Prevalence and Bayesian Phylogenetics of Enteroviruses Derived From Environmental Surveillance Around Polio Vaccine Switch Period in Shandong Province, China

Environmental surveillance reveals co-circulation of distinctive lineages of enteroviruses in southwest China's border cities, 2020-2022

AIMS

Enteroviruses are significant human pathogens associated with a range of mild to severe diseases. This study aims to understand the diversity and genetic characterization of enteroviruses circulated in southwest China's border cities by using environmental surveillance.

METHODS AND RESULTS

A total of 96 sewage samples were collected in three border cities and a port located in Yunnan Province, China from July 2020 to June 2022. After cell culture and VP1 sequencing, a total of 590 enterovirus isolates were identified, belonging to 21 types. All PV strains were Sabin-like with ≤6 nucleotide mutations in the VP1 coding region. Echovirus 6, echovirus 21 (a rare serotype in previous studies), and coxsackievirus B5 were the predominant serotypes, which accounted for 21.19%, 18.31%, and 13.39% of the total isolates, respectively. The prevalence of the common serotypes varied across different border cities and periods. Phylogenetic analysis revealed the presence of multiple evolutionary lineages for E21, E6, and E30, some of which formed distinct branches.

CONCLUSIONS

High diversity of enteroviruses and distinct lineages of predominant serotypes circulated in southwest China's border cities.

Whole Genomic Sequence Analysis of Human Adenovirus Species C Shows Frequent Recombination in Tianjin, China

Human adenovirus species C (HAdV-C) is frequently detected in China and worldwide. For the first time, 16 HAdV-C strains were isolated from sewage water (14 strains) and hospitalised children with diarrhoea (2 strains,) in Tianjin, China. Nearly complete genome data were successfully obtained for these viruses. Subsequently, genomic and bioinformatics analyses of the 16 HAdV-C strains were performed. A phylogenetic tree of the complete HAdV-C genome divided these strains into three types: HAdV-C1, HAdV-C2, HAdV-C5. Phylogenetic analysis based on the fiber gene showed similar outcomes to analyses of the hexon gene and complete HAdV-C genomes, whereas the penton gene sequences showed more variation than previously reported. Furthermore, analysis of the whole-genome sequencing revealed seven recombination patterns transmitted in Tianjin, of which at least four patterns have not been previously reported. However, the penton base gene sequences of the HAdV-C species had significantly lower heterogeneity than those of the hexon and fiber gene sequences of recombinant isolates; that is, many strains were distinct in origin, but shared hexon and fiber genes. These data illustrate the importance of frequent recombination in the complexity of the HAdV-C epidemic in Tianjin, thus emphasising the necessity for HAdV-C sewage and virological monitoring in China.

Outbreaks of Circulating Vaccine-derived Poliovirus in the World Health Organization Western Pacific Region, 2000-2021

The World Health Organization Western Pacific Region (WPR) has maintained the polio-free status for more than two decades. At the global level, there were only 6 confirmed polio cases due to wild type 1 poliovirus in Pakistan, Afghanistan, and Malawi in 2021, therefore, the risk of the importation of wild poliovirus from the endemic countries to the WPR is considerably lower than ever before. On the other hand, the risk of polio outbreaks associated with circulating vaccine-derived polioviruses (cVDPVs) still cannot be ignored even in the WPR. Since late 2010s, cVDPV outbreaks in the WPR have appeared to be more extensive in frequency and magnitude. Moreover, the emergence of concomitant polio outbreaks of type 1 and type 2 cVDPVs in the Philippines and Malaysia during 2019-2020 has highlighted the remaining risk of cVDPV outbreaks in high-risk areas and/or communities in the WPR. The previous cVDPV outbreaks in the WPR have been rapidly and effectively controlled, however, the future risk of polio outbreaks associated with cVDPVs needs to be reconsidered and polio immunization and surveillance strategies should be updated accordingly.

