Comparison of SARS-CoV-2 indirect and direct RT-qPCR detection methods

BACKGROUND

Sensitive, rapid, and accessible diagnostics continue to be critical to track the COVID-19 pandemic caused by the SARS-CoV-2 virus. RT-qPCR is the gold standard test, and comparison of methodologies and reagents, utilizing patient samples, is important to establish reliable diagnostic pipelines.

METHODS

Here, we assessed indirect methods that require RNA extraction with direct RT-qPCR on patient samples. Four different RNA extraction kits (Qiagen, Invitrogen, BGI and Norgen Biotek) were compared. For detection, we assessed two recently developed Taqman-based modules (BGI and Norgen Biotek), a SYBR green-based approach (NEB Luna Universal One-Step Kit) with published and newly-developed primers, and clinical results (Seegene STARMag RNA extraction system and Allplex 2019-nCoV RT-qPCR assay). We also tested and optimized direct, extraction-free detection using these RT-qPCR systems and performed a cost analysis of the different methods evaluated here.

RESULTS

Most RNA isolation procedures performed similarly, and while all RT-qPCR modules effectively detected purified viral RNA, the BGI system provided overall superior performance (lower detection limit, lower Ct values and higher sensitivity), generating comparable results to original clinical diagnostic data, and identifying samples ranging from 65 copies to 2.1 × 105 copies of viral genome/μl. However, the BGI detection system is more expensive than other options tested here. With direct RT-qPCR, simply adding an RNase inhibitor greatly improved detection, without the need for any other treatments (e.g. lysis buffers or boiling). The best direct methods detected ~ 10 fold less virus than indirect methods, but this simplified approach reduced sample handling, as well as assay time and cost.

CONCLUSIONS

With extracted RNA, the BGI RT-qPCR detection system exhibited superior performance over the Norgen system, matching initial clinical diagnosis with the Seegene Allplex assay. The BGI system was also suitable for direct, extraction-free analysis, providing 78.4% sensitivity. The Norgen system, however, still accurately detected samples with a clinical Ct < 33 from extracted RNA, provided significant cost savings, and was superior to SYBR green assays that exhibited reduced specificity.

Circulating NK-cell subsets in renal allograft recipients with anti-HLA donor-specific antibodies

Detection of posttransplant donor-specific anti-HLA antibodies (DSA) constitutes a risk factor for kidney allograft loss. Together with complement activation, NK-cell antibody-dependent cell mediated cytotoxicity (ADCC) has been proposed to contribute to the microvascular damage associated to humoral rejection. In the present observational exploratory study, we have tried to find a relationship of circulating donor-specific and non donor-specific anti-HLA antibodies (DSA and HLA non-DSA) with peripheral blood NK-cell subsets and clinical features in 393 renal allograft recipients. Multivariate analysis indicated that retransplantation and pretransplant sensitization were associated with detection of posttransplant DSA. Recipient female gender, DR mismatch and acute rejection were significantly associated with posttransplant DSA compared to HLA non-DSA. In contrast with patients without detectable anti-HLA antibodies, DSA and HLA non-DSA patients displayed lower proportions of NK-cells, associated with increased CD56(bright) and NKG2A(+) subsets, the latter being more marked in DSA cases. These differences appeared unrelated to retransplantation, previous acute rejection or immunosuppressive therapy. Although preliminary and observational in nature, our results suggest that the assessment of the NK-cell immunophenotype may contribute to define signatures of alloreactive humoral responses in renal allograft recipients.

Flat-on lamellae in spin-coated, stable films of poly(propylene azelate)

Thin films (5-500 nm thick) of the linear aliphatic polyester (3,7) poly(propylene azelate) (PPAz) were prepared by spin-coating of CHCl(3) polymer solutions with different polymer concentrations. The morphology and structure of the spin-coated thin films were investigated by atomic force microscopy (AFM) and by grazing incidence wide-angle X-ray scattering (GIWAXS) techniques. AFM revealed the continuous nature of the flat, spherulitic films which are stable against dewetting even for polymer coatings as thin as 15 nm. GIWAXS patterns revealed a high crystal orientation of the films. A sharp reflection on the meridian whose spacing is related to the polymer chain unit length (c-axis) supports the presence of flat-on lamellae morphology in the whole range of film thicknesses investigated. The flat-on lamellae morphology is also supported by AFM images. A triclinic unit cell with the c*-axis perpendicular to the substrate is proposed for PPAz. The repulsion of the long aliphatic spacer by the Si-substrate is invoked as the main reason for the flat-on morphology observed.

Structure and morphology of thin films of linear aliphatic polyesters prepared by spin-coating

Thin films, with thicknesses from 10 to 400 nm of linear aliphatic polyesters (X, Y), based on propylenediol (X = 3) and on dicarboxylic acid of different chain length (Y = 2, 3, and 4 CH(2) units) were prepared by spin coating of CHCl(3) polymer solutions with different polymer concentrations. Morphology and structure of the spin coated thin films were investigated by atomic force microscopy (AFM) and by grazing incidence X-ray scattering techniques at small, (GISAXS) and wide angles (GIWAXS). AFM revealed a strong dewetting for all three polymers for coatings thinner than 100 nm. The polymer films are clearly semicrystalline for thicknesses higher than 50 nm. GIWAXS of the thicker films revealed their oriented crystalline nature. An edge-on-lamellae morphology is clearly shown by the AFM-phase images even for relatively thin films. SAXS with the beam parallel to the sample plane also support the presence of lamellae perpendicular to the substrate. The use of a mu-beam helped to interpret the GIWAXS patterns and allowed to obtain oriented WAXS patterns from melt solidified filaments. Thus, a crystal chain packing is proposed for the three polymers and consequently the indexing of the observed reflections. Accordingly, the polymer chains lie parallel to the substrate being the bc plane of the monoclinic crystal unit cell parallel to the substrate.

