Monkeypox Virus in Wastewater Samples from Santiago Metropolitan Region, Chile

Sewage surveillance provides useful epidemiologic and public health information on viral infections at the population level. We detected monkeypox virus DNA from sewage samples covering 85% of the population in Santiago Metropolitan Region Chile. We also isolated infective viruses from those samples. Wastewater surveillance could complement clinical surveillance for monkeypox virus.

Norovirus, Hepatitis A and SARS-CoV-2 surveillance within Chilean rural wastewater treatment plants based on different biological treatment typologies

During the COVID-19 pandemic, wastewater from WWTPs became an interesting source of epidemiological surveillance. However, there is uncertainty about the influence of treatment type on virus removal. The aim of this study was to assess viral surveillance within wastewater treatment plants (WWTPs) based on different biological treatments. Seasonal monitoring (autumn-winter and spring-summer) was conducted in 10 Chilean rural WWTPs, which were based on activated sludge, aerated lagoons, bio-discs, constructed wetlands, vermifilters and mixed systems. Viruses were measured (influent/effluent) by the RT-qPCR technique, using a commercial kit for SARS-CoV-2, NoV GI, NoV GII, and HAV. The detection of SARS-CoV-2 viral variants by genotyping was performed using SARS-CoV-2 Mutation Assays (ThermoFisher Scientific, USA). JC polyomavirus detection (control), as well as a qPCR technique. Results showed that SARS-CoV-2, NoV GI and GII were detected in influents at values between <5 and 462, 0 to 28, and 0 to 75 GC/mL, respectively. HAV was not detected among the studied WWTPs. The monitored WWTPs removed these viruses at percentages between 0 and 100 %. WWTPs based on activated sludge with bio-discs demonstrated to be the most efficient at removing SARS-CoV-2 (up to 98 %) and NoV GI and GII (100 %). Meanwhile, bio-discs technologies were the least efficient for viral removal, due to biofilm detachment, which could also adsorb viral aggregates. A correlation analysis established that solids, pH, and temperature are the most influential parameters in viral removal. Wastewater-based surveillance at WWTP allowed for the detection of Omicron before the Chilean health authorities notified its presence in the population. In addition, surveillance of viruses and other microorganisms could help assess the potential public health risk of wastewater recycling.

Changing molecular epidemiology of Hepatitis A virus in Santiago, Chile from 2010 to 2021

OBJECTIVES

Hepatitis A (HAV) virus causes asymptomatic to life-treating fulminant hepatitis. During infection, patients show large viral excretion in their stools. Resistance of HAV to environmental conditions, allows us to recover viral nucleotide sequences from wastewater and trace its evolutionary history.

METHODS

We characterize twelve years of HAV circulation in wastewater from Santiago, Chile, and conducted phylogenetic analyses to decipher the dynamics of circulating lineages.

RESULTS

We observed the exclusive circulation of the HAV IA genotype. The molecular epidemiologic analyses showed a steady circulation of a dominant lineage with low genetic diversity (d = 0,007) between 2010 and 2017. An outbreak of Hepatitis A associated with men who have sex with men, in 2017 was associated with the irruption of a new lineage. Remarkably, a dramatic change in the dynamic of HAV circulation was observed in the period post-outbreak; between 2017 and 2021 when 4 different lineages were transiently detected. Exhaustive phylogenetic analyses indicate that these lineages were introduced and possibly derived from isolates from other Latin American countries.

CONCLUSION

The HAV circulation in recent years in Chile is rapidly changing and suggests that this phenomenon could be a consequence of massive population migrations in Latin America caused by political instability and natural disasters.

Performance of SARS-CoV-2 rapid antigen test compared with real-time RT-PCR in asymptomatic individuals

Screening, testing and contact tracing plays a pivotal role in control of the COVID-19 pandemic. To enable this it is necessary to increase the testing capacity. This study compared a SARS-CoV-2 rapid antigen test (RAT) and RT-PCR in 842 asymptomatic individuals from Tarapacá, Chile. A sensitivity of 69.86%, specificity of 99.61%, PPV of 94.44% and NPP of 97.22% with Ct values (Ct > 27) that were significantly higher among individuals with false-negative RAT were reported. These results support the fact that RAT might have a significant impact on the identification of asymptomatic carriers in areas that lack suitable laboratories to perform SARS-CoV-2 real-time RT-PCR diagnostics, or the results take more than 24-48 h, as well as zones with high traffic of individuals such as border/customs, airports, interregional bus, train stations or in any mass testing campaign requiring rapid results.

JC polyomavirus circulation in one-year surveillance in wastewater in Santiago, Chile

Human polyomavirus JC (JCPyV) is a widely distributed viral agent and because it high resistance against environmental conditions it is frequently recovered from diverse sources of water and is considered a good marker for human pollution. Phylogenetic analysis of JCPyV isolated in different part of the world has revealed 7 genotypes, which have been associated with specific populations or ethnics groups. This feature has been used to trace pre-historic and historic human migration patterns across the world. Although there are many reports describing genotypes distribution around the world, data on JCPyV genotypes in the southernmost areas of South America are scarce. The goal of this study is to detect and characterize the JCPyV that circulates in Santiago, Chile using sewage samples from wastewater treatment plants (WWTP). Sewage samples were obtained monthly during 1 year from three WWTPs which together process about 80% of wastewater generated in the city of Santiago, Chile. Our results show that JCPyV profusely circulates in Santiago, Chile, because it was detected in 80.56% of the samples, reinforcing the use of JCPyV as a feasible marker to assess human environmental pollution. JCPyV was detected in high frequency in influents and effluents samples, with the largest WWTPs showing the highest percentage of detection and viral loads. In the phylogenetic analysis the Chilean sequences clustered mainly with genotype 2A (Asian genotype). This is similar to that previously reported from Buenos Aires, Argentina and divergent to data from Brazil, where the circulation of European subtypes 1 and 4 and African subtypes 3 and 6 has been described.