A State-of-the-Art Scoping Review on SARS-CoV-2 in Sewage Focusing on the Potential of Wastewater Surveillance for the Monitoring of the COVID-19 Pandemic.

The outbreak of coronavirus infectious disease-2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has rapidly spread throughout the world. Several studies have shown that detecting SARS-CoV-2 in untreated wastewater can be a useful tool to identify new outbreaks, establish outbreak trends, and assess the prevalence of infections. On 06 May 2021, over a year into the pandemic, we conducted a scoping review aiming to summarize research data on SARS-CoV-2 in sewage. Papers dealing with raw sewage collected at wastewater treatment plants, sewer networks, septic tanks, and sludge treatment facilities were included in this review. We also reviewed studies on sewage collected in community settings such as private or municipal hospitals, healthcare facilities, nursing homes, dormitories, campuses, airports, aircraft, and cruise ships. The literature search was conducted using the electronic databases PubMed, EMBASE, and Web Science Core Collection. This comprehensive research yielded 1090 results, 66 of which met the inclusion criteria and are discussed in this review. Studies from 26 countries worldwide have investigated the occurrence of SARS-CoV-2 in sewage of different origin. The percentage of positive samples in sewage ranged from 11.6 to 100%, with viral concentrations ranging from ˂LOD to 4.6 × 108 genome copies/L. This review outlines the evidence currently available on wastewater surveillance: (i) as an early warning system capable of predicting COVID-19 outbreaks days or weeks before clinical cases; (ii) as a tool capable of establishing trends in current outbreaks; (iii) estimating the prevalence of infections; and (iv) studying SARS-CoV-2 genetic diversity. In conclusion, as a cost-effective, rapid, and reliable source of information on the spread of SARS-CoV-2 and its variants in the population, wastewater surveillance can enhance genomic and epidemiological surveillance with independent and complementary data to inform public health decision-making during the ongoing pandemic.

Seroepidemiological Studies of Arboviruses in Africa.

The literature on sero-epidemiological studies of flaviviral infections in the African continent is quite scarce. Much of the viral epidemiology studies have been focussing on diseases such as HIV/AIDS because of their sheer magnitude and impact on the lives of people in the various affected countries. Increasingly disease outbreaks caused by arboviruses such as the recent cases of chikungunya virus, dengue virus and yellow fever virus have prompted renewed interest in studying these viruses. International agencies from the US, several EU nations and China are starting to build collaborations to build capacity in many African countries together with established institutions to conduct these studies. The Tofo Advanced Study Week (TASW) was established to bring the best scientists from the world to the tiny seaside town of Praia do Tofo to rub shoulders with African virologists and discuss cutting-edge science and listen to the work of researchers in the field. In 2015 the 1st TASW focussed on Ebola virus. The collections of abstracts from participants at the 2nd TASW which focused on Dengue and Zika virus as well as presentations on other arboviruses are collated in this chapter.

The burden of hepatitis C virus in Cameroon: Spatial epidemiology and historical perspective.

Cameroon is thought to have one of the highest prevalences of hepatitis C virus (HCV) infection in the world (4.9% among adults). A marked cohort effect exists in several communities where ≈50% of the elderly are infected. Better assessment of HCV distribution is needed for planning treatment programmes. We tested for HCV antibodies 14 150 capillary blood samples collected during the 2011 Demographic and Health Survey, whose participants were representative of the Cameroonian population aged 15-49 (both genders) and 50-59 years (men only). Historical data on exposure to medical care were collected and factors associated with HCV assessed through logistic regression and geospatial analyses. To estimate prevalence in all persons aged ≥15 years, we used data from the survey for the 15-59 years fraction and modelled a cohort effect for older individuals. The nationwide HCV prevalence was 0.81% for the 15-49 years group, and 2.51% for all individuals aged ≥15 years. Only 0.2% of individuals aged 15-19 were seropositive. Among participants aged 15-44 years, HCV was associated with age, rural residence and, for males, with ritual circumcision. For those aged 45-59 years, HCV was associated with age and access to medical care in the late 1950s. Prevalence of HCV seropositivity in Cameroon is half of previous estimates. Nationwide surveys are essential to rationalize resources allocation. The high prevalence among older cohorts, a colonial legacy, has had little spillover into younger cohorts. HCV-free generations might be attainable in countries not plagued with intravenous drug abuse.

