Diagnostic Nucleic Acid Amplification Test Research Articles

Calibrating COVID-19 community transmission risk levels to reflect infection prevalence

Many organizations, including the US Centers for Disease Control and Prevention, have developed risk indexes to help determine community transmission levels for the ongoing COVID-19 pandemic. These risk indexes are largely based on newly reported cases and percentage of positive SARS-CoV-2 diagnostic nucleic acid amplification tests, which are well-established as biased estimates of COVID-19 transmission. However, transmission risk indexes should accurately and precisely communicate community risks to decision-makers and the public. Therefore, transmission risk indexes would ideally quantify actual, and not just reported, levels of disease prevalence or incidence. Here, we develop a robust data-driven framework for determining and communicating community transmission risk levels using reported cases and test positivity. We use this framework to evaluate the previous CDC community risk level metrics that were proposed as guidelines for determining COVID-19 transmission risk at community level in the US. Using two recently developed data-driven models for COVID-19 transmission in the US to compute community-level prevalence, we show that there is substantial overlap of prevalence between the different community risk levels from the previous CDC guidelines. Using our proposed framework, we redefined the risk levels and their threshold values. We show that these threshold values would have substantially reduced the overlaps of underlying community prevalence between counties/states in different community risk levels between 3/19/2020–9/9/2021. Our study demonstrates how the previous CDC community risk level indexes could have been calibrated to infection prevalence to improve their power to accurately determine levels of COVID-19 transmission in local communities across the US. This method can be used to inform the design of future COVID-19 transmission risk indexes.

Use of At-Home COVID-19 Tests - United States, August 23, 2021-March 12, 2022.

COVID-19 testing provides information regarding exposure and transmission risks, guides preventative measures (e.g., if and when to start and end isolation and quarantine), identifies opportunities for appropriate treatments, and helps assess disease prevalence (1). At-home rapid COVID-19 antigen tests (at-home tests) are a convenient and accessible alternative to laboratory-based diagnostic nucleic acid amplification tests (NAATs) for SARS-CoV-2, the virus that causes COVID-19 (2-4). With the emergence of the SARS-CoV-2 B.1.617.2 (Delta) and B.1.1.529 (Omicron) variants in 2021, demand for at-home tests increased† (5). At-home tests are commonly used for school- or employer-mandated testing and for confirmation of SARS-CoV-2 infection in a COVID-19-like illness or following exposure (6). Mandated COVID-19 reporting requirements omit at-home tests, and there are no standard processes for test takers or manufacturers to share results with appropriate health officials (2). Therefore, with increased COVID-19 at-home test use, laboratory-based reporting systems might increasingly underreport the actual incidence of infection. Data from a cross-sectional, nonprobability-based online survey (August 23, 2021-March 12, 2022) of U.S. adults aged ≥18 years were used to estimate self-reported at-home test use over time, and by demographic characteristics, geography, symptoms/syndromes, and reasons for testing. From the Delta-predominant period (August 23-December 11, 2021) to the Omicron-predominant period (December 19, 2021-March 12, 2022)§ (7), at-home test use among respondents with self-reported COVID-19-like illness¶ more than tripled from 5.7% to 20.1%. The two most commonly reported reasons for testing among persons who used an at-home test were COVID-19 exposure (39.4%) and COVID-19-like symptoms (28.9%). At-home test use differed by race (e.g., self-identified as White [5.9%] versus self-identified as Black [2.8%]), age (adults aged 30-39 years [6.4%] versus adults aged ≥75 years [3.6%]), household income (>$150,000 [9.5%] versus $50,000-$74,999 [4.7%]), education (postgraduate degree [8.4%] versus high school or less [3.5%]), and geography (New England division [9.6%] versus West South Central division [3.7%]). COVID-19 testing, including at-home tests, along with prevention measures, such as quarantine and isolation when warranted, wearing a well-fitted mask when recommended after a positive test or known exposure, and staying up to date with vaccination,** can help reduce the spread of COVID-19. Further, providing reliable and low-cost or free at-home test kits to underserved populations with otherwise limited access to COVID-19 testing could assist with continued prevention efforts.

Cervicovaginal Microbiota Predicts Neisseria gonorrhoeae Clinical Presentation.

