assay was positive in 238 (94.1%), including all samples with Ct values < 30 (220/220) for the N2 target and 18/33 samples with N2 Ct values ≥ 30. Results were confirmed by SARS-CoV-2 genomic sequencing in 50/50 samples (100%). Subsequent addition of the 452R probe did not affect performance for the original targets, and probes for 452Q and 484Q performed similarly to LNA-modified probes. Conclusion The Spike SNP assay provides fast, inexpensive and sensitive detection of specific mutations associated with SARS-CoV-2 VOCs, and the assay can be quickly modified to detect new mutations in the receptor binding domain. Similar analytical performance of LNA-modified and unmodified probes presents options for future assay customization that balance the shorter probe length (LNAs) and increased accessibility (unmodified). The Spike SNP assay, if implemented across laboratories offering SARS-CoV-2 testing, could greatly increase capacity for variant detection and surveillance globally. Disclosures Colleen S. Kraft, MD, MSc, Rebiotix (Individual(s) Involved: Self): Advisor or Review Panel member

8.
Viruses ; 13(12)2021 11 23.
Article in English | MEDLINE | ID: covidwho-1542793

ABSTRACT

Evidence varies as to how far aerosols spread from individuals infected with SARS-CoV-2 in hospital rooms. We investigated the presence of aerosols containing SARS-CoV-2 inside of dedicated COVID-19 patient rooms. Three National Institute for Occupational Safety and Health BC 251 two-stage cyclone samplers were set up in each patient room for a six-hour sampling period. Samplers were place on tripods, which each held two samplers at various heights above the floor. Extracted samples underwent reverse transcription polymerase chain reaction for selected gene regions of the SARS-CoV-2 virus nucleocapsid. Patient medical data were compared between participants in rooms where virus-containing aerosols were detected and those where they were not. Of 576 aerosols samples collected from 19 different rooms across 32 participants, 3% (19) were positive for SARS-CoV-2, the majority from near the head and foot of the bed. Seven of the positive samples were collected inside a single patient room. No significant differences in participant clinical characteristics were found between patients in rooms with positive and negative aerosol samples. SARS-CoV-2 viral aerosols were detected from the patient rooms of nine participants (28%). These findings provide reassurance that personal protective equipment that was recommended for this virus is appropriate given its spread in hospital rooms.


Subject(s)
COVID-19/virology , Patients' Rooms , SARS-CoV-2/isolation & purification , Adult , Aged , Aged, 80 and over , COVID-19/diagnosis , Coronavirus Nucleocapsid Proteins/genetics , Hospitals , Humans , Middle Aged , Patients' Rooms/statistics & numerical data , Phosphoproteins/genetics , RNA, Viral/genetics , SARS-CoV-2/genetics
9.
J Clin Microbiol ; 59(12): e0144621, 2021 11 18.
Article in English | MEDLINE | ID: covidwho-1522905

ABSTRACT

To provide an accessible and inexpensive method to surveil for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutations, we developed a multiplex real-time reverse transcription-PCR (rRT-PCR) assay, the Spike single-nucleotide polymorphism (SNP) assay, to detect specific mutations in the spike receptor binding domain. A single primer pair was designed to amplify a 348-bp region of spike, and probes were initially designed to detect K417, E484K, and N501Y. The assay was evaluated using characterized variant sample pools and residual nasopharyngeal samples. Variant calls were confirmed by SARS-CoV-2 genome sequencing in a subset of samples. Subsequently, a fourth probe was designed to detect L452R. The lower limit of 95% detection was 2.46 to 2.48 log10 genome equivalents (GE)/ml for the three initial targets (∼1 to 2 GE/reaction). Among 253 residual nasopharyngeal swabs with detectable SARS-CoV-2 RNA, the Spike SNP assay was positive in 238 (94.1%) samples. All 220 samples with threshold cycle (CT) values of <30 for the SARS-CoV-2 N2 target were detected, whereas 18/33 samples with N2 CT values of ≥30 were detected. Spike SNP results were confirmed by sequencing in 50/50 samples (100%). Addition of the 452R probe did not affect performance for the original targets. The Spike SNP assay accurately identifies SARS-CoV-2 mutations in the receptor binding domain, and it can be quickly modified to detect new mutations that emerge.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Mutation , RNA, Viral/genetics , Real-Time Polymerase Chain Reaction , Reverse Transcription
11.
J Clin Microbiol ; 59(11): e0156421, 2021 10 19.
Article in English | MEDLINE | ID: covidwho-1480239

