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  1. Article ; Online: SLIDE: Saliva-Based SARS-CoV-2 Self-Testing with RT-LAMP in a Mobile Device.

    Tang, Zifan / Cui, Jiarui / Kshirsagar, Aneesh / Liu, Tianyi / Yon, Michele / Kuchipudi, Suresh V / Guan, Weihua

    ACS sensors

    2022  Volume 7, Issue 8, Page(s) 2370–2378

    Abstract: Regular, accurate, rapid, and inexpensive self-testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is urgently needed to quell pandemic propagation. The existing at-home nucleic acid testing (NAT) test has high sensitivity and ... ...

    Abstract Regular, accurate, rapid, and inexpensive self-testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is urgently needed to quell pandemic propagation. The existing at-home nucleic acid testing (NAT) test has high sensitivity and specificity, but it requires users to mail the sample to the central lab, which often takes 3-5 days to obtain the results. On the other hand, rapid antigen tests for the SARS-CoV-2 antigen provide a fast sample to answer the test (15 min). However, the sensitivity of antigen tests is 30 to 40% lower than nucleic acid testing, which could miss a significant portion of infected patients. Here, we developed a fully integrated SARS-CoV-2 reverse transcription loop-mediated isothermal amplification (RT-LAMP) device using a self-collected saliva sample. This platform can automatically handle the complexity and can perform the functions, including (1) virus particles' thermal lysis preparation, (2) sample dispensing, (3) target sequence RT-LAMP amplification, (4) real-time detection, and (5) result report and communication. With a turnaround time of less than 45 min, our device achieved the limit of detection (LoD) of 5 copies/μL of the saliva sample, which is comparable with the LoD (6 copies/μL) using FDA-approved quantitative real-time polymerase chain reaction (qRT-PCR) assays with the same heat-lysis saliva sample preparation method. With clinical samples, our platform showed a good agreement with the results from the gold-standard RT-PCR method. These results show that our platform can perform self-administrated SARS-CoV-2 nucleic acid testing by laypersons with noninvasive saliva samples. We believe that our self-testing platform will have an ongoing benefit for COVID-19 control and fighting future pandemics.
    MeSH term(s) COVID-19/diagnosis ; Computers, Handheld ; Humans ; Molecular Diagnostic Techniques ; Nucleic Acid Amplification Techniques ; Nucleic Acids ; SARS-CoV-2/genetics ; Saliva ; Self-Testing ; Sensitivity and Specificity
    Chemical Substances Nucleic Acids
    Language English
    Publishing date 2022-08-03
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 2379-3694
    ISSN (online) 2379-3694
    DOI 10.1021/acssensors.2c01023
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Rapid detection of novel coronavirus SARS-CoV-2 by RT-LAMP coupled solid-state nanopores

    Tang, Zifan / Nouri, Reza / Dong, Ming / Yang, Jianbo / Greene, Wallace / Zhu, Yusheng / Yon, Michele / Nair, Meera Surendran / Kuchipudi, Suresh V. / Guan, Weihua

    Biosensors & bioelectronics. 2022 Feb. 01, v. 197

    2022  

    Abstract: The current pandemic of COVID-19 caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) has raised significant public health concerns. Rapid and accurate testing of SARS-CoV-2 is urgently needed for early detection and control of the ... ...

    Abstract The current pandemic of COVID-19 caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) has raised significant public health concerns. Rapid and accurate testing of SARS-CoV-2 is urgently needed for early detection and control of the disease spread. Here, we present an RT-LAMP coupled glass nanopore digital counting method for rapid detection of SARS-CoV-2. We validated and compared two one-pot RT-LAMP assays targeting nucleocapsid (N) and envelop (E) genes. The nucleocapsid assay was adopted due to its quick time to positive and better copy number sensitivity. For qualitative positive/negative classification of a testing sample, we used the glass nanopore to digitally count the RT-LAMP amplicons and benchmarked the event rate with a threshold. Due to its intrinsic single molecule sensitivity, nanopore sensors could capture the amplification dynamics more rapidly (quick time to positive). We validated our RT-LAMP coupled glass nanopore digital counting method for SARS-CoV-2 detection by using both spiked saliva samples and COVID-19 clinical nasopharyngeal swab samples. The results obtained showed excellent agreement with the gold standard RT-PCR assay. With its integration capability, the electronic nanopore digital counting platform has significant potential to provide a rapid, sensitive, and specific point-of-care assay for SARS-CoV-2.
    Keywords COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; biosensors ; glass ; nanopores ; nucleocapsid ; pandemic ; point-of-care systems ; public health ; rapid methods ; reverse transcription loop-mediated isothermal amplification ; saliva
    Language English
    Dates of publication 2022-0201
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 1011023-9
    ISSN 1873-4235 ; 0956-5663
    ISSN (online) 1873-4235
    ISSN 0956-5663
    DOI 10.1016/j.bios.2021.113759
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Complete Genome Sequence of a Bovine Coronavirus Isolated from a Goat in Pennsylvania, USA.

