Viral Etiological Agent(s) of Respiratory Tract Infections in Symptomatic Individuals during the Second Wave of COVID-19 Pandemic: A Single Drive-Thru Mobile Collection Site Study

Abstract

One of the tools to contain the SARS-CoV-2 pandemic was to increase the number of performed tests and to improve the access to diagnostics. To this effect, mobile collection sites (MCSs) were established. This study was performed on samples collected at the MCS between November 2020 and March 2021. We aimed to confirm/exclude SARS-CoV-2, differentiate SARS-CoV-2 variants, and detect other respiratory pathogens. SARS-CoV-2 and other respiratory viruses were identified by RT-qPCRs. A total of 876 (46.35%) SARS-CoV-2 positive specimens in the diagnostic tests were identified. The wild-type variant was determined in 667 (76.14%) samples; the remaining 209 (23.86%) samples specimens were identified as Alpha variant. A total of 51 (5.6%) non-SARS-CoV-2 cases were detected in retrospective studies. These accounted for 33 cases of mono-infection including rhinovirus (RV), human adenovirus (HAdV), human metapneumovirus (HMPV), enterovirus (EV), and influenza virus, and 18 cases of co-infection (SARS-CoV-2 with RV or HAdV or HMPV, and RV with EV). Our research shows that the results obtained from the MCS have value in epidemiological studies, reflecting national trends on a micro scale. Although the spread of COVID-19 is a major public health concern, SARS-CoV-2 is not the only pathogen responsible for respiratory infections.

Differentiation of SARS-CoV-2 Variants Using RT-qPCRs by Targeting Recurrent Mutation Sites: A Diagnostic Laboratory Experience from Multi-Center Regional Study, August 2020–December 2021, Poland

“…The first illness peak appeared in October–November 2020 (first wave), followed by another in February–March 2021 (second wave), and then October–December 2021 (third wave). The number of positive SARS-CoV-2 cases identified during the routine diagnostics in the NMI reflected a nationwide trend, with peaks in the first and second waves, as we already noted in our previously report [ 29 ]. A renewed increase in the number of positive samples occurred in the autumn/winter period (full data not shown, partial data in Figure 1 ), coinciding with the time of the third wave of COVID-19 in the country.…”

“…Interestingly, previous data reported that this variant appeared in Poland in December 2020 [ 37 , 42 ]. Since its emergence, the Alpha variant has gradually increased its proportion in the following months, as we already observed in our previous survey [ 29 ]. Between March and June 2021, the variant accounted for more than 92% of all recognized cases; this finding also reflects national data, in which the Alpha variant was responsible for the second wave of the epidemic [ 42 ].…”

“…A limitation of the study was that not all samples were examined, but only those for which the CT values of the analyzed genes in RT-qPCRs were less than 30. Therefore, in the remaining cases, a specific variants were not defined, potentially underestimating their numbers; this is evidenced by our earlier study, that included all positive samples from the mobile collection site from this study (MCS1) [ 29 ]; however, it should be noted that the prevalence of the Alpha variant in the overall virus population remained similar in both investigations.…”

“…There are only few publications tracing SARS-CoV-2 variants in Poland [ 29 , 34 , 35 , 36 , 37 ]. Most of them based on analysis of viral genomic data deposited at the Global Initiative on Sharing All Influenza Data (GISAID) [ 5 ]; it currently contains 83,764 sequences from Poland [ 5 ].…”

Implementation of a Mobile Application based on the Convolutional Neural Network for the Diagnosis of Pneumonia

“…Respiratory infections contribute to high mortality rates worldwide, accounting for more than 4.5 million deaths per year, especially in low-and middle-income countries [1]. These infections cause upper respiratory tract diseases such as rhinitis, sinusitis, pharyngitis, and lower respiratory tract diseases such as bronchitis and pneumonia [2].…”