ABSTRACT

The utility of rapid antigen testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is measured within the context for which it is applied; diagnostic accuracy must be considered in determining if rapid antigen testing is appropriate for the clinical situation. In this issue of the Journal of Clinical Microbiology, J. N. Kanji, D. T. Proctor, W. Stokes, B. M. Berenger, et al. (J Clin Microbiol 59:e01411-21, 2021, https://doi.org/10.1128/JCM.01411-21) evaluate two rapid antigen tests that demonstrate high false-positive rates in asymptomatic health care workers. The assays may not be useful in situations where there is a shortage of staff, such as health care settings, since isolation would occur unnecessarily for these employees.


Subject(s)
COVID-19 , SARS-CoV-2 , Health Personnel , Humans , Immunologic Tests , Vaccination
12.
Clin Infect Dis ; 73(7): e1790-e1794, 2021 10 05.
Article in English | MEDLINE | ID: covidwho-1455276

ABSTRACT

BACKGROUND: Previous research has shown that rooms of patients with coronavirus disease 2019 (COVID-19) present the potential for healthcare-associated transmission through aerosols containing severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). However, data on the presence of these aerosols outside of patient rooms are limited. We investigated whether virus-containing aerosols were present in nursing stations and patient room hallways in a referral center with critically ill COVID-19 patients. METHODS: Eight National Institute for Occupational Safety and Health BC 251 2-stage cyclone samplers were set up throughout 6 units, including nursing stations and visitor corridors in intensive care units and general medical units, for 6 h each sampling period. Samplers were placed on tripods which held 2 samplers positioned 102 cm and 152 cm above the floor. Units were sampled for 3 days. Extracted samples underwent reverse transcription polymerase chain reaction for selected gene regions of the SARS-CoV-2 virus nucleocapsid and the housekeeping gene human RNase P as an internal control. RESULTS: The units sampled varied in the number of laboratory-confirmed COVID-19 patients present on the days of sampling. Some of the units included patient rooms under negative pressure, while most were maintained at a neutral pressure. Of 528 aerosol samples collected, none were positive for SARS-CoV-2 RNA by the estimated limit of detection of 8 viral copies/m3 of air. CONCLUSIONS: Aerosolized SARS-CoV-2 outside of patient rooms was undetectable. While healthcare personnel should avoid unmasked close contact with each other, these findings may provide reassurance for the use of alternatives to tight-fitting respirators in areas outside of patient rooms during the current pandemic.


Subject(s)
COVID-19 , SARS-CoV-2 , Critical Illness , Humans , RNA, Viral/genetics , Referral and Consultation , United States
14.
Clin Infect Dis ; 72(5): e154-e157, 2021 03 01.
Article in English | MEDLINE | ID: covidwho-1387787

ABSTRACT

To assess the impact of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic on seasonal respiratory viruses, absolute case counts and viral reproductive rates from 2019-2020 were compared against previous seasons. Our findings suggest that the public health measures implemented to reduce SARS-CoV-2 transmission significantly reduced the transmission of other respiratory viruses.