    Chothe, Shubhada K / Byukusenge, Maurice / Sekhwal, Manoj K / Li, Lingling / LaBella, Lindsey Cecelia / Jakka, Padmaja / Palchak, Kay / Barry, Rhiannon / Yon, Michele / Nissly, Ruth H / Kelly, Kathleen M / Jayarao, Bhushan M / Surendran Nair, Meera / Kuchipudi, Suresh V

    Microbiology resource announcements

    2023  Volume 12, Issue 6, Page(s) e0012223

    Abstract: We report a complete genome sequence of bovine coronavirus (BCoV) isolated from a goat in the state of Pennsylvania in 2022. BCoV often causes calf scours and winter dysentery in cattle. ...

    Abstract We report a complete genome sequence of bovine coronavirus (BCoV) isolated from a goat in the state of Pennsylvania in 2022. BCoV often causes calf scours and winter dysentery in cattle.
    Language English
    Publishing date 2023-05-03
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/mra.00122-23
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: SARS-CoV-2 Prevalence and Variant Surveillance among Cats in Pittsburgh, Pennsylvania, USA.

    Ramasamy, Santhamani / Gontu, Abhinay / Neerukonda, Sabarinath / Ruggiero, Diana / Morrow, Becky / Gupta, Sheweta / Amirthalingam, Saranya / Hardham, John M / Lizer, Joshua T / Yon, Michele / Nissly, Ruth H / Jakka, Padmaja / Chothe, Shubhada K / LaBella, Lindsey C / Tewari, Deepanker / Nair, Meera Surendran / Kuchipudi, Suresh V

    Viruses

    2023  Volume 15, Issue 7

    Abstract: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infects many mammals, and SARS-CoV-2 circulation in nonhuman animals may increase the risk of novel variant emergence. Cats are highly susceptible to SARS-CoV-2 infection, and there were cases ... ...

    Abstract Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infects many mammals, and SARS-CoV-2 circulation in nonhuman animals may increase the risk of novel variant emergence. Cats are highly susceptible to SARS-CoV-2 infection, and there were cases of virus transmission between cats and humans. The objective of this study was to assess the prevalence of SARS-CoV-2 variant infection of cats in an urban setting. We investigated the prevalence of SARS-CoV-2 variant infections in domestic and community cats in the city of Pittsburgh (
    MeSH term(s) Animals ; Humans ; SARS-CoV-2/genetics ; COVID-19/epidemiology ; COVID-19/veterinary ; Pennsylvania ; Prevalence ; Antibodies, Viral ; RNA ; Antibodies, Neutralizing ; Mammals
    Chemical Substances Antibodies, Viral ; RNA (63231-63-0) ; Antibodies, Neutralizing
    Language English
    Publishing date 2023-06-30
    Publishing country Switzerland
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v15071493
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: A Novel Real-Time PCR Assay for the Rapid Detection of Virulent

    Kuchipudi, Suresh V / Surendran Nair, Meera / Yon, Michele / Gontu, Abhinay / Nissly, Ruth H / Barry, Rhiannon / Greenawalt, Denver / Pierre, Traci / Li, Lingling / Thirumalapura, Nagaraja / Tewari, Deepanker / Jayarao, Bhushan

    Frontiers in veterinary science

    2021  Volume 8, Page(s) 604675

    Abstract: Streptococcus ... ...

    Abstract Streptococcus equi
    Language English
    Publishing date 2021-02-12
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2834243-4
    ISSN 2297-1769
    ISSN 2297-1769
    DOI 10.3389/fvets.2021.604675
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Rapid detection of novel coronavirus SARS-CoV-2 by RT-LAMP coupled solid-state nanopores.