Epidemiological evaluation of sewage surveillance as a tool to detect the presence of COVID-19 cases in a low case load setting

In low prevalence settings the development of sensitive and specific quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR) tests to detect SARS-CoV-2 (the virus causing COVID-19) in sewage presents the possibility of using sewage sampling as a diagnostic test for the presence of infected people in the catchment of the sampled sewer. However, the usefulness of such surveillance has not been quantified. In this study in the Australian state of Victoria between August and October 2020 the location of each known SARS-CoV-2-infected person was determined on each day from two days before onset to 55 days after, in 46 metropolitan and rural sewer catchments sampled weekly – a total of 71 positive and 275 negative samples, and 354,155 person-days of location data. These were categorised by time since onset and distance from the sampling site. The odds of detection in sewage were between 5 and 20 times higher where known cases were present, with less effect of distance than time since onset. Using positive qRT-PCR in a sewage sample as a diagnostic test not just for viral RNA in the sample, but for the presence of known infected people in the catchment on the same day, the sensitivity was moderate (31% to 76%) and the specificity high (87% to 94%). The odds of detection were increased with increased numbers of known infected people but decreased with increased distance and time since onset. The probability of detection of the viral subgenome in sewage samples was about 10% when one known infected person was present, and this increased with higher numbers of known infected people and greater proximity to the sampling site. Sewage surveillance can be used to detect people infected with SARS-CoV-2 in the catchment, directing a search for infectious clinical cases and other public health actions. However, detection at least eight weeks after onset may be due to existing cases rather than new ones, and, although not zero, the probability of detecting a single case is low.

High Heterogeneity of Echoviruses in Brazilian Children with Acute Gastroenteritis

Echoviruses (E) are a diverse group of viruses responsible for various pathological conditions in humans including aseptic meningitis, myocarditis, and acute flaccid paralysis. The detection and identification of echovirus genotypes in clinical samples is challenging due to its high genetic diversity. Here, we report the complete genome sequences of nine echoviruses, obtained by next-generation sequencing of 238 fecal samples from individuals with gastroenteritis in regions of Brazil. Detected viruses were classified into six genotypes: Three E1 sequences (BRA/TO-028, BRA/TO-069 and BRA/TO-236), one E3 (BRA/TO-018), one E11 (BRA/TO-086), one E20 (BRA/TO-016), two E29 (BRA/TO-030 and BRA/TO-193), and one E30 sequence (BRA/TO-032). Phylogenetic analysis indicated that the echoviruses E1 and E29 circulating in Brazil are divergent from strains circulating worldwide. The genotype diversity identified in our study may under-represent the total echovirus diversity in Brazil because of the small sample size and the restricted geographical distribution covered by the survey.

Environmental Surveillance through Next-Generation Sequencing to Unveil the Diversity of Human Enteroviruses beyond the Reported Clinical Cases

The knowledge about circulation of Human Enteroviruses (EVs) obtained through medical diagnosis in Argentina is scarce. Wastewater samples monthly collected in Córdoba, Argentina during 2011-2012, and then in 2017-2018 were retrospectively studied to assess the diversity of EVs in the community. Partial VP1 gene was amplified by PCR from wastewater concentrates, and amplicons were subject of next-generation sequencing and genetic analyses. There were 41 EVs detected, from which ~50% had not been previously reported in Argentina. Most of the characterized EVs (60%) were detected at both sampling periods, with similar values of intratype nucleotide diversity. Exceptions were enterovirus A71, coxsackievirus B4, echovirus 14, and echovirus 30, which diversified in 2017-2018. There was a predominance of types from EV-C in 2017-2018, evidencing a common circulation of these types throughout the year in the community. Interestingly, high genetic similarity was evidenced among environmental strains of echovirus 30 circulating in 2011-2012 and co-temporal isolates obtained from patients suffering aseptic meningitis in different locations of Argentina. This study provides an updated insight about EVs circulating in an important region of South America, and suggests a valuable role of wastewater-based epidemiology in predicting outbreaks before the onset of cases in the community.