Kolhe Lab | MCG Path - Pandemic Response

Pandemic Response and Emergency Preparedness

The SARS-CoV-2 pandemic has placed significant unexpected demands on CLIA laboratories. Compounded by supply chain constraints & the need to validate multiple alternatives & create new testing modalities, laboratories have not only been placed front & center of this pandemic but have been tasked with providing perhaps the most significant piece to understanding the dynamics of this pandemic through testing.

Laboratories have adapted to these challenges by adopting a multifaceted strategy including assay development & validation, that is, cost-effective, accurate, time-efficient & can cater to mass testing in the face of significant supply chain failures. It also forced them to make significant changes to their regular workflow as they adapted to new diagnostic tests & sample volumes.

We developed the CLIA LDT assay for COVID-19 screening and testing on March 15th, 2020. (CLIA validation, FDA submission, and testing) We were the 1st laboratory in the southeast United States to go live with COVID-19 testing in a CLIA setting. Our novel approach of using a primer-probe set from IDT helped us not to be dependent on the bottlenecked supply chain from China. In the first phase of the pandemic, our laboratory validated 2 RT-PCR assays to test ∼1000 samples/day & rapidly modified procedures & validated various preanalytical & analytical steps to overcome the supply chain constraints that would have otherwise derailed testing efforts.

Further, the pooling strategy was validated for wide-scale population screening using nasopharyngeal swab samples & saliva samples. The translational research arm of the laboratory pursued several initiatives to understand the variable clinical manifestations that this virus presented in the population. The phylogenetic evolution of the virus was investigated using next-generation sequencing technology. The following figure & table summarize our journey as the laboratory has sought to adapt & continue to positively contribute to the unprecedented demands & challenges of this rapidly evolving pandemic.

Contributions to Pandemic Response and Emergency Preparedness

Testing for SARS-CoV-2 has lagged in many countries due to a lack of adequate test kits and bottlenecks in the analytical process. We investigated the feasibility and accuracy of a sample pooling approach for wide-scale population screening for COVID-19. The sample pooling strategy has the potential to catch up with testing needs with minimal turnaround times. This strategy also facilitates enormous savings on laboratory supplies, extraction, and PCR kits, which can be in short supply during a pandemic.

The advantages of this innovative approach include the potential of catching up with testing, clearing back-logged samples, reducing turnaround times, and ensuring enormous savings on RNA extraction and/or testing kits and laboratory supplies. This would relieve the pressure mounting on laboratories for increased testing, hopefully making a significant contribution to the control of this pandemic. Besides, this strategy may enable effective and consistent disease surveillance, as many states and countries begin to reopen businesses, airports, public gatherings, and work environments. Monitoring spikes in the number of cases in groups of individuals in the same environment will facilitate rapid and early containment.

Laboratories should also adopt a multi-pronged strategy in the development of assays that are cost-effective, accurate, and time-efficient, that cater to mass testing under differing clinical scenarios, and that are uninterrupted or sustainable in case of supply chain failures, and that enhance further research and understanding of COVID-19. Paying attention to laboratory management will facilitate smooth operations. Currently, resources to equip laboratories have been awarded or increased to meet the need for COVID-19 testing. Careful consideration of an effective COVID-19 testing program, plus a look into how these resources can be redefined for improved testing beyond COVID-19 and/or a better preparedness for future outbreaks is needed.

Developed CLIA LDT assay for COVID-19 screening and testing on March 15th, 2020 (CLIA validation, FDA submission, and testing)

We were the 1st laboratory in the southeast United States to go live with COVID-19 testing in a CLIA setting. Our novel approach of using a primer-probe set from IDT helped us not to be dependent on the bottlenecked supply chain from China.

“Pooling samples” as an approach for COVID-19 screening and testing (CLIA validation, FDA submission, and testing)

Sahajpal NS, Mondal AK, Njau A, Ananth S, Jones K, Ahluwalia PK, Ahluwalia M, Jilani Y, Chaubey A, Hegde M, Kota V, Rojiani A, Kolhe R. Proposal of RT-PCR-Based Mass Population Screening for Severe Acute Respiratory Syndrome Coronavirus 2 (Coronavirus Disease 2019). J Mol Diagn. 2020 Oct;22(10):1294-1299. doi: 10.1016/j.jmoldx.2020.07.001. PMID: 32738298

Saliva as a sample type for COVID-19 screening and testing (CLIA validation, FDA submission, and testing)

Sahajpal NS, Mondal AK, Ananth S, Njau A, Ahluwalia P, Kota V, Caspary K, Ross TM, Farrell M, Shannon MP, Fulzele S, Chaubey A, Hegde M, Rojiani AM, Kolhe R. Clinical Validation of a Sensitive Test for Saliva Collected in Healthcare and Community Settings with Pooling Utility for Severe Acute Respiratory Syndrome Coronavirus 2 Mass Surveillance. J Mol Diagn. 2021 Jul;23(7):788-795. doi: 10.1016/j.jmoldx.2021.04.005. PMID: 33957320

SalivaSTAT: Direct-PCR and pooling of saliva samples bypassing RNA extraction (CLIA validation, FDA submission, and testing)