Neisseria gonorrhoeae infection of the female lower genital tract can present with a spectrum of phenotypes ranging from asymptomatic carriage to symptomatic cervical inflammation, or cervicitis. The factors that contribute to the development of asymptomatic or symptomatic infections are largely uncharacterized. We conducted a pilot study to assess differences in the cervicovaginal microbial community of patients presenting with symptomatic vs. asymptomatic N. gonorrhoeae infections to a sexually transmitted infections (STI) clinic. DNA was isolated from cervicovaginal swab specimens from women who tested positive for N. gonorrhoeae infection using a clinical diagnostic nucleic acid amplification test. We performed deep sequencing of 16S ribosomal RNA gene amplicons, followed by microbiome analyses with QIIME, and species-specific real-time PCR to assess the composition of microbial communities cohabitating the lower genital tract with the infecting N. gonorrhoeae. Specimens collected from asymptomatic individuals with N. gonorrhoeae infection and no co-infection with Chlamydia trachomatis and/or Trichomonas vaginalis carried Lactobacillus-dominant microbial communities more frequently than symptomatic patients without co-infection. When compared to asymptomatic individuals, symptomatic women had microbial communities characterized by more diverse and heterogenous bacterial taxa, typically associated with bacterial vaginosis (BV) [Prevotella, Sneathia, Mycoplasma hominis, and Bacterial Vaginosis-Associated Bacterium-1 (BVAB1)/“Candidatus Lachnocurva vaginae”]. Both symptomatic and asymptomatic N. gonorrhoeae patients with additional STI co-infection displayed a BV-like microbial community. These findings suggest that Lactobacillus-dominant vaginal microbial community may protect individuals from developing symptoms during lower genital tract infection with N. gonorrhoeae.

Initial study on TMPRSS2 p.Val160Met genetic variant in COVID-19 patients

BackgroundCoronavirus disease 2019 (COVID-19) is a global health problem that causes millions of deaths worldwide. The clinical manifestation of COVID-19 widely varies from asymptomatic infection to severe pneumonia and systemic inflammatory disease. It is thought that host genetic variability may affect the host’s response to the virus infection and thus cause severity of the disease. The SARS-CoV-2 virus requires interaction with its receptor complex in the host cells before infection. The transmembrane protease serine 2 (TMPRSS2) has been identified as one of the key molecules involved in SARS-CoV-2 virus receptor binding and cell invasion. Therefore, in this study, we investigated the correlation between a genetic variant within the human TMPRSS2 gene and COVID-19 severity and viral load.ResultsWe genotyped 95 patients with COVID-19 hospitalised in Dr Soetomo General Hospital and Indrapura Field Hospital (Surabaya, Indonesia) for the TMPRSS2 p.Val160Met polymorphism. Polymorphism was detected using a TaqMan assay. We then analysed the association between the presence of the genetic variant and disease severity and viral load. We did not observe any correlation between the presence of TMPRSS2 genetic variant and the severity of the disease. However, we identified a significant association between the p.Val160Met polymorphism and the SARS-CoV-2 viral load, as estimated by the Ct value of the diagnostic nucleic acid amplification test. Furthermore, we observed a trend of association between the presence of the C allele and the mortality rate in patients with severe COVID-19.ConclusionOur data indicate a possible association between TMPRSS2 p.Val160Met polymorphism and SARS-CoV-2 infectivity and the outcome of COVID-19.

Diagnostic Performance of an Antigen Test with RT-PCR for the Detection of SARS-CoV-2 in a Hospital Setting - Los Angeles County, California, June-August 2020.

Prompt and accurate detection of SARS-CoV-2, the virus that causes COVID-19, has been important during public health responses for containing the spread of COVID-19, including in hospital settings (1-3). In vitro diagnostic nucleic acid amplification tests (NAAT), such as real-time reverse transcription-polymerase chain reaction (RT-PCR) can be expensive, have relatively long turnaround times, and require experienced laboratory personnel.* Antigen detection tests can be rapidly and more easily performed and are less expensive. The performance† of antigen detection tests, compared with that of NAATs, is an area of interest for the rapid diagnosis of SARS-CoV-2 infection. The Quidel Sofia 2 SARS Antigen Fluorescent Immunoassay (FIA) (Quidel Corporation) received Food and Drug Administration Emergency Use Authorization for use in symptomatic patients within 5 days of symptom onset (4). The reported test positive percentage agreement§ between this test and an RT-PCR test result is 96.7% (95% confidence interval [CI]=83.3%-99.4%), and the negative percentage agreement is 100.0% (95% CI=97.9%-100.0%) in symptomatic patients.¶ However, performance in asymptomatic persons in a university setting has shown lower sensitivity (5); assessment of performance in a clinical setting is ongoing. Data collected during June 30-August 31, 2020, were analyzed to compare antigen test performance with that of RT-PCR in a hospital setting. Among 1,732 paired samples from asymptomatic patients, the antigen test sensitivity was 60.5%, and specificity was 99.5% when compared with RT-PCR. Among 307 symptomatic persons, sensitivity and specificity were 72.1% and 98.7%, respectively. Health care providers must remain aware of the lower sensitivity of this test among asymptomatic and symptomatic persons and consider confirmatory NAAT testing in high-prevalence settings because a false-negative result might lead to failures in infection control and prevention practices and cause delays in diagnosis, isolation, and treatment.

