As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing and/or sequencing capacity, which can also introduce biases1–3. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing4,5. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We developed and deployed improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detected emerging variants of concern up to 14 days earlier in wastewater samples, and identified multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.

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As SARS-CoV-2 becomes an endemic pathogen, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing/sequencing capacity, which can also introduce biases. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here, we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We develop and deploy improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detect emerging variants of concern up to 14 days earlier in wastewater samples, and identify multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.

Background: Cutaneous manifestation of COVID 19 in children has not yet been reviewed systematically and hence this review gives a future direction to the clinicians to be vigilant for skin presentations during such pandemic.Methodology: The review was done as per the guidelines of PRISMA and literature search was done on PubMed database using keywords as COVID-19, children and skin in different combinations. Articles published in English with cases of age 1 month to 18 years were eligible. The outcome included varied aspects of cutaneous and COVID-19 infection. The review protocol was not registered.Results: Of 51 publications identified, 13 studies containing 149 children met the eligibility criteria. Acrally located erythematous maculopapular lesion was the most common finding in 138 children. Erythema multiforme, varicella like exanthem and Kawasaki disease like presentations were reported in the rest of the cases. The duration of the skin lesion was 1-2 weeks in 43%. Skin biopsy done in 18 cases revealed superficial & deep perivascular and peri-eccrine lymphocytic infiltrate & lymphocytic vasculitis. RT-PCR was positive in 13.8% cases. Serological markers for HSV, parvovirus B19 analyzed across various studies, were found negative, except for mycoplasma pneumoniae in 2 of 20 cases tested.Discussion: Clinicopathologic analysis established chilblains like lesion in 43% cases with no confirmed etiology like cold exposure, autoimmune dysfunction, drug reaction, or viral infection. The usual cephalo-caudal spread of a viral exanthem was also missing. However, a low number of discussed cases was a limitation of the study.Conclusion: In the absence of any confirmed etiology for such cutaneous manifestations, the possibility of COVID-19 should be explored and evaluated thoroughly during such pandemic.