Historical epidemiology of hepatitis C virus in select countries-volume 4.

Due to the introduction of newer, more efficacious treatment options, there is a pressing need for policy makers and public health officials to develop or adapt national hepatitis C virus (HCV) control strategies to the changing epidemiological landscape. To do so, detailed, country-specific data are needed to characterize the burden of chronic HCV infection. In this study of 17 countries, a literature review of published and unpublished data on HCV prevalence, viraemia, genotype, age and gender distribution, liver transplants and diagnosis and treatment rates was conducted, and inputs were validated by expert consensus in each country. Viraemic prevalence in this study ranged from 0.2% in Hong Kong to 2.4% in Taiwan, while the largest viraemic populations were in Nigeria (2 597 000 cases) and Taiwan (569 000 cases). Diagnosis, treatment and liver transplant rates varied widely across the countries included in this analysis, as did the availability of reliable data. Addressing data gaps will be critical for the development of future strategies to manage and minimize the disease burden of hepatitis C.

Hepatitis B, C, and E infection among HIV-infected patients in Franceville, Gabon: retrospective cross-sectional study.

Access to antiretrovirals has increased the life expectancy of patients living with HIV. However, HIV-viral hepatitis coinfections in countries endemic for these infections make management more difficult. To determine the extent of these coinfections in Gabon, we investigated markers of hepatitis B, C, and E viruses in 762 adults infected with HIV-1 by ELISA. We used real-time PCR to quantify plasma HBV DNA (HBV VL) and amplified HCV and HEV RNA by nested RT-PCR and PCR.The seroprevalence of chronic hepatitis B infection was 9.3 %. Among patients with isolated HBcAc profiles, the prevalence of occult hepatitis B infection was 26.7 %, for a real prevalence (detectable CV-HBV) of 17.3 % of the total population. HCV seroprevalence was 8.8 %. Of the 67 HIV-positive patients, 76.1 % had replicative profiles (detectable HCV RNA), that is, 6.7 % of the total population. For hepatitis E, seroprevalence was 3.5 %. No case of chronic HEV infection was found. In conclusion, this study highlights a high rate of HIV-Hepatitis B, C and E coinfections in Gabon. In addition, we show the interest of looking for chronic infections (replicative profiles) in HIV-infected patients in Gabon. The establishment of technical platforms for this type of research, accessible to middle-income countries, is necessary.

Correction: Temporal Patterns of Influenza A and B in Tropical and Temperate Countries: What Are the Lessons for Influenza Vaccination?

[This corrects the article DOI: 10.1371/journal.pone.0152310.].

HIV-1 subtyping using phylogenetic analysis of pol gene sequences.

HIV-1 pol gene sequencing is now used routinely in France to identify mutations associated with resistance to reverse transcriptase (RT) or protease (PR) inhibitors. These sequences may also provide other information, such as the HIV-1 subtype. HIV-1 subtyping was compared using the RT and PR gene sequences to heteroduplex mobility assay (HMA) of the envelope gene. The RT and PR genes of 51 samples that had been subtyped earlier by HMA were sequenced. Sequences were aligned and subtypes were determined by phylogenetic analysis with reference HIV sequences. HMA gave the following subtypes: A (20), B (19), C (1), D (3), F (1), G (3) and CRF01-AE (4). Phylogenetic analysis of the RT gene gave: A (5), B (19), C (2), D (3), F (1), G (6), J (2), CRF01_AE (4), CFR02_AG (7) and undetermined (2). PR gene analysis did not infer subtypes with sufficient confidence. HMA and RT subtyping was not in agreement in nine cases. RT subtyping can identify CFR02_AG and CRF01_AE variants from A subtype RT. It was shown that phylogenetic analysis of the RT gene could provide a useful method for HIV-1 subtyping. The length of the amplicon and the relative performance of each primer pair used in this study favoured RT sequences as a subtyping tool. One potential advantage over env subtyping HMA is the ability to identify some circulating recombinant forms (CRFs).