Perepliotchikov Yuri, Ziv-Baran Tomer, Hindiyeh Musa, Manor Yossi, Sofer Danit, Moran-Gilad Jacob, Stephens Laura, Mendelson Ella, Weil Merav, Bassal Ravit, Anis Emilia, Singer Shepherd Roee, Kaliner Ehud, Cooper Gillian, Majumdar Manasi, Markovich Michal, Ram Daniela, Grotto Itamar, Gamzu Ronni, Martin Javier, Shulman Lester M
Central Virology Laboratory, Sheba Medical Center, Tel Hashomer, Ramat Gan 52621, Israel.
School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel.
Vaccines (Basel). 2021 Aug 6;9(8):870. doi: 10.3390/vaccines9080870.
Response to and monitoring of viral outbreaks can be efficiently focused when rapid, quantitative, kinetic information provides the location and the number of infected individuals. Environmental surveillance traditionally provides information on location of populations with contagious, infected individuals since infectious poliovirus is excreted whether infections are asymptomatic or symptomatic. Here, we describe development of rapid (1 week turnaround time, TAT), quantitative RT-PCR of poliovirus RNA extracted directly from concentrated environmental surveillance samples to infer the number of infected individuals excreting poliovirus. The quantitation method was validated using data from vaccination with bivalent oral polio vaccine (bOPV). The method was then applied to infer the weekly number of excreters in a large, sustained, asymptomatic outbreak of wild type 1 poliovirus in Israel (2013) in a population where >90% of the individuals received three doses of inactivated polio vaccine (IPV). Evidence-based intervention strategies were based on the short TAT for direct quantitative detection. Furthermore, a TAT shorter than the duration of poliovirus excretion allowed resampling of infected individuals. Finally, the method documented absence of infections after successful intervention of the asymptomatic outbreak. The methodologies described here can be applied to outbreaks of other excreted viruses such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), where there are (1) significant numbers of asymptomatic infections; (2) long incubation times during which infectious virus is excreted; and (3) limited resources, facilities, and manpower that restrict the number of individuals who can be tested and re-tested.
当快速、定量的动力学信息能够提供感染个体的位置和数量时，对病毒爆发的应对和监测就能高效地聚焦。传统的环境监测可提供有关具有传染性的感染个体所在人群位置的信息，因为无论感染是无症状还是有症状，传染性脊髓灰质炎病毒都会排出体外。在此，我们描述了一种快速（周转时间为1周，TAT）的脊髓灰质炎病毒RNA定量逆转录聚合酶链反应（RT-PCR）方法，该方法直接从浓缩的环境监测样本中提取RNA，以推断排出脊髓灰质炎病毒的感染个体数量。使用来自双价口服脊髓灰质炎疫苗（bOPV）接种的数据对定量方法进行了验证。然后将该方法应用于推断以色列2013年大规模、持续、无症状的野生型1型脊髓灰质炎病毒爆发中每周的病毒排出者数量，该人群中超过90%的个体接种了三剂灭活脊髓灰质炎疫苗（IPV）。基于证据的干预策略基于直接定量检测的短周转时间。此外，短于脊髓灰质炎病毒排出持续时间的周转时间允许对感染个体进行重新采样。最后，该方法记录了无症状爆发成功干预后无感染情况。这里描述的方法可应用于其他排出病毒的爆发，如严重急性呼吸综合征冠状病毒2（SARS-CoV-2），其中存在（1）大量无症状感染；（2）在排出传染性病毒期间有较长的潜伏期；以及（3）资源、设施和人力有限，限制了可检测和重新检测的个体数量。
