Determination of the cycle threshold value of the Xpert Xpress SARS-CoV-2/Flu/RSV test that corresponds to the presence of infectious SARS-CoV-2 in anterior nasal swabs.

Despite having high analytical sensitivities and specificities, qualitative SARS-CoV-2 nucleic acid amplification tests (NAATs) cannot distinguish infectious from non-infectious virus in clinical samples. In this study, we determined the highest cycle threshold (Ct) value of the SARS-CoV-2 targets in the Xpert Xpress SARS-CoV-2/Flu/RSV (Xpert 4plex) test that corresponded to the presence of detectable infectious SARS-CoV-2 in anterior nasal swab samples. A total of 111 individuals with nasopharyngeal swab specimens that were initially tested by the Xpert Xpress SARS-CoV-2 test were enrolled. A healthcare worker subsequently collected anterior nasal swabs from all SARS-CoV-2-positive individuals, and those specimens were tested by the Xpert 4plex test, viral culture, and laboratory-developed assays for SARS-CoV-2 replication intermediates. SARS-CoV-2 Ct values from the Xpert 4plex test were correlated with data from culture and replication intermediate testing to determine the Xpert 4plex assay Ct value that corresponded to the presence of infectious virus. Ninety-eight of the 111 (88.3%) individuals initially tested positive by the Xpert Xpress SARS-CoV-2 test. An anterior nasal swab specimen collected from positive individuals a median of 2 days later (range, 0-9 days) tested positive for SARS-CoV-2 by the Xpert 4plex test in 39.8% (39/98) of cases. Of these samples, 13 (33.3%) were considered to contain infectious virus based on the presence of cultivable virus and replication intermediates, and the highest Ct value observed for the Xpert 4plex test in these instances was 26.3. Specimens that yielded Ct values of ≤26.3 when tested by the Xpert 4plex test had a likelihood of containing infectious SARS-CoV-2; however, no infectious virus was detected in specimens with higher Ct values.IMPORTANCEUnderstanding the correlation between real-time PCR test results and the presence of infectious SARS-CoV-2 may be useful for informing patient management and workforce return-to-work or -duty. Further studies in different patient populations are needed to correlate Ct values or other biomarkers of viral replication along with the presence of infectious virus in clinical samples.

Two novel recombinant human mastadenovirus D genotypes associated with acute respiratory illness.

Two novel genotypes of species human mastadenovirus D designated 109 and 110 were isolated from three epidemiologically unrelated cases of acute respiratory disease detected in January 2018 by surveillance efforts at the California/Mexico border. Both genotypes represent examples of intertypic recombination. Genotype D109 is most closely related to genotype D56 (97.68% genomic similarity) and features a type D22-like penton base, a type D19-like hexon gene, and a type D9-like fiber [P22/H19/F9]. On the other hand, genotype D110 is most closely related to type D22 (96.94% genomic similarity) and features a type D67-like penton base, a novel hexon gene, and a type D9-like fiber [P67/H110/F9]. Importantly, the fibers of both novel genotypes are highly similar to those of genotypes D56 and D59, which have also been isolated from a few cases of respiratory infections. The present report shows data contributing to the understanding of the molecular determinants of the expanded tissue tropism of certain members of species HAdV-D.

Spotted fever group rickettsiae canine serosurveillance near the US-Mexico border in California.

BACKGROUND: Dogs are vulnerable to pathogens transmitted by brown dog ticks. An epidemic of Rocky Mountain spotted fever (RMSF) is underway in Mexicali, a Mexican city bordering California affecting people and dogs; several human cases have been reported in California residents who travelled to Mexico. To evaluate risks of RMSF, we conducted seroprevalence surveys in Imperial County in 2016 and 2017 using dogs as sentinels. METHODS: Blood was collected from 752 dogs and was tested for antibodies against R. rickettsii, E. canis and A. phagocytophilum (as a proxy for A. platys). Samples were considered seropositive to spotted fever group rickettsia (SFGR) if the R. rickettsia titre was ≥1:64 and seropositive to E. canis and A. phagocytophilum if the titre was ≥1:32. Owners provided information on dog age, exposure risks, health status and tick prevention. We assessed associations between SFGR seropositivity and driving distance to the nearest US-Mexico border crossing station, whether proximity to a border crossing increased likelihood of taking dogs across the border, and whether distance to the border was associated with seropositivity. Logistic regression was performed to assess relationships between the titre classes and other predictor variables. RESULTS: 12.2% of dogs were seropositive against SFGR. Dogs close to the border were significantly more likely to be taken across the border and to be seropositive. Risk factors that increased seropositivity included owners seeing ticks on the dog (OR = 1.9), being an adult dog, travel to Mexico (OR = 3.0) and living in a rural area (OR = 4.0). There was statistically significant co-exposure to SFGR and Anaplasma spp. CONCLUSION: Surveillance for brown dog tick-vectored pathogens can help identify dogs and people at risk for RMSF. Tick prevention, particularly in dogs, and surveillance of tick-borne pathogens can help prevent the spread of rickettsioses and other diseases in this dynamic border region.