Division of Diagnostic and Applied Microbiology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 2B4.01, Walter C. Mackenzie Centre, Provincial Laboratory of Public Health, 8440 - 112 Street, Edmonton, AB, T6G 2J2, Canada.
Alberta Precision Laboratories - Public Health Laboratory (ProvLab), Edmonton, AB, Canada.
Virol J. 2021 May 1;18(1):93. doi: 10.1186/s12985-021-01545-9.
SARS-CoV-2 infection can present with a broad clinical differential that includes many other respiratory viruses; therefore, accurate tests are crucial to distinguish true COVID-19 cases from pathogens that do not require urgent public health interventions. Co-circulation of other respiratory viruses is largely unknown during the COVID-19 pandemic but would inform strategies to rapidly and accurately test patients with respiratory symptoms.
This study retrospectively examined 298,415 respiratory specimens collected from symptomatic patients for SARS-CoV-2 testing in the three months since COVID-19 was initially documented in the province of Alberta, Canada (March-May, 2020). By focusing on 52,285 specimens that were also tested with the Luminex Respiratory Pathogen Panel for 17 other pathogens, this study examines the prevalence of 18 potentially co-circulating pathogens and their relative rates in prior years versus since COVID-19 emerged, including four endemic coronaviruses.
SARS-CoV-2 was identified in 2.2% of all specimens. Parallel broad multiplex testing detected additional pathogens in only 3.4% of these SARS-CoV-2-positive specimens: significantly less than in SARS-CoV-2-negative specimens (p < 0.0001), suggesting very low rates of SARS-CoV-2 co-infection. Furthermore, the overall co-infection rate was significantly lower among specimens with SARS-CoV-2 detected (p < 0.0001). Finally, less than 0.005% of all specimens tested positive for both SARS-CoV-2 and any of the four endemic coronaviruses tested, strongly suggesting neither co-infection nor cross-reactivity between these coronaviruses.
Broad respiratory pathogen testing rarely detected additional pathogens in SARS-CoV-2-positive specimens. While helpful to understand co-circulation of respiratory viruses causing similar symptoms as COVID-19, ultimately these broad tests were resource-intensive and inflexible in a time when clinical laboratories face unprecedented demand for respiratory virus testing, with further increases expected during influenza season. A transition from broad, multiplex tests toward streamlined diagnostic algorithms targeting respiratory pathogens of public health concern could simultaneously reduce the overall burden on clinical laboratories while prioritizing testing of pathogens of public health importance. This is particularly valuable with ongoing strains on testing resources, exacerbated during influenza seasons.
SARS-CoV-2 感染可能表现出广泛的临床差异，其中包括许多其他呼吸道病毒；因此，准确的检测对于将真正的 COVID-19 病例与不需要紧急公共卫生干预的病原体区分开来至关重要。在 COVID-19 大流行期间，其他呼吸道病毒的共同传播情况在很大程度上尚不清楚，但这将为制定策略提供信息，以便快速准确地检测有呼吸道症状的患者。
本研究回顾性分析了自 2020 年 3 月加拿大艾伯塔省首次记录 COVID-19 以来的三个月内，298415 份有症状患者的呼吸道标本进行 SARS-CoV-2 检测。通过重点关注 52285 份同时使用 Luminex 呼吸道病原体检测试剂盒检测了 17 种其他病原体的标本，本研究检查了 18 种潜在共同传播病原体的流行率及其相对于前几年和 COVID-19 出现以来的相对比率，包括四种内源性冠状病毒。
SARS-CoV-2 在所有标本中的检出率为 2.2%。平行的广谱多重检测仅在 SARS-CoV-2 阳性标本的 3.4%中检测到其他病原体：显著低于 SARS-CoV-2 阴性标本（p<0.0001），表明 SARS-CoV-2 合并感染率非常低。此外，在检测到 SARS-CoV-2 的标本中，总体合并感染率显著较低（p<0.0001）。最后，所有检测标本中，同时检测到 SARS-CoV-2 和四种内源性冠状病毒中任何一种的标本不到 0.005%，强烈表明这些冠状病毒之间没有合并感染或交叉反应。
广谱呼吸道病原体检测很少在 SARS-CoV-2 阳性标本中检测到其他病原体。虽然有助于了解引起 COVID-19 类似症状的呼吸道病毒的共同传播，但最终这些广谱检测在临床实验室面临前所未有的呼吸道病毒检测需求时既耗费资源又缺乏灵活性，预计在流感季节会进一步增加。从广谱、多重检测向针对公共卫生关注的呼吸道病原体的简化诊断算法的转变可以同时减轻临床实验室的整体负担，同时优先检测具有公共卫生重要性的病原体。在流感季节，检测资源紧张的情况下，这一点尤其有价值。