Subject(s)
COVID-19 , Viruses , Humans , Pandemics , SARS-CoV-2 , Seasons , United States/epidemiology
15.
Ocul Immunol Inflamm ; 29(4): 743-750, 2021 May 19.
Article in English | MEDLINE | ID: covidwho-1379400

ABSTRACT

PURPOSE: To assess the prevalence of retinopathy and its association with systemic morbidity and laboratory indices of coagulation and inflammatory dysfunction in severe COVID-19. DESIGN: Retrospective, observational cohort study. METHODS: Adult patients hospitalized with severe COVID-19 who underwent ophthalmic examination from April to July 2020 were reviewed. Retinopathy was defined as one of the following: 1) Retinal hemorrhage; 2) Cotton wool spots; 3) Retinal vascular occlusion. We analyzed medical comorbidities, sequential organ failure assessment (SOFA) scores, clinical outcomes, and laboratory values for their association with retinopathy. RESULTS: Thirty-seven patients with severe COVID-19 were reviewed, the majority of whom were female (n = 23, 62%), Black (n = 26, 69%), and admitted to the intensive care unit (n = 35, 95%). Fourteen patients had retinopathy (38%) with retinal hemorrhage in 7 (19%), cotton wool spots in 8 (22%), and a branch retinal artery occlusion in 1 (3%) patient. Patients with retinopathy had higher SOFA scores than those without retinopathy (8.0 vs. 5.3, p = .03), higher rates of respiratory failure requiring invasive mechanical ventilation and shock requiring vasopressors (p < .01). Peak D-dimer levels were 28,971 ng/mL in patients with retinopathy compared to 12,575 ng/mL in those without retinopathy (p = .03). Peak CRP was higher in patients with cotton wool spots versus those without cotton wool spots (354 mg/dL vs. 268 mg/dL, p = .03). Multivariate logistic regression modeling showed an increased risk of retinopathy with higher peak D-dimers (aOR 1.32, 95% CI 1.01-1.73, p = .04) and male sex (aOR 9.6, 95% CI 1.2-75.5, p = .04). CONCLUSION: Retinopathy in severe COVID-19 was associated with greater systemic disease morbidity involving multiple organs. Given its association with coagulopathy and inflammation, retinopathy may offer insight into disease pathogenesis in patients with severe COVID-19.


Subject(s)
COVID-19/epidemiology , Retinal Diseases/epidemiology , SARS-CoV-2 , COVID-19/diagnosis , Follow-Up Studies , Hospitalization/trends , Morbidity , Retrospective Studies , Severity of Illness Index , United States/epidemiology
17.
Clin Transl Gastroenterol ; 12(6): e00363, 2021 06 09.
Article in English | MEDLINE | ID: covidwho-1262701

ABSTRACT

INTRODUCTION: Mounting evidence demonstrates potential for fecal-oral transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The US Food and Drug Administration now requires SARS-CoV-2 testing of potential feces donors before the use of stool manufactured for fecal microbiota transplantation. We sought to develop and validate a high-sensitivity SARS-CoV-2 reverse transcriptase polymerase chain reaction (RT-PCR) procedure for testing stool specimens. METHODS: A modified extraction method was used with an RT-PCR assay adapted from the Centers for Disease Control and Prevention PCR protocol for respiratory specimens. Contrived specimens were created using pre-COVID-19 banked stool specimens and spiking in known concentrations of SARS-CoV-2-specific nucleic acid. The highest transcript concentration at which 2/2 or 1/2 SARS-CoV-2 targets were detected in 9/10 replicates was defined as the dual-target limit and single-target limit of detection, respectively. The clinical performance of the assay was evaluated with stool samples collected from 17 nasopharyngeal swab RT-PCR-positive patients and 14 nasopharyngeal RT-PCR-negative patients. RESULTS: The dual-target and single-target limit of detection were 56 copies/µL and 3 copies/µL, respectively. SARS-CoV-2 was detected at concentrations as low as 0.6 copies/µL. Clinical stool samples from known COVID-19-positive patients demonstrated the detection of SARS-CoV-2 in stool up to 29 days from symptom onset with a high agreement with nasopharyngeal swab tests (kappa statistic of 0.95, P value < 0.001). DISCUSSION: The described RT-PCR test is a sensitive and flexible approach for the detection of SARS-CoV-2 in stool specimens. We propose an integrated screening approach that incorporates this stool test to support continuation of fecal microbiota transplantation programs.


Subject(s)
COVID-19 Testing/methods , COVID-19/transmission , Fecal Microbiota Transplantation/methods , Feces/virology , SARS-CoV-2/genetics , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19/virology , COVID-19 Testing/statistics & numerical data , Centers for Disease Control and Prevention, U.S./standards , Fecal Microbiota Transplantation/statistics & numerical data , Humans , Nasopharynx/virology , RNA, Viral/genetics , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/isolation & purification , Tissue Donors/supply & distribution , United States
18.
Future Microbiol ; 16: 439-443, 2021 04.
Article in English | MEDLINE | ID: covidwho-1181329

ABSTRACT

The COVID-19 pandemic has changed the way we practice medicine and lead our lives. In addition to pulmonary symptoms; COVID-19 as a syndrome has multisystemic involvement including frequent gastrointestinal symptoms such as diarrhea. Due to microbiome alterations with COVID-19 and frequent antibiotic exposure, COVID-19 can be complicated by Clostridioides difficile infection. Co-infection with these two can be associated with a high risk of complications. Infection control measures in hospitals is enhanced due to the COVID-19 pandemic which in turn appears to reduce the incidence of hospital-acquired infections such as C. difficile infection. Another implication of COVID-19 and its potential transmissibility by stool is microbiome-based therapies. Potential stool donors should be screened COVID-19 symptoms and be tested for COVID-19.


Subject(s)
COVID-19 , Clostridium Infections , Coinfection , Cross Infection/prevention & control , Feces , Pandemics/prevention & control , COVID-19/epidemiology , COVID-19/transmission , Clostridioides difficile/isolation & purification , Clostridium Infections/diagnosis , Clostridium Infections/epidemiology , Clostridium Infections/therapy , Coinfection/diagnosis , Coinfection/epidemiology , Fecal Microbiota Transplantation , Feces/microbiology , Feces/virology , Humans , Infection Control , SARS-CoV-2/isolation & purification
20.
J Clin Microbiol ; 59(1)2020 12 17.
Article in English | MEDLINE | ID: covidwho-991749

ABSTRACT

Broad testing for respiratory viruses among persons under investigation (PUIs) for SARS-CoV-2 has been performed inconsistently, limiting our understanding of alternative viral infections and coinfections in these patients. RNA metagenomic next-generation sequencing (mNGS) offers an agnostic tool for the detection of both SARS-CoV-2 and other RNA respiratory viruses in PUIs. Here, we used RNA mNGS to assess the frequencies of alternative viral infections in SARS-CoV-2 RT-PCR-negative PUIs (n = 30) and viral coinfections in SARS-CoV-2 RT-PCR-positive PUIs (n = 45). mNGS identified all viruses detected by routine clinical testing (influenza A [n = 3], human metapneumovirus [n = 2], and human coronavirus OC43 [n = 2], and human coronavirus HKU1 [n = 1]). mNGS also identified both coinfections (1, 2.2%) and alternative viral infections (4, 13.3%) that were not detected by routine clinical workup (respiratory syncytial virus [n = 3], human metapneumovirus [n = 1], and human coronavirus NL63 [n = 1]). Among SARS-CoV-2 RT-PCR-positive PUIs, lower cycle threshold (CT ) values correlated with greater SARS-CoV-2 read recovery by mNGS (R2, 0.65; P < 0.001). Our results suggest that current broad-spectrum molecular testing algorithms identify most respiratory viral infections among SARS-CoV-2 PUIs, when available and implemented consistently.


Subject(s)
Betacoronavirus/isolation & purification , COVID-19/diagnosis , Coronavirus OC43, Human/isolation & purification , Influenza A virus/isolation & purification , Metapneumovirus/isolation & purification , SARS-CoV-2/isolation & purification , Betacoronavirus/genetics , COVID-19 Nucleic Acid Testing/methods , Coinfection/virology , Coronavirus OC43, Human/genetics , Genome, Viral/genetics , High-Throughput Nucleotide Sequencing , Humans , Influenza A virus/genetics , Metagenome , Metagenomics , Metapneumovirus/genetics , SARS-CoV-2/genetics
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