Respiratory virus coinfections with severe acute respiratory coronavirus virus 2 (SARS-CoV-2) continue to be rare one year into the coronavirus disease 2019 (COVID-19) pandemic in Alberta, Canada (June 2020-May 2021).

To assess the burden of respiratory virus coinfections with severe acute respiratory coronavirus virus 2 (SARS-CoV-2), this study reviewed 4,818 specimens positive for SARS-CoV-2 and tested using respiratory virus multiplex testing. Coinfections with SARS-CoV-2 were uncommon (2.8%), with enterovirus or rhinovirus as the most prevalent target (88.1%). Respiratory virus coinfection with SARS-CoV-2 remains low 1 year into the coronavirus disease 2019 (COVID-19) pandemic.

Evaluation of the ID NOW among symptomatic individuals during the Omicron wave.

Introduction. Starting in December, 2020, the ID NOW was implemented throughout the province of Alberta, Canada (population 4.4 million) in various settings.Gap statement. ID NOW's test performance with SARS-CoV-2 Omicron variant BA.1 is unknown.Aim. To assess the ID NOW performance among symptomatic individuals during the BA.1 Omicron wave and compare it to previous SARS-CoV-2 variant waves.Methodology. The ID NOW was assessed in two locations among symptomatic individuals: rural hospitals and community assessment centres (AC) during the period 5-18 January 2022. Starting 5 January, Omicron represented >95 % of variants detected in our population. For every individual tested, two swabs were collected: one for ID NOW testing and the other for either reverse-transcriptase polymerase chain reaction (RT-PCR) confirmation of negative ID NOW results or for variant testing of positive ID NOW results.Results. A total of 3041 paired samples were analysed (1139 RT-PCR positive). From this, 1873 samples were from 42 COVID-19 AC and 1168 from 69 rural hospitals. ID NOW sensitivity for symptomatic individuals presenting to community AC and rural hospitals was 96.0 % [95 % confidence interval (CI) 94.5-97.3 %, n=830 RT-PCR positive], and 91.6 % (95 % CI 87.9-94.4 %, n=309 RT-PCR positive), respectively. SARS-CoV-2 positivity rate was very high for both populations (44.3 % at AC, 26.5 % in hospital).Conclusions. Sensitivity of ID NOW SARS-CoV-2, compared to RT-PCR, is very high during the BA.1 Omicron wave, and is significantly higher when compared to previous SARS-CoV-2 variant waves.

Prospective population-level validation of the Abbott ID NOW severe acute respiratory syndrome coronavirus 2 device implemented in multiple settings for testing asymptomatic and symptomatic individuals.

OBJECTIVE: Diagnostic evaluation of the ID NOW coronavirus disease 2019 (COVID-19) assay in various real-world settings among symptomatic and asymptomatic individuals. METHODS: Depending on the setting, the ID NOW testing was performed using oropharyngeal swabs (OPSs) taken from patients with symptoms suggestive of COVID-19, asymptomatic close contacts, or asymptomatic individuals as part of outbreak point prevalence screening. From January to April 2021, a select number of sites switched from using OPS to combined oropharyngeal and nasal swab (O + NS) for ID NOW testing. For every individual tested, two swabs were collected by a health care worker: one swab (OPS or O + NS) for ID NOW testing and a separate swab (OPS or nasopharyngeal swab) for RT-PCR. RESULTS: A total of 129 112 paired samples were analysed (16 061 RT-PCR positive). Of these, 81 697 samples were from 42 COVID-19 community collection sites, 16 924 samples were from 69 rural hospitals, 1927 samples were from nine emergency shelters and addiction treatment facilities, 23 802 samples were from six mobile units that responded to 356 community outbreaks, and 4762 O + NS swabs were collected from three community collection sites and one emergency shelter. The ID NOW assay sensitivity was the highest among symptomatic individuals presenting to community collection sites (92.5%; 95% CI, 92.0-93.0%) and the lowest for asymptomatic individuals associated with community outbreaks (73.9%; 95% CI, 69.8-77.7%). Specificity was >99% in all populations tested. DISCUSSION: The sensitivity of ID NOW severe acute respiratory syndrome coronavirus 2 testing is the highest when used in symptomatic community populations not seeking medical care. Sensitivity and positive predictive value drop by approximately 10% when tested on asymptomatic populations. Using combined oropharyngeal and nasal swabs did not improve the performance of ID NOW assay.

Face Masks Impact Auditory and Audiovisual Consonant Recognition in Children With and Without Hearing Loss.

Teachers and students are wearing face masks in many classrooms to limit the spread of the coronavirus. Face masks disrupt speech understanding by concealing lip-reading cues and reducing transmission of high-frequency acoustic speech content. Transparent masks provide greater access to visual speech cues than opaque masks but tend to cause greater acoustic attenuation. This study examined the effects of four types of face masks on auditory-only and audiovisual speech recognition in 18 children with bilateral hearing loss, 16 children with normal hearing, and 38 adults with normal hearing tested in their homes, as well as 15 adults with normal hearing tested in the laboratory. Stimuli simulated the acoustic attenuation and visual obstruction caused by four different face masks: hospital, fabric, and two transparent masks. Participants tested in their homes completed auditory-only and audiovisual consonant recognition tests with speech-spectrum noise at 0 dB SNR. Adults tested in the lab completed the same tests at 0 and/or -10 dB SNR. A subset of participants from each group completed a visual-only consonant recognition test with no mask. Consonant recognition accuracy and transmission of three phonetic features (place of articulation, manner of articulation, and voicing) were analyzed using linear mixed-effects models. Children with hearing loss identified consonants less accurately than children with normal hearing and adults with normal hearing tested at 0 dB SNR. However, all the groups were similarly impacted by face masks. Under auditory-only conditions, results were consistent with the pattern of high-frequency acoustic attenuation; hospital masks had the least impact on performance. Under audiovisual conditions, transparent masks had less impact on performance than opaque masks. High-frequency attenuation and visual obstruction had the greatest impact on place perception. The latter finding was consistent with the visual-only feature transmission data. These results suggest that the combination of noise and face masks negatively impacts speech understanding in children. The best mask for promoting speech understanding in noisy environments depend on whether visual cues will be accessible: hospital masks are best under auditory-only conditions, but well-fit transparent masks are best when listeners have a clear, consistent view of the talker's face.

Evolving strategy for an evolving virus: Development of real-time PCR assays for detecting all SARS-CoV-2 variants of concern.

In order to detect the SARS-CoV-2 variants of concern (VOCs), five real-time reverse transcriptase PCR (rRT-PCR) assays were designed to target the critical discriminatory mutations responsible for the following amino acid changes in the spike protein: two Δ69-70 + N501Y + E gene triplexes (one optimized for Alpha [B.1.1.7] and one optimized for Omicron [B.1.1.529]), a K417N + 242-244 wild-type duplex, a K417T + E484K duplex, and a L452R + P681 + E484Q triplex. Depending on the assay, sensitivity was 98.97-100% for the detection of known VOC-positive samples, specificity was 97.2-100%, limit of detection was 2-116 copies/reaction, intra- and interassay variability was less than 5%, and no cross-reactivity with common respiratory pathogens was observed with any assay. A subset of rRT-PCR- positive VOC samples were further characterized by genome sequencing. A comparison of the lineage designation by the VOC rRT-PCR assays and genome sequencing for the detection of the Alpha, Beta, Gamma, Delta and Omicron variants showed clinical sensitivities of 99.97-100 %, clinical specificities of 99.6-100 %, positive predictive values of 99.8-100%, and negative predictive values of 99.98-100 %. We have implemented these rRT-PCR assays targeting discriminatory single nucleotide polymorphisms for ongoing VOC screening of SARS-CoV-2 positive samples for surveillance purposes. This has proven extremely useful in providing close to real-time molecular surveillance to monitor the emergence of Alpha, the replacement of Alpha by Delta, and the replacement of Delta by Omicron. While the design, validation and implementation of the variant specific PCR targets is an ever-evolving approach, we find the turn-around-time, high throughput and sensitivity to be a useful complementary approach for SARS-CoV-2 genome sequencing for surveillance purposes in the province of Alberta, Canada.

Effects of word familiarity and receptive vocabulary size on speech-in-noise recognition among young adults with normal hearing.

