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1.
Appl Environ Microbiol ; 88(16): e0119222, 2022 Aug 23.
Article in English | MEDLINE | ID: covidwho-1962071
2.
Appl Environ Microbiol ; 88(12): e0050422, 2022 06 28.
Article in English | MEDLINE | ID: covidwho-1879112

ABSTRACT

Multiple pathways of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission have been examined, and the role of contaminated foods as a source of SARS-CoV-2 exposure has been suggested. As many cases of SARS-CoV-2 have been linked to meat processing plants, it may be that conditions in live animal markets and slaughterhouses or meat processing plant procedures transfer viral particles to meat, poultry, and seafood during animal slaughter, processing, storage, or transport. Because of the potential for contamination of foods such as beef, chicken, pork, or fish, the goal of this study was to evaluate the survival of a lipid enveloped RNA bacteriophage, phi 6, as well as two animal coronaviruses, murine hepatitis virus (MHV) and transmissible gastroenteritis virus (TGEV), as SARS-CoV-2 surrogates for their survival under various meat and fish cold-storage conditions over 30 days. Viral surrogates differed in survival, depending on food product and temperature, but overall, viruses survived for extended periods of time at high concentrations at both refrigerated and frozen temperatures. The ability of SARS-CoV-2 viral surrogates like Phi 6 and animal coronaviruses to survive for varying extents on some meat and fish products when stored refrigerated or frozen is a significant and concerning finding. Continued efforts are needed to prevent contamination of foods and food processing surfaces, worker hands, and food processing utensils such as knives, and there is a need to better address the lack of or inadequate disinfection of these foods prior to meat packaging. IMPORTANCE The ability of SARS-CoV-2 viral surrogates like Phi 6 and animal coronaviruses to survive for long periods on meat and fish products at cold temperatures emphasizes the need for rigorous and sustained food sanitation and hygiene in the harvest, transport, processing, and distribution of these foods.


Subject(s)
COVID-19 , Murine hepatitis virus , Animals , Cattle , Fish Products , Meat , Mice , SARS-CoV-2
3.
Front Public Health ; 9: 783832, 2021.
Article in English | MEDLINE | ID: covidwho-1591474

ABSTRACT

Reports of COVID-19 cases potentially attributed to fomite transmission led to the extensive use of various disinfectants to control viral spread. Alternative disinfectants, such as essential oils, have emerged as a potential antimicrobial. Four essential oil blends were tested on three different surfaces inoculated with a coronavirus surrogate, bacteriophage Phi 6, and a bacterial indicator, Staphylococcus aureus. Log10 concentration reductions were analyzed using GraphPad Prism software. Data collected in this study show that the application of dilute essential oil disinfectants using a spray delivery device is an effective way to reduce concentrations of bacterial and viral microorganisms on ceramic, stainless steel, and laminate surfaces. Surrogate viruses were reduced up to 6 log10 PFU and bacterial were reduced up to 4 log10 CFU. Although surfaces are no longer considered a high risk fomite for COVID-19 transmission, the disinfection of microorganisms on surfaces remains an important consideration for high touch areas in hospitals, waiting rooms, etc. The application of spray disinfectants, based on essential oil blends, provides a rapid and effective means to reduce microbial contamination on high-touched surfaces.


Subject(s)
COVID-19 , Disinfectants , Oils, Volatile , Disinfectants/pharmacology , Disinfection , Humans , Oils, Volatile/pharmacology , SARS-CoV-2
4.
Open Forum Infect Dis ; 7(5): ofaa134, 2020 May.
Article in English | MEDLINE | ID: covidwho-1455337

ABSTRACT

From October to December 2018, periodic bioaerosol sampling was conducted at a live bird market in Kunshan, China. Sixty-six (55%) of 120 samples had molecular evidence of avian influenza viruses. Four yielded live H9N2 virus after egg culture.

5.
Trop Dis Travel Med Vaccines ; 6: 13, 2020.
Article in English | MEDLINE | ID: covidwho-718156

ABSTRACT

BACKGROUND: In a year-long pneumonia etiology study conducted June 2017 to May 2018 in Sarawak, Malaysia, 599 patients' nasopharyngeal swab specimens were studied with real-time polymerase chain reaction (rPCR)/ reverse-transcription (rRT-PCR) assays for respiratory pathogens known to contribute to the high burden of lower respiratory tract infections. The study team sought to compare real-time assay results with panspecies conventional molecular diagnostics to compare sensitivities and learn if novel viruses had been missed. METHODS: Specimens were studied for evidence of adenovirus (AdV), enterovirus (EV) and coronavirus (CoV) with panspecies gel-based nested PCR/RT-PCR assays. Gene sequences of specimens positive by panspecies assays were sequenced and studied with the NCBI Basic Local Alignment Search Tool software. RESULTS: There was considerable discordance between real-time and conventional molecular methods. The real-time AdV assay found a positivity of 10.4%; however, the AdV panspecies assay detected a positivity of 12.4% and the conventional AdV-Hexon assay detected a positivity of 19.6%. The CoV and EV panspecies assays similarly detected more positive specimens than the real-time assays, with a positivity of 7.8% by the CoV panspecies assay versus 4.2% by rRT-PCR, and 8.0% by the EV panspecies assay versus 1.0% by rRT-PCR. We were not able to ascertain virus viability in this setting. While most discordance was likely due to assay sensitivity for previously described human viruses, two novel, possible zoonotic AdV were detected. CONCLUSIONS: The observed differences in the two modes of amplification suggest that where a problem with sensitivity is suspected, real-time assay results might be supplemented with panspecies conventional PCR/RT-PCR assays.

