Investigation of SARS-CoV-2 spread and identification of variants in sewers has been demonstrated to accurately detect prevalence of viral strains and is advantageous to clinical sampling in population catchment size. Herein, we utilized an established nationwide system of wastewater sampling and viral concentration approaches to perform large-scale surveillance of SARS-CoV-2 variants in nine different locations across Israel that were sampled from August 2020 to February 2021 and sequenced (n=58). Viral sequences obtained from the wastewater samples had high coverages of the genome, and mutation analyses successfully identified the penetration of the B.1.1.7 variant into Israel in December 2020 in the central and north regions, and its spread into additional regions in January and February 2021, corresponding with clinical sampling results. Moreover, the wastewater analysis identified the B.1.1.7 variant in December 2020 in regions in which non-sufficient clinical sampling was available. Other variants of concern examined, including P.1 (Brazil/Manaus), B.1.429 (USA/California), B.1.526 (USA/New York), A.23.1 (Uganda) and B.1.525 (Unknown origin), did not show consistently elevated frequencies. This study exemplifies that surveillance by sewage is a robust approach which allows to monitor the diversity of SARS-CoV-2 strains circulating in the community. Most importantly, this approach can pre-identify the emergence of epidemiologically or clinically relevant mutations/variants, aiding in public health decision making.

ABSTRACT

The COVID-19 pandemic and the fast global spread of the disease resulted in unprecedented decline in world trade and travel. A critical priority is, therefore, to quickly develop serological diagnostic capacity and identify individuals with past exposure to SARS-CoV-2. In this study serum samples obtained from 309 persons infected by SARS-CoV-2 and 324 of healthy, uninfected individuals as well as serum from 7 COVID-19 patients with 4–7 samples each ranging between 1–92 days post first positive PCR were tested by an “in house” ELISA which detects IgM, IgA and IgG antibodies against the receptor binding domain (RBD) of SARS-CoV-2. Sensitivity of 47%, 80% and 88% and specificity of 100%, 98% and 98% in detection of IgM, IgA and IgG antibodies, respectively, were observed. IgG antibody levels against the RBD were demonstrated to be up regulated between 1–7 days after COVID-19 detection, earlier than both IgM and IgA antibodies. Study of the antibody kinetics of seven COVID 19 patients revealed that while IgG levels are high and maintained for at least 3 months, IgM and IgA levels decline after a 35–50 days following infection. Altogether, these results highlight the usefulness of the RBD based ELISA, which is both easy and cheap to prepare, to identify COVID-19 patients even at the acute phase. Most importantly our results demonstrate that measuring IgG levels alone is both sufficient and necessary to diagnose past exposure to SARS-CoV-2.

BackgroundPolio eradication is an extraordinary globally coordinated health program in terms of its magnitude and reach, leading to the elimination of wild poliovirus (WPV) in most parts of the world. In 2013, a silent outbreak of WPV was detected in Israel, a country using an inactivated polio vaccine (IPV) exclusively since 2005. The outbreak was detected using environmental surveillance (ES) of sewage reservoirs. Stool surveys indicated the outbreak to be restricted mainly to children under the age of 10 in the Bedouin population of southern Israel. In order to curtail the outbreak, a nationwide vaccination campaign using oral polio vaccine (OPV) was conducted, targeting all children under 10.MethodsA transmission model, fitted to the results of the stool surveys, with additional conditions set by the ES measurements, was used to evaluate the prevalence of WPV in Bedouin children and the effectiveness of the vaccination campaign. Employing the parameter estimates of the model fitting, the model was used to investigate the effect of alternative timings, coverages and dosages of the OPV campaign on the outcome of the outbreak.ResultsThe mean estimate for the mean reproductive number was 1.77 (95 % credible interval, 1.46–2.30). With seasonal variation, the reproductive number maximum range was between zero and six. The mean estimate for the mean infectious periods was 16.8 (8.6–24.9) days. The modeling indicates the OPV campaign was effective in curtailing the outbreak. The mean estimate for the attack rate in Bedouin children under 10 at the end of 2014 was 42 % (22–65 %), whereas without the campaign the mean projected attack rate was 57 % (35–74 %). The campaign also likely shortened the duration of the outbreak by a mean estimate of 309 (2–846) days. A faster initiation of the OPV campaign could have reduced the incidence of WPV even if a lower coverage was reached, at the risk of prolonging the outbreak.ConclusionsOPV campaigns are essential for interrupting WPV transmission, even in a developed country setting with a high coverage of IPV. In this setting, establishing ES of WPV circulation is particularly crucial for early detection and containment of an outbreak.Electronic supplementary materialThe online version of this article (doi:10.1186/s12916-016-0637-z) contains supplementary material, which is available to authorized users.

Wild poliovirus type 1 (WPV1) introduction into southern Israel in early 2013 was detected by routine environmental surveillance. The virus was identified genetically as related to the South Asian (SOAS) R3A lineage endemic to Pakistan in 2012. Intensified, high-throughput environmental surveillance using advanced molecular methods played a critical role in documenting and locating sustained transmission throughout 2013 and early 2014 in the absence of any acute flaccid paralysis. It guided the public health responses, including stool-based surveillance and serosurveys, to determine the point prevalence in silent excretors and measured the effect of vaccination campaigns with inactivated polio vaccine and bivalent oral polio vaccine on stopping transmission.

No abstract

No abstract

We evaluated the performance of the Simplexa Flu A/B & RSV kit on 170 prospective respiratory samples using a modified protocol, supplied by the manufacturer, that eliminates the RNA extraction step. Overall, compared against our laboratory-developed assay, the assay's sensitivity, specificity, and positive and negative predictive values were 95.1%, 99.6%, 98.7%, and 98.6%, respectively.