Association of SARS-CoV-2 Seropositive Antibody Test With Risk of Future Infection

Understanding the effect of serum antibodies to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on susceptibility to infection is important for identifying at-risk populations and could have implications for vaccine deployment. The study purpose was to evaluate evidence of SARS-CoV-2 infection based on diagnostic nucleic acid amplification test (NAAT) among patients with positive vs negative test results for antibodies in an observational descriptive cohort study of clinical laboratory and linked claims data. The study created cohorts from a deidentified data set composed of commercial laboratory tests, medical and pharmacy claims, electronic health records, and hospital chargemaster data. Patients were categorized as antibody-positive or antibody-negative according to their first SARS-CoV-2 antibody test in the database. Primary end points were post-index diagnostic NAAT results, with infection defined as a positive diagnostic test post-index, measured in 30-day intervals (0-30, 31-60, 61-90, >90 days). Additional measures included demographic, geographic, and clinical characteristics at the time of the index antibody test, including recorded signs and symptoms or prior evidence of coronavirus 2019 (COVID) diagnoses or positive NAAT results and recorded comorbidities. The cohort included 3 257 478 unique patients with an index antibody test; 56% were female with a median (SD) age of 48 (20) years. Of these, 2 876 773 (88.3%) had a negative index antibody result, and 378 606 (11.6%) had a positive index antibody result. Patients with a negative antibody test result were older than those with a positive result (mean age 48 vs 44 years). Of index-positive patients, 18.4% converted to seronegative over the follow-up period. During the follow-up periods, the ratio (95% CI) of positive NAAT results among individuals who had a positive antibody test at index vs those with a negative antibody test at index was 2.85 (95% CI, 2.73-2.97) at 0 to 30 days, 0.67 (95% CI, 0.6-0.74) at 31 to 60 days, 0.29 (95% CI, 0.24-0.35) at 61 to 90 days, and 0.10 (95% CI, 0.05-0.19) at more than 90 days. In this cohort study, patients with positive antibody test results were initially more likely to have positive NAAT results, consistent with prolonged RNA shedding, but became markedly less likely to have positive NAAT results over time, suggesting that seropositivity is associated with protection from infection. The duration of protection is unknown, and protection may wane over time.

Addressing the rising rates of gonorrhea and drug-resistant gonorrhea: There is no time like the present.

Increasing rates of gonococcal (GC) infection and antimicrobial resistant (AMR) GC, are a serious public health concern for Canada and around the world. Previously recommended treatments are ineffective against many of the gonorrhea strains circulating today. The current recommendation for combination therapy is now being threatened by globally emerging and increasingly resistant strains. It is important that coordinated efforts be made now to ensure these new global strains do not become established in Canada. Otherwise, we will be faced with the possibility of persistent GC infection which can lead to pelvic inflammatory disease, infertility and chronic pelvic pain in women; and epididymitis in men. The presence of GC can also increase the risk of HIV acquisition and transmission.There are a number of reasons why we are facing this public health threat. GC infection is often asymptomatic and it is highly transmissible. People may hesitate to seek testing (or to offer testing). Treatment is complex: recommendations vary by site of infection and risk of resistance. Sexual contact during travel is an important source of imported emerging resistant global strains. The new screening and diagnostic Nucleic Acid Amplification Test (NAAT) is excellent but has decreased the number of cultures being done and therefore our capacity to track AMR-GC.There are four key actions that clinicians and front-line public health professionals can take to stem the increase in rates of GC and drug resistant GC. First, normalize and increase GC screening based on risk factors and emphasize the need for safer sex practices. NAAT is useful for screening, but culture is still needed for extra-genital sites. Second, conduct pretravel counselling and include a travel history as part of the risk assessment. Third, use culture along with NAAT to establish the diagnosis and follow up for test-of-cure. Finally, refer to the most current Canadian Guidelines on Sexually Transmitted Infections or provincial/territorial recommendations on combination therapies for patients and their contacts as recommendations may have changed in response to evolving AMR-GC trends.