    Tang, Zifan / Nouri, Reza / Dong, Ming / Yang, Jianbo / Greene, Wallace / Zhu, Yusheng / Yon, Michele / Nair, Meera Surendran / Kuchipudi, Suresh V / Guan, Weihua

    Biosensors & bioelectronics

    2021  Volume 197, Page(s) 113759

    Abstract: The current pandemic of COVID-19 caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) has raised significant public health concerns. Rapid and accurate testing of SARS-CoV-2 is urgently needed for early detection and control of the ... ...

    Abstract The current pandemic of COVID-19 caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) has raised significant public health concerns. Rapid and accurate testing of SARS-CoV-2 is urgently needed for early detection and control of the disease spread. Here, we present an RT-LAMP coupled glass nanopore digital counting method for rapid detection of SARS-CoV-2. We validated and compared two one-pot RT-LAMP assays targeting nucleocapsid (N) and envelop (E) genes. The nucleocapsid assay was adopted due to its quick time to positive and better copy number sensitivity. For qualitative positive/negative classification of a testing sample, we used the glass nanopore to digitally count the RT-LAMP amplicons and benchmarked the event rate with a threshold. Due to its intrinsic single molecule sensitivity, nanopore sensors could capture the amplification dynamics more rapidly (quick time to positive). We validated our RT-LAMP coupled glass nanopore digital counting method for SARS-CoV-2 detection by using both spiked saliva samples and COVID-19 clinical nasopharyngeal swab samples. The results obtained showed excellent agreement with the gold standard RT-PCR assay. With its integration capability, the electronic nanopore digital counting platform has significant potential to provide a rapid, sensitive, and specific point-of-care assay for SARS-CoV-2.
    MeSH term(s) Biosensing Techniques ; COVID-19 ; Humans ; Molecular Diagnostic Techniques ; Nanopores ; Nucleic Acid Amplification Techniques ; RNA, Viral ; SARS-CoV-2 ; Sensitivity and Specificity
    Chemical Substances RNA, Viral
    Language English
    Publishing date 2021-11-02
    Publishing country England
    Document type Journal Article
    ZDB-ID 1011023-9
    ISSN 1873-4235 ; 0956-5663
    ISSN (online) 1873-4235
    ISSN 0956-5663
    DOI 10.1016/j.bios.2021.113759
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Mitochondrial DNA analysis of 114 hairs measuring less than 1 cm from a 19-year-old homicide

    Melton Terry / Dimick Gloria / Higgins Bonnie / Yon Michele / Holland Charity

    Investigative Genetics, Vol 3, Iss 1, p

    2012  Volume 12

    Abstract: Abstract Background Mitochondrial DNA analysis is typically applied to degraded skeletal remains and telogen or rootless hairs. Data on the application of the method to very small hairs less than 0.5 cm from an age-matched and -challenged sample set are ... ...

    Abstract Abstract Background Mitochondrial DNA analysis is typically applied to degraded skeletal remains and telogen or rootless hairs. Data on the application of the method to very small hairs less than 0.5 cm from an age-matched and -challenged sample set are lacking. Methods One hundred fourteen hairs sized less than 1 cm from a 1993 case were analyzed for mitochondrial DNA according to laboratory standard operating procedures. For some hairs, a screening approach was applied, which permitted some samples, such as victim hairs on victim clothing, to be eliminated from the process quickly. Degraded samples were amplified with “mini-primers,” and 12S species testing was applied when non-human hairs were encountered. Results Partial to full control region human mitochondrial DNA profiles or species identifications (non-human species) were obtained from 93% of hairs under 1 cm, 92% of hairs under 5 mm, and 90% of hairs under 3.5 mm. Nineteen of 21 hairs 2 mm or less gave full or partial profiles. Among 128 hairs of all sizes tested in the case, 9 gave no results, 3 were canine in origin, and 73 did not exclude six known individuals tested in the case. Twenty-two hairs had nine additional profiles that were observed two or more times each. Twenty-one hairs showed singleton types not matching each other or any individual. Conclusions Crime scene hairs that are both aged and small are often judged to be unsuitable for either hair microscopy or DNA analysis. This study of age-matched challenged small hairs indicates that even the smallest probative crime scene hairs are suitable for mitochondrial DNA analysis and can provide useful data.
    Keywords Casework ; mtDNA ; Hair ; Analysis ; Small ; Aged ; Degraded ; Genetics ; QH426-470 ; Biology (General) ; QH301-705.5 ; Science ; Q ; DOAJ:Genetics ; DOAJ:Biology ; DOAJ:Biology and Life Sciences
    Subject code 590
    Language English
    Publishing date 2012-07-01T00:00:00Z
    Publisher BioMed Central
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Draft Genome Sequences of Two Virulent Streptococcus equi subsp.