Having a large receptive vocabulary benefits speech-in-noise recognition for young children, though this is not always the case for older children or adults. These observations could indicate that effects of receptive vocabulary size on speech-in-noise recognition differ depending on familiarity of the target words, with effects observed only for more recently acquired and less frequent words. Two experiments were conducted to evaluate effects of vocabulary size on open-set speech-in-noise recognition for adults with normal hearing. Targets were words acquired at 4, 9, 12 and 15 years of age, and they were presented at signal-to-noise ratios (SNRs) of -5 and -7 dB. Percent correct scores tended to fall with increasing age of acquisition (AoA), with the caveat that performance at -7 dB SNR was better for words acquired at 9 years of age than earlier- or later-acquired words. Similar results were obtained whether the AoA of the target words was blocked or mixed across trials. Differences in word duration appear to account for nonmonotonic effects of AoA. For all conditions, a positive correlation was observed between recognition and vocabulary size irrespective of target word AoA, indicating that effects of vocabulary size are not limited to recently acquired words. This dataset does not support differential assessment of AoA, lexical frequency, and other stimulus features known to affect lexical access.

Influence of Postponed Follow-Up after Cochlear Implant Activation during the COVID-19 Pandemic on Aided Sound Field Detection and Speech Recognition.

INTRODUCTION: The objective of this study was to assess the influence of postponing the first post-activation follow-up due to the COVID-19 pandemic on the aided sound field detection thresholds and speech recognition of cochlear implant (CI) users. METHODS: A retrospective review was performed at a tertiary referral center. Two groups of adult CI recipients were evaluated: (1) patients whose first post-activation follow-up was postponed due to COVID-19 closures (postponed group; n = 10) and (2) a control group that attended recommended post-activation follow-ups prior to the COVID-19 pandemic (control group; n = 18). For both groups, electric thresholds were estimated at initial activation based on comfort levels and were measured behaviorally at subsequent post-activation follow-ups. For the control group, behavioral thresholds were measured at the 1-month follow-up. For the postponed group, behavioral thresholds were not measured until 3 months post-activation since the 1-month follow-up was postponed. The aided pure-tone average (PTA) and word recognition results were compared between groups at the 3-month follow-up and at an interim visit 2-9 weeks later. RESULTS: At the 3-month follow-up, the postponed group had significantly poorer word recognition (23 vs. 42%, p = 0.027) and aided PTA (42 vs. 37 dB HL, p = 0.041) than the control group. No significant differences were observed between 3-month data from the control group and interim data from the postponed group. CONCLUSIONS: The postponed follow-up after CI activation was associated with poorer outcomes, both in terms of speech recognition and aided audibility. However, these detrimental effects were reversed following provision of an individualized map, with behaviorally measured electric threshold and comfort levels. While adult CI recipients demonstrate an improvement in speech recognition with estimated electric thresholds, the present results suggest that behavioral mapping within the initial weeks of device use may support optimal outcomes.

Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance.

SARS-CoV-2 variants of concern (VOCs) have emerged as a global threat to the COVID-19 pandemic response. We implemented a combined approach to quickly detect known VOCs while continuously monitoring for evolving mutations of the virus. To rapidly detect VOCs, two real-time reverse transcriptase PCR assays were designed and implemented, targeting the spike gene H69/V70 deletion and the N501Y mutation. The H69/V70 deletion and N501Y mutation assays demonstrated accuracies of 98.3% (95% CI 93.8 to 99.8) and 100% (95% CI 96.8 to 100), limits of detection of 1,089 and 294 copies/ml, and percent coefficients of variation of 0.08 to 1.16% and 0 to 2.72% for the two gene targets, respectively. No cross-reactivity with common respiratory pathogens was observed with either assay. Implementation of these tests allowed the swift escalation in testing for VOCs from 2.2% to ∼100% of all SARS-CoV-2-positive samples over 12 January to 9 February 2021, and resulted in the detection of a rapid rise of B.1.1.7 cases within the province of Alberta, Canada. A prospective comparison of the VOC assays to genome sequencing for the detection of B.1.1.7, combined detection of P.1 and B.1.351, and wild-type (i.e., non-VOC) lineages showed sensitivities of 98.2 to 100%, specificities of 98.9 to 100%, positive predictive values of 76.9% to 100%, and negative predictive values of 96 to 100%. Variant screening results inform sampling strategies for regular surveillance by genome sequencing, thus allowing rapid identification of known VOCs while continuously monitoring the evolution of SARS-CoV-2 in the province. IMPORTANCE Different strains, or variants, of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, the virus that causes COVID-19) have emerged that have higher levels of transmission, less susceptibility to our immune response, and possibly cause more severe disease than previous strains of the virus. Rapid detection of these variants of concern is important to help contain them and prevent them from spreading widely within the population. This study describes two newly developed tests that are able to identify and differentiate the variants of concern from regular strains of SARS-CoV-2. These tests are faster and simpler than the main, gold standard method of identifying variants of concern (genome sequencing). These tests also demonstrated a high correlation with genome sequencing and allowed for the rapid and accurate detection of the rise of B.1.1.7 (one of the variants of concern) in the province of Alberta, Canada.

Influence of Protective Face Coverings on the Speech Recognition of Cochlear Implant Patients.

OBJECTIVES: The objectives were to characterize the effects of wearing face coverings on: 1) acoustic speech cues, and 2) speech recognition of patients with hearing loss who listen with a cochlear implant. METHODS: A prospective cohort study was performed in a tertiary referral center between July and September 2020. A female talker recorded sentences in three conditions: no face covering, N95 mask, and N95 mask plus a face shield. Spectral differences were analyzed between speech produced in each condition. The speech recognition in each condition for twenty-three adult patients with at least 6 months of cochlear implant use was assessed. RESULTS: Spectral analysis demonstrated preferential attenuation of high-frequency speech information with the N95 mask plus face shield condition compared to the other conditions. Speech recognition did not differ significantly between the uncovered (median 90% [IQR 89%-94%]) and N95 mask conditions (91% [IQR 86%-94%]; P = .253); however, speech recognition was significantly worse in the N95 mask plus face shield condition (64% [IQR 48%-75%]) compared to the uncovered (P < .001) or N95 mask (P < .001) conditions. CONCLUSIONS: The type and combination of protective face coverings used have differential effects on attenuation of speech information, influencing speech recognition of patients with hearing loss. In the face of the COVID-19 pandemic, there is a need to protect patients and clinicians from spread of disease while maximizing patient speech recognition. The disruptive effect of wearing a face shield in conjunction with a mask may prompt clinicians to consider alternative eye protection, such as goggles, in appropriate clinical situations. LEVEL OF EVIDENCE: 3 Laryngoscope, 131:E2038-E2043, 2021.

Evaluation of Six Commercial Mid- to High-Volume Antibody and Six Point-of-Care Lateral Flow Assays for Detection of SARS-CoV-2 Antibodies.

Coronavirus disease (COVID) serological tests are essential to determine the overall seroprevalence of a population and to facilitate exposure estimates within that population. We performed a head-to-head assessment of enzyme immunoassays (EIAs) and point-of-care lateral flow assays (POCTs) to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies. Demographics, symptoms, comorbidities, treatment, and mortality of patients whose sera were used were also reviewed. Six EIAs (Abbott, Affinity, Bio-Rad, DiaSorin, Euroimmun, and Roche) and six POCTs (BTNX, Biolidics, Deep Blue, Genrui, Getein BioTech, and Innovita) were evaluated for the detection of SARS-CoV-2 antibodies in known COVID-19-infected individuals. Sensitivity of EIAs ranged from 50 to 100%, with only four assays having overall sensitivities of >95% after 21 days after symptom onset. Notably, cross-reactivity with other respiratory viruses (parainfluenza virus [PIV-4] [n = 5], human metapneumovirus [hMPV] [n = 3], rhinovirus/enterovirus [n = 1], CoV-229E [n = 2], CoV-NL63 [n = 2], and CoV-OC43 [n = 2]) was observed; however, overall specificity of EIAs was good (92 to 100%; all but one assay had specificity above 95%). POCTs were 0 to 100% sensitive >21 days after onset, with specificity ranging from 96 to 100%. However, many POCTs had faint banding and were often difficult to interpret. Serology assays can detect SARS-CoV-2 antibodies as early as 10 days after symptom onset. Serology assays vary in their sensitivity based on the marker (IgA/IgM versus IgG versus total) and by manufacturer; however, overall only 4 EIAs and 4 POCTs had sensitivities of >95% >21 days after symptom onset. Cross-reactivity with other seasonal coronaviruses is of concern. Serology assays should not be used for the diagnosis of acute infection but rather in carefully designed serosurveys to facilitate understanding of seroprevalence in a population and to identify previous exposure to SARS-CoV-2.