The Swedish new variant of Chlamydia trachomatis (nvCT) remains undetected by many European laboratories as revealed in the recent PCR/NAT ring trial organised by INSTAND e.V., Germany

The May 2009 round of INSTAND's ring trial "Chlamydia trachomatis detection PCR/NAT" included a sample with high amount of the Swedish new variant of C. trachomatis (nvCT). A spectrum of at least 12 different commercial diagnostic nucleic acid amplification tests (NAATs) and many different in house NAATs were applied by the 128 participating laboratories which reported 152 results. Approximately 80% of the results correctly reported the presence of C. trachomatis in the nvCT specimen. The nvCT sample was mainly missed, as expected, by participants using the Roche COBAS Amplicor CT/NG (15.5% of reported results) but also by several participants using in house NAATs. The trend towards using nvCT-detecting NAATs is obvious and in addition to the new dual-target NAATs from Roche and Abbott, and BD ProbeTec ET, also a number of new CE mark-certified commercial tests from smaller diagnostic companies as well as many different in house NAATs were used. Laboratories using commercial or in house NAATs that do not detect the nvCT are encouraged to carefully monitor their C. trachomatis incidence, participate in appropriate external quality assurance and controls schemes, and consider altering their testing system. The reliable detection of low amounts of the wildtype C. trachomatis strain in other samples of the ring trial set indicates a good diagnostic performance of all applied commercial NAATs while also detecting the nvCT strain.

The prevalence of genital Chlamydia trachomatis in Australia 1997 - 2004: a systematic review

To determine by systematic review the prevalence of genital chlamydial infection in Australia between 1997 and 2004. Electronic literature databases, reference lists, and conference proceedings were searched and health agencies and jurisdictions were contacted for published and unpublished reports. Studies were eligible if they offered a diagnostic nucleic acid amplification test to consecutive individuals presenting during the study period. As a summary measure of the available data, mean prevalence rates, weighted by sample size and irrespective of participant age, were calculated for the population sub-groups. 40 studies of 50 populations and 40,587 individuals met the inclusion criteria, but only one of these was population-based. The use of non-systematic methodologies prevented an assessment of time trends and a statistical comparison of population sub-groups. The mean overall prevalence of genital chlamydial infection was 4.6% (95% CI 4.4-4.8%), reflecting over-sampling of high-risk groups. The mean community-based rates were 7.5% (95% CI 6.4-8.6%) and 8.7% (95% CI 7.9-9.7%) for Indigenous men and women, and 1.5% (95% CI 1.1-1.9%) and 1.4% (95% CI 0.9-2.0%) for non-Indigenous men and women. The overall mean estimates for other groups were 3.3% (95% CI 3.0-3.7%) for female attendees of sexual health and related clinics, 5.6% (95% CI 4.9-6.4%) for adolescents and young adults, 3.3% (95% CI 2.8-3.9%) for sex workers, and 1.6% (95% CI 1.2-2.0%) for urethral infection in men who have sex with men. Clinic-based estimates were generally, although not consistently, higher than community-based estimates. There is no serial population-based data for sexually active young men and women, but the available age-specific rates suggest under-ascertainment by the routine surveillance systems. The prevalence of genital chlamydial infection in Indigenous Australians and young adults is unacceptably high and quality epidemiological studies are urgently required to supplement the routinely collected national notification data.

Use of applied biosystems 7900HT sequence detection system and Taqman assay for detection of quinolone-resistant Neisseria gonorrhoeae.

Mutations in quinolone resistance-determining regions (QRDRs) have been associated with quinolone-resistant Neisseria gonorrhoeae (QRNG). Since diagnostic nucleic acid amplification tests for gonococci are now in frequent use, molecular detection of QRNG could facilitate surveillance in the absence of culture. Here we describe a real-time molecular assay for detecting QRDR mutations in gonococci.