    Surendran Nair, Meera / Byukusenge, Maurice / Li, Lingling / Nissly, Ruth H / Cavener, Victoria S / Yon, Michele / Barry, Rhiannon / Natesan, Pazhanivel / Thirumalapura, Nagaraja / Tewari, Deepanker / Jayarao, Bhushan M / Kuchipudi, Suresh V

    Microbiology resource announcements

    2020  Volume 9, Issue 42

    Abstract: Draft genome sequences of two outbreak isolates ... ...

    Abstract Draft genome sequences of two outbreak isolates of
    Language English
    Publishing date 2020-10-15
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/MRA.00974-20
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: A Highly Sensitive and Specific Probe-Based Real-Time PCR for the Detection of

    Kuchipudi, Suresh V / Yon, Michele / Surendran Nair, Meera / Byukusenge, Maurice / Barry, Rhiannon M / Nissly, Ruth H / Williams, Jen / Pierre, Traci / Mathews, Tammy / Walner-Pendleton, Eva / Dunn, Patricia / Barnhart, Denise / Loughrey, Sean / Davison, Sherrill / Kelly, Dona J / Tewari, Deepanker / Jayarao, Bhushan M

    Frontiers in veterinary science

    2021  Volume 8, Page(s) 609126

    Abstract: Avibacterium ... ...

    Abstract Avibacterium paragallinarum
    Language English
    Publishing date 2021-04-12
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2834243-4
    ISSN 2297-1769
    ISSN 2297-1769
    DOI 10.3389/fvets.2021.609126
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Transmission history of SARS-CoV-2 in humans and white-tailed deer.

    Willgert, Katriina / Didelot, Xavier / Surendran-Nair, Meera / Kuchipudi, Suresh V / Ruden, Rachel M / Yon, Michele / Nissly, Ruth H / Vandegrift, Kurt J / Nelli, Rahul K / Li, Lingling / Jayarao, Bhushan M / Levine, Nicole / Olsen, Randall J / Davis, James J / Musser, James M / Hudson, Peter J / Kapur, Vivek / Conlan, Andrew J K

    Scientific reports

    2022  Volume 12, Issue 1, Page(s) 12094

    Abstract: The emergence of a novel pathogen in a susceptible population can cause rapid spread of infection. High prevalence of SARS-CoV-2 infection in white-tailed deer (Odocoileus virginianus) has been reported in multiple locations, likely resulting from ... ...

    Abstract The emergence of a novel pathogen in a susceptible population can cause rapid spread of infection. High prevalence of SARS-CoV-2 infection in white-tailed deer (Odocoileus virginianus) has been reported in multiple locations, likely resulting from several human-to-deer spillover events followed by deer-to-deer transmission. Knowledge of the risk and direction of SARS-CoV-2 transmission between humans and potential reservoir hosts is essential for effective disease control and prioritisation of interventions. Using genomic data, we reconstruct the transmission history of SARS-CoV-2 in humans and deer, estimate the case finding rate and attempt to infer relative rates of transmission between species. We found no evidence of direct or indirect transmission from deer to human. However, with an estimated case finding rate of only 4.2%, spillback to humans cannot be ruled out. The extensive transmission of SARS-CoV-2 within deer populations and the large number of unsampled cases highlights the need for active surveillance at the human-animal interface.
    MeSH term(s) Animals ; COVID-19/epidemiology ; COVID-19/prevention & control ; COVID-19/transmission ; COVID-19/veterinary ; Deer/virology ; Environmental Monitoring ; Humans ; Risk Assessment ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification ; Viral Zoonoses/epidemiology ; Viral Zoonoses/transmission ; Viral Zoonoses/virology
    Language English
    Publishing date 2022-07-15
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-022-16071-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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