6.
J Clin Virol ; 128: 104391, 2020 07.
Article in English | MEDLINE | ID: covidwho-252517

ABSTRACT

BACKGROUND: During the past two decades, three novel coronaviruses (CoVs) have emerged to cause international human epidemics with severe morbidity. CoVs have also emerged to cause severe epidemics in animals. A better understanding of the natural hosts and genetic diversity of CoVs are needed to help mitigate these threats. OBJECTIVE: To design and evaluate a molecular diagnostic tool for detection and identification of all currently recognized and potentially future emergent CoVs from the Orthocoronavirinae subfamily. STUDY DESIGN AND RESULTS: We designed a semi-nested, reverse transcription RT-PCR assay based upon 38 published genome sequences of human and animal CoVs. We evaluated this assay with 14 human and animal CoVs and 11 other non-CoV respiratory viruses. Through sequencing the assay's target amplicon, the assay correctly identified each of the CoVs; no cross-reactivity with 11 common respiratory viruses was observed. The limits of detection ranged from 4 to 4 × 102 copies/reaction, depending on the CoV species tested. To assess the assay's clinical performance, we tested a large panel of previously studied specimens: 192 human respiratory specimens from pneumonia patients, 5 clinical specimens from COVID-19 patients, 81 poultry oral secretion specimens, 109 pig slurry specimens, and 31 aerosol samples from a live bird market. The amplicons of all RT-PCR-positive samples were confirmed by Sanger sequencing. Our assay performed well with all tested specimens across all sample types. CONCLUSIONS: This assay can be used for detection and identification of all previously recognized CoVs, including SARS-CoV-2, and potentially any emergent CoVs in the Orthocoronavirinae subfamily.


Subject(s)
Bird Diseases/diagnosis , Coronavirus Infections/diagnosis , Coronavirus/isolation & purification , Molecular Diagnostic Techniques/methods , Pneumonia, Viral/diagnosis , Reverse Transcriptase Polymerase Chain Reaction/methods , Swine Diseases/diagnosis , Animals , Betacoronavirus/genetics , Betacoronavirus/isolation & purification , Bird Diseases/virology , Birds , COVID-19 , Coronavirus/genetics , Coronavirus Infections/virology , Genetic Variation , Humans , Pandemics , Pneumonia, Viral/virology , SARS Virus/genetics , SARS Virus/isolation & purification , SARS-CoV-2 , Swine , Swine Diseases/virology
7.
PLoS One ; 15(5): e0233117, 2020.
Article in English | MEDLINE | ID: covidwho-244945

ABSTRACT

Severe acute respiratory illness (SARI) is a major cause of death and morbidity in low- and middle-income countries, however, the etiologic agents are often undetermined due to the lack of molecular diagnostics in hospitals and clinics. To examine evidence for select viral infections among patients with SARI in northern Vietnam, we studied 348 nasopharyngeal samples from military and civilian patients admitted to 4 hospitals in the greater Hanoi area from 2017-2019. Initial screening for human respiratory viral pathogens was performed in Hanoi, Vietnam at the National Institute of Hygiene and Epidemiology (NIHE) or the Military Institute of Preventative Medicine (MIPM), and an aliquot was shipped to Duke-NUS Medical School in Singapore for validation. Patient demographics were recorded and used to epidemiologically describe the infections. Among military and civilian cases of SARI, 184 (52.9%) tested positive for one or more respiratory viruses. Influenza A virus was the most prevalent virus detected (64.7%), followed by influenza B virus (29.3%), enterovirus (3.8%), adenovirus (1.1%), and coronavirus (1.1%). Risk factor analyses demonstrated an increased risk of influenza A virus detection among military hospital patients (adjusted OR, 2.0; 95% CI, 1.2-3.2), and an increased risk of influenza B virus detection among patients enrolled in year 2017 (adjusted OR, 7.9; 95% CI, 2.7-22.9). As influenza A and B viruses were commonly associated with SARI and are treatable, SARI patients entering these hospitals would benefit if the hospitals were able to adapt onsite molecular diagnostics.


Subject(s)
Pneumonia/epidemiology , Severe Acute Respiratory Syndrome/epidemiology , Severe Acute Respiratory Syndrome/virology , Adolescent , Adult , Coronavirus/isolation & purification , Enterovirus/isolation & purification , Female , Humans , Influenza A virus/isolation & purification , Influenza B virus/isolation & purification , Influenza, Human/epidemiology , Influenza, Human/virology , Male , Middle Aged , Military Facilities/statistics & numerical data , Pneumonia/virology , Vietnam/epidemiology , Young Adult
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