Lamba Sanjay, Ganesan Sutharsan, Daroch Namrta, Paul Kiran, Joshi Soumya Gopal, Sreenivas Darshan, Nataraj Annamalai, Srikantaiah Vishwanath, Mishra Rakesh, Ramakrishnan Uma, Ishtiaq Farah
Tata Institute for Genetics and Society, GKVK Post, Bellary Road, Bengaluru, 560065, India.
National Centre for Biological Sciences, TIFR, Bellary Road, Bengaluru, 560065, India.
Lancet Reg Health Southeast Asia. 2023 Apr;11:100151. doi: 10.1016/j.lansea.2023.100151. Epub 2023 Jan 18.
Environmental surveillance (ES) of a pathogen is crucial for understanding the community load of disease. As an early warning system, ES for SARS-CoV-2 has complemented routine diagnostic surveillance by capturing near real-time virus circulation at a population level.
In this longitudinal study conducted between January 2022 and June 2022 in 28 sewershed sites in Bengaluru city (∼11 million inhabitants), we quantified weekly SARS-CoV-2 RNA concentrations to track infection dynamics and provide evidence of change in the relative abundance of emerging variants.
We describe an early warning system using the exponentially weighted moving average control chart and demonstrate how SARS-CoV-2 RNA concentrations in wastewater correlated with clinically diagnosed new COVID-19 cases, with the trends appearing 8-14 days earlier in wastewater than in clinical data. This was further corroborated by showing that the estimated number of infections is strongly correlated with SARS-CoV-2 RNA copies detected in the wastewater. Using a deconvolution matrix, we detected emerging variants of concern up to two months earlier in wastewater samples. In addition, we found a huge diversity in variants detected in wastewater compared to clinical samples. The findings from this study have been discussed regularly with local authorities to inform policy-making decisions.
Our study highlights that quantifying viral titre, correlating it with a known number of cases in the area, and combined with genomic surveillance helps in tracking variants of concern (VOC) over time and space, enabling timely and making informed policy decisions.
This work has been supported by funding from the Rockefeller Foundation grant to National Centre for Biological Sciences, TIFR) and the Indian Council of Medical Research grant to (FI) Tata Institute for Genetics and Society and Tata Trusts.
病原体的环境监测（ES）对于了解疾病的社区负荷至关重要。作为一种早期预警系统，SARS-CoV-2的环境监测通过在人群层面捕获近乎实时的病毒传播情况，对常规诊断监测起到了补充作用。
在2022年1月至2022年6月期间于班加罗尔市（约1100万居民）的28个下水道流域站点进行的这项纵向研究中，我们对每周的SARS-CoV-2 RNA浓度进行了量化，以追踪感染动态，并为新出现变异株相对丰度的变化提供证据。
我们描述了一种使用指数加权移动平均控制图的早期预警系统，并展示了废水中SARS-CoV-2 RNA浓度如何与临床诊断的新增COVID-19病例相关，废水里的趋势比临床数据中早8 - 14天出现。通过表明估计的感染数与废水中检测到的SARS-CoV-2 RNA拷贝数密切相关，这一点得到了进一步证实。使用反卷积矩阵，我们在废水样本中比临床样本早两个月检测到令人担忧的新出现变异株。此外，我们发现与临床样本相比，在废水中检测到的变异株具有巨大的多样性。本研究的结果已定期与地方当局进行讨论，以为决策提供信息。
我们的研究强调，量化病毒滴度、将其与该地区已知病例数相关联，并结合基因组监测，有助于在时间和空间上追踪令人担忧的变异株（VOC），从而能够及时做出明智的政策决策。
这项工作得到了洛克菲勒基金会向国家生物科学中心（TIFR）提供的资助以及印度医学研究理事会向塔塔遗传学与社会研究所和塔塔信托基金（FI）提供的资助。
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