Dynamics of respiratory viruses other than SARS-CoV-2 during the COVID-19 pandemic in Madrid, Spain.

The COVID-19 pandemic and the implemented control measures have impacted the circulation of respiratory-transmitted pathogens. In this report, we present data from a retrospective study that included 17,883 specimens conducted between 2018 and 2022 in our facility, describing the dynamics of circulation of the main respiratory viruses. We observed a significant decrease in all viral detections (other than SARS-CoV-2) starting from March 2020. However, rhinovirus maintained comparable levels to the pre-pandemic period. Additionally, influenza viruses were not detected during the 2020-2021 season, and respiratory syncytial virus (RSV) exhibited a shift in its seasonality, with an epidemic peak occurring in the summer of 2021.

The emergence, impact, and evolution of human metapneumovirus variants from 2014 to 2021 in Spain.

BACKGROUND: Human metapneumovirus (HMPV) is an important aetiologic agent of respiratory tract infection (RTI). This study aimed to describe the prevalence, genetic diversity, and evolutionary dynamics of HMPV. METHODS: Laboratory-confirmed HMPV were characterised based on partial-coding G gene sequences with MEGA.v6.0. WGS was performed with Illumina, and evolutionary analyses with Datamonkey and Nextstrain. RESULTS: HMPV prevalence was 2.5%, peaking in February-April and with an alternation in the predominance of HMPV-A and -B until the emergence of SARS-CoV-2, not circulating until summer and autumn-winter 2021, with a higher prevalence and with the almost only circulation of A2c111dup. G and SH proteins were the most variable, and 70% of F protein was under negative selection. Mutation rate of HMPV genome was 6.95 × 10-4 substitutions/site/year. CONCLUSION: HMPV showed a significant morbidity until the emergence of SARS-CoV-2 pandemic in 2020, not circulating again until summer and autumn 2021, with a higher prevalence and with almost the only circulation of A2c111dup, probably due to a more efficient immune evasion mechanism. The F protein showed a very conserved nature, supporting the need for steric shielding. The tMRCA showed a recent emergence of the A2c variants carrying duplications, supporting the importance of virological surveillance.

Detection of BK polyomavirus genotypes to predict the development of BK polyomavirus-associated complications in kidney transplant recipients: A retrospective analysis.

OBJECTIVES: This study focused on the role that BK polyomavirus (BKPyV) genotypes can play in the development of BKPyV-associated complications in renal transplant recipients. METHODS: A retrospective observational study (January 2015 to April 2018) was conducted by analyzing BKPyV genotypes in 180 blood samples with detectable BKPyV viral load (VL) > 1000 copies/mL, from 63 renal transplant recipients. VL and BKPyV genotypes detections were based on real-time PCR (rt-PCR)-specific assays. RESULTS: Forty-four patients (44/63 [69.8%]) were men, and the median age was 55.0 (interquartile range 49.0-66.0 years). Eleven patients had clinical manifestations (11/63 [17.5%]). The most frequently detected genotypes were I (14/63 [22.2%]) and II (13/63 [20.6%]). Half of the patients (33/63 [52.4%]) had a mixed genotype, most with genotypes I and II (25/33 [75.8%]). Patients with infection by mixed genotypes showed VLs that were detected earlier (in the first year after transplantation) than those with a single genotype (25/33 [75.8%] vs 13/30 [43.3%], P = .009) and demonstrated greater risk of developing clinical manifestations associated with BKPyV (odds ratio 12.609, 95% confidence interval 1.503-105.807). Moreover, patients with first BKPyV VL > 10 000 copies/mL more frequently presented mixed genotypes (12/16 [75.0%] vs 21/47 [44.7%], P = .036). CONCLUSIONS: The probability of developing clinical manifestations is higher in infections by mixed genotypes. Therefore, the detection of BKPyV genotypes by rt-PCR can provide relevant information to stratify patients' risk of BKPyV-associated complications and guide the clinical management of BKPyV infection in kidney transplant recipients.

Lack of clinical significance for molecular detection of respiratory viruses in bronchoalveolar lavage samples.

The clinical significance of molecular detection of respiratory viruses in bronchoalveolar lavage (BAL) samples is poorly defined. We performed an observational retrospective study including all patients who underwent a BAL procedure in our institution, regardless of the reason for bronchoscopy, from January 2015 to December 2018. Respiratory viruses were detected by real-time polymerase chain reaction with a commercial multiplex panel, and a cell culture was performed to detect cytomegalovirus and herpes simplex virus. Positive results were correlated with clinical symptoms and patients' characteristics. Of 540 BAL samples analyzed, 113 (20.9%) were positive for any respiratory virus. Viral detection was significantly associated with respiratory symptoms (83.2% vs. 68.9%, p = .004) and radiological infiltrates (67.3% vs. 52.2%, p = .006). The most frequent viruses detected were rhinovirus (42/113, 37.2%), influenza virus (20/113, 17.7%), and parainfluenza virus (PIV) (16/113, 14.2%). Respiratory pathogens codetections were found in 51/113 (45.1%) BAL samples, including more than one virus (16/51, 31.4%), fungi (8/51, 15.7%), and bacteria (9/51, 17.6%). Viral detection was significantly higher in immunocompromised patients (26.5% vs. 16.9%; p = .022). PIV and human metapneumovirus were mostly observed in lung (50.0%, 8/16) and hemopoietic transplant recipients (25%, 2/8), respectively, with clinical repercussions. Our data underline that molecular diagnosis allows identification of viral agents as the etiology of respiratory infections; however, the high frequency of codetections hinders identification of the agent responsible for the current respiratory symptomatology. Immunocompromised patients are the target population in whom to investigate the presence of respiratory viruses in their BAL samples.

Feasible alternatives to DBS in the retrospective diagnosis of congenital cytomegalovirus infection.

BACKGROUND: Retrospective diagnosis of congenital cytomegalovirus (cCMV) infection may be challenging mainly because of the high variable sensitivity of PCR on dried blood spots (DBS) samples. OBJECTIVES: To compare cytomegalovirus (CMV) viral load (VL) values in different samples obtained at birth from infants with cCMV infection. To evaluate dried umbilical cord (DUC) samples as an alternative to DBS. STUDY DESIGN: Saliva and/or urine, peripheral blood (PB), and DBS from 16 infants with confirmed cCMV infection were collected at birth. CMV VL were determined by DNA extraction and real-time polymerase chain reaction (rt-PCR). In two cases, VL was determined from DUC samples. RESULTS: Six (37.5 %) of the 16 infants were symptomatic, and 10 (62.5 %) were asymptomatic. The CMV VL found in saliva (median: 1,958,525 [IQR: 597,683-3,483,843] IU/mL) and in urine (median: 691,865 [IQR: 188,489.5-3,175,696] UI/mL) were both higher than those found in PB (median: 1115 [IQR: 364-4,002] IU/mL), p: 0.0001). Symptomatic infants presented 100 % of detectable VL in PB and 50 % in DBS. Asymptomatic infants showed 75 % of detectable VL in PB and 30 % in DBS. The VL in DUC were 22,341, 9754 IU/mL and 994 IU/mL. CONCLUSIONS: When VL was detectable in PB, the values were lower than in saliva or urine, in both symptomatic and asymptomatic cases of cCMV. The low sensitivity in DBS samples could be due to low blood volume content, making CMV VL undetectable even when using optimised extraction and PCR protocols. In our limited experience, DUC could play a complementary diagnostic role when DBS VL is undetectable.

Comparison of the Panther Fusion and Allplex assays for the detection of respiratory viruses in clinical samples.

Respiratory viral infections are the most frequent clinical syndrome affecting both children and adults, and early detection is fundamental to avoid infection-related risks and reduce the healthcare costs incurred by unnecessary antibiotic treatments. In this study, performance characteristics of two commercial methods, the Panther Fusion® assay (Hologic Inc., San Diego, CA, USA) were compared to Allplex™ respiratory panels (Seegene, Seoul, South Korea) for the detection of influenza A (Flu A), influenza B (Flu B), respiratory syncytial virus (RSV), parainfluenza virus (PIV), human metapneumovirus (hMPV), rhinovirus (RV) and adenovirus (AdV) targets. A total of 865 specimens collected prospectively and retrospectively were included, and discordant results were further examined using another commercial product, R-GENE™ respiratory kits (bioMérieux, Marcy l'Etoile, France). There was high agreement between both methods, with 98.6% concordance and a kappa (k) value of 0.9 (95% CI: 0.89-0.92). A specific analysis of both methods for each viral agent demonstrated comparable sensitivity and specificity, both ranging from 0.83 to 1 with good predictive values for the prospective part of the study. Good agreement between both methods was also found for the κ values obtained (ranging from 97.55% to 98.9%), with the lowest for hMPV (k = 0.83, 95% CI: 0.75-0.91) and RV (k = 0.73, 95% CI: 0.65-0.81). Amplification efficiency, measured according to the value of the cycle threshold (Ct) obtained in each of the amplifications in both tests, was significantly better with Panther Fusion for Flu A, Flu B, hMPV and RV. Regarding discordant results, R-GENE showed higher agreement with Panther Fusion-positive specimens (negative for Allplex; n = 28/71, 34.9%) than with Allplex-positive samples (negative for Panther Fusion; n = 7/49, 14.3%). In summary, Panther Fusion proved to be a more efficient fully-automated methodology, requiring shorter hands-on and turnaround times than Allplex.

BK virus viral load: analysis of the requests received by the microbiology laboratory and clinical involvement of the issued results.

Automation of viral diagnosis has led to an increase of BK virus (BKV) viral load (VL) requests. The aim of this study was to assess the suitability of serum creatinine (SCr) for controlling the demand and to study the clinical characteristics of BKV infection. This is a retrospective study including patients with BKV VL request during April-July 2017. Clinical records and SCr were analyzed. Five hundred samples from 333 patients were included; 61.4% of samples were from males (55.5 ± 14.8 years), and all belonged to transplant recipients (86.4% renal). BKV VL was detectable in 40 samples (8.0%) from 23 patients (6.9%), who presented high SCr (100% vs. 90.9%, P = 0.038). Most of detectable VLs (62.5%) belonged to patients in their first year post-transplant. Six patients with detectable VL (26.1%) developed clinical manifestations, most of them (83.3%) had a first BKV VL greater than 10,000 copies/mL (P = 0.001). In conclusion, SCr would be useful to identify suitable specimens for BKV VL testing without missing cases.