Genetic typing of Malassezia pachydermatis from different domestic animals

In the present study, random amplification of polymorphic DNA, which detects DNA polymorphism in fungal genomic DNA, was applied for genetic typing of Malassezia pachydermatis isolates. Fifty-five isolates from different domestic animals and body sites and the neotype strain CBS 1879 were characterized. Primers M13 and OPT-20 were used to analyse their genetic relatedness and similarity. This technique allowed us to distinguish four different genetic types. The predominant genetic type was observed in isolates recovered from different anatomical locations in all animals. It was the only genetic type found in cats, horse, goat and pig. The other three genetic types were observed only in isolates from external ear canals of dogs. Types II and IV were only recovered from external otitic ears and type III from healthy ears. An animal was colonised by more than one type of M. pachydermatis and different genetic types were detected in the same body site. Some genetic types were only isolated from diseased skin.

Molecular analysis of Malassezia sympodialis-related strains from domestic animals

Recently, several new lipid-dependent species belonging to the genus Malassezia have been described. Some of them, such as Malassezia dermatis, Malassezia nana, and the tentatively named "Malassezia equi," have similar phenotypes and are genetically close to Malassezia sympodialis Simmons et Gueho 1990. DNA characterization by D1/D2 26S rRNA gene and internal transcribed spacer (ITS)-5.8S rRNA gene sequencing analysis of lipid-dependent strains from different animal species close to M. sympodialis is described and illustrated. Phylogenetic analysis of both the D1/D2 regions of 26S rRNA gene and ITS-5.8S rRNA gene sequences showed four distinct clusters. Cluster I included isolates from different animal species (horse, pig, and lamb) and the type culture of M. sympodialis. Cluster II included isolates from horses grouping close to the "M. equi" AJ305330 sequence. Cluster III comprised isolates mainly from goats. Cluster IV contained isolates mainly from cats grouping together with the M. nana AB075224 sequence. This last cluster included isolates from healthy and external otitic ears. All of these strains had identical 26S rRNA gene and ITS regions. It is not clear whether the value of these genetic differences is for the definition of species or whether they only demonstrate genetic variation among strains from different origins within M. sympodialis, which are in the course of differentiation and probably adaptation to specific animal hosts.

AIDS-related illness trajectories in Mexico: findings from a qualitative study in two marginalized communities

This paper describes findings from a recent study examining how people affected directly and indirectly by the HIV/AIDS epidemic cope with HIV-related illness in Mexico. One-hundred-and-thirteen in-depth interviews were conducted with key informants in two contrasting communities: Ciudad Netzahualcóyotl (an economically marginalized community) and the gay community in Mexico City (a sexually marginalized community). This paper describes the AIDS-related wellness/illness careers or trajectories followed by individuals in both communities, and identifies critical points for material and emotional intervention. This career comprises four stages: (1) life before infection; (2) life surrounding the discovery of seropositivity; (3) living as an HIV-positive person; and (4) facing death. Comparisons are drawn between the processes of adjustment and coping found in both communities. In Ciudad Netzahualcóyotl, wellness/illness careers are closely linked to prevailing poverty and oppression, as well as the sense of urgency in which local people live their lives. In the case of the gay community, wellness/illness careers are associated with the intolerance and social repression faced by homosexual men. The paper concludes by suggesting possible interventions to improve the lives of people with HIV/AIDS in Mexico today.

[Management strategies in HIV/AIDS at the family level]

OBJECTIVE

To identify the critical points of the trajectories of the families of persons with AIDS which may serve as a basis to develop educational and support programs.

THEORY AND METHODS

A qualitative investigation was conducted in 1995 in Ciudad Netzahualcóyotl, State of Mexico, Mexico. Rapid Assessment Procedures (RAP) were applied to determine the social, economic, demographic and cultural context of persons with HIV/AIDS in the community. Forty-six in-depth interviews were applied to persons with AIDS, their families and people from their social networks.

RESULTS

The main aspects of the family response to the HIV/ AIDS are characterized, and it is demonstrated that it is possible to identify critical points in such a response which can be targeted through specific interventions. In Ciudad Netzahualcóyotl, a context of poverty, a migrating tradition, and gender social relations are the basis of the acceptance or rejection of persons with AIDS. The main finding refers to the ambiguos attitude, ranging from rejection to support, displayed by family members of persons with AIDS. This pattern varies according to the history and specific conditions of each family.

CONCLUSIONS

Specific health interventions are proposed to support families with one or more persons with AIDS.

Functional and biochemical features of alcohol dehydrogenase in four species of the obscura group of Drosophila

The biochemical features of ADH of four Drosophila species of the obscura group have been studied. The relationship between ethanol tolerance and ADH activity has been investigated. Propan-2-ol and acetone concentrations have been determined in propan-2-ol treated flies and ADH activity has been followed during 96 h of propan-2-ol treatment. Data on the ADH system confirm constructed phylogenies based on electrophoretic variation and chromosome homologies.