Poliovirus Laboratory Based Surveillance: An Overview

Evaluation of the Acute Flaccid Paralysis Virological Surveillance System in Polio-Free Morocco, 2010–2018

Background. The goal of Acute flaccid paralysis (AFP) surveillance is to comprehensively investigate and report any case of a child below 15 years with a floppy weakness. This is essential for the poliovirus eradication initiative. Objective. In this study, we analyzed the results of nine-year surveillance (2010–2018) of AFP in Morocco. Method. This was a descriptive, retrospective study of cases with AFP routinely documented at the National Referral Laboratory of Polio (NRLP) from 2010 to 2018. Results. Among the 884 AFP cases identified and analyzed, we identified 11 polioviruses as Sabin-like vaccine strains (PSL). PSL were isolated in 11 samples of AFP cases received at the laboratory, including one PSL1, three PSL2 + PSL3, one PSL1 + PSL2, and one PSL1 + 2 + 3. The annualized nonpolio AFP rate per 100,000 children under 15 years ranged from 0.84 during 2011–2015 to 2.29 in 2018. The stool adequacy indicator was poor and may be improved with better delivery times and maintaining the cold chain. The incidence of isolated nonpolio enteroviruses (NPEV) varied between 2.27% and 12.6%, with the average not exceeding 6.35%; the incidence remained low compared to the indicator set by the World Health Organization (WHO). Conclusion. Morocco was certified polio-free by WHO in 2015, and since then no cases of wild poliovirus have been reported. Overall, although the nonpolio AFP rate has risen to the WHO standard, stool adequacy and the proportion of nonpolio enteroviruses need to be improved. The laboratory can adopt alternative techniques, independent of cell culture, to ensure that imported cases of poliovirus are not missed, especially in this era of eradication.

Spatial analysis of genetic clusters and epidemiologic factors related to wild poliovirus type 1 persistence in Afghanistan and Pakistan

Following the certification of the World Health Organization Region of Africa as free of serotype 1 wild poliovirus (WPV1) in 2020, Afghanistan and Pakistan represent the last remaining WPV1 reservoirs. As efforts continue in these countries to progress to eradication, there is an opportunity for a deeper understanding of the spatiotemporal characteristics and epidemiological risk factors associated with continual WPV1 circulation in the region. Using poliovirus surveillance data from 2017-2019, we used pairwise comparisons of VP1 nucleotide sequences to illustrate the spatiotemporal WPV1 dispersal to identify key sources and destinations of potentially infected, highly mobile populations. We then predicted the odds of WPV1 detection at the district level using a generalized linear model with structural indicators of health, security, environment, and population demographics. We identified evidence of widespread population mobility based on WPV1 dispersal within and between the countries, and evidence indicating five districts in Afghanistan (Arghandab, Batikot, Bermel, Muhamandara and Nawzad) and four districts in Pakistan (Charsada, Dera Ismail Khan, Killa Abdullah and Khyber) act as cross-border WPV1 circulation reservoirs. We found that the probability of detecting WPV1 in a district increases with each armed conflict event (OR = 1·024, +- 0·008), level of food insecurity (OR = 1·531, +-0·179), and mean degrees Celsius during the months of greatest precipitation (OR = 1·079, +- 0·019). Our results highlight the multidisciplinary complexities contributing to the continued transmission of WPV1 in Afghanistan and Pakistan. We discuss the implications of our results, stressing the value of coordination during this final chapter of the wild polio virus eradication initiative.

Cell culture demonstrates superior sensitivity over one step real time RT PCR and nested VP1 amplification for Enteroviruses

This study evaluated and compared the sensitivity profile of routine cell culture, nested VP1 amplification and one step real time RT PCR for Enteroviruses. Serially diluted spiked samples of four model viruses (EV71, CVA16, CVB5 and PV1) and 32 true positive samples including Poliovirus (PV1 & PV3), Coxsackie virus (CVB5, CVB3, CVB1 & CVA4, 10, 16), Echovirus (Echo 6, 7, 11, 13, 18, 25 & 30) and Enterovirus 71 (E71), and 32 true negative stool samples were subjected to cell culture, nested RT PCR and one step real time RT PCR. The result of sensitivity test indicated superior sensitivity with one step real time RT PCR (75 %, 24/32) against cell culture (71.9 %, 23/32) and nested RT PCR (65.6 %, 21/32). The most specific test was cell culture (100 %, 32/32), followed by nested RT PCR (96.9 %, 31/32). Positive predictive values were 100 %: 23/23, 95.5 %; 21/22 and 88.9 %; 24/27, for cell culture, nested RT PCR and one step real time RT PCR, respectively, and one step real time RT PCR had the highest negative predictive value (78.4 %, 29/37). Overall result indicate relatively high analytical sensitivity with all the tests, suggesting superior performance by cell culture. Therefore, cell culture is the gold standard. However, considering intensive nature of cell cultures and prolong window for results, it is wise to consider one step real time RT PCR in routine diagnosis for its added advantages. Meanwhile, selecting a combination of tests can maximize detection, depending on the laboratory strength.

Surveillance and laboratory detection for non-polio enteroviruses in the European Union/European Economic Area, 2016

Enteroviruses (EVs) cause severe outbreaks of respiratory and neurological disease as illustrated by EV-D68 and EV-A71 outbreaks, respectively. We have mapped European laboratory capacity for identification and characterisation of non-polio EVs to improve preparedness to respond to (re)-emerging EVs linked to severe disease. An online questionnaire on non-polio EV surveillance and laboratory detection was submitted to all 30 European Union (EU)/European Economic Area (EEA) countries. Twenty-nine countries responded; 26 conducted laboratory-based non-polio EV surveillance, and 24 included neurological infections in their surveillance. Eleven countries have established specific surveillance for EV-D68 via sentinel influenza surveillance (n = 7), typing EV-positive respiratory samples (n = 10) and/or acute flaccid paralysis surveillance (n = 5). Of 26 countries performing non-polio EV characterisation/typing, 10 further characterised culture-positive EV isolates, whereas the remainder typed PCR-positive but culture-negative samples. Although 19 countries have introduced sequence-based EV typing, seven still rely entirely on virus isolation. Based on 2015 data, six countries typed over 300 specimens mostly by sequencing, whereas 11 countries characterised under 50 EV-positive samples. EV surveillance activity varied between EU/EEA countries, and did not always specifically target patients with neurological and/or respiratory infections. Introduction of sequence-based typing methods is needed throughout the EU/EEA to enhance laboratory capacity for the detection of EVs.

Insights from a Systematic Search for Information on Designs, Costs, and Effectiveness of Poliovirus Environmental Surveillance Systems

Poliovirus surveillance plays a critical role in achieving and certifying eradication and will play a key role in the polio endgame. Environmental surveillance can provide an opportunity to detect circulating polioviruses prior to the observation of any acute flaccid paralysis cases. We completed a systematic review of peer-reviewed publications on environmental surveillance for polio including the search terms "environmental surveillance" or "sewage," and "polio," "poliovirus," or "poliomyelitis," and compared characteristics of the resulting studies. The review included 146 studies representing 101 environmental surveillance activities from 48 countries published between 1975 and 2016. Studies reported taking samples from sewage treatment facilities, surface waters, and various other environmental sources, although they generally did not present sufficient details to thoroughly evaluate the sewage systems and catchment areas. When reported, catchment areas varied from 50 to over 7.3 million people (median of 500,000 for the 25% of activities that reported catchment areas, notably with 60% of the studies not reporting this information and 16% reporting insufficient information to estimate the catchment area population size). While numerous studies reported the ability of environmental surveillance to detect polioviruses in the absence of clinical cases, the review revealed very limited information about the costs and limited information to support quantitative population effectiveness of conducting environmental surveillance. This review motivates future studies to better characterize poliovirus environmental surveillance systems and the potential value of information that they may provide in the polio endgame.

Whole Genome Sequencing of Enterovirus species C Isolates by High-Throughput Sequencing: Development of Generic Primers

Enteroviruses are among the most common viruses infecting humans and can cause diverse clinical syndromes ranging from minor febrile illness to severe and potentially fatal diseases. Enterovirus species C (EV-C) consists of more than 20 types, among which the three serotypes of polioviruses, the etiological agents of poliomyelitis, are included. Biodiversity and evolution of EV-C genomes are shaped by frequent recombination events. Therefore, identification and characterization of circulating EV-C strains require the sequencing of different genomic regions. A simple method was developed to quickly sequence the entire genome of EV-C isolates. Four overlapping fragments were produced separately by RT-PCR performed with generic primers. The four amplicons were then pooled and purified prior to being sequenced by a high-throughput technique. The method was assessed on a panel of EV-Cs belonging to a wide-range of types. It can be used to determine full-length genome sequences through de novo assembly of thousands of reads. It was also able to discriminate reads from closely related viruses in mixtures. By decreasing the workload compared to classical Sanger-based techniques, this method will serve as a precious tool for sequencing large panels of EV-Cs isolated in cell cultures during environmental surveillance or from patients, including vaccine-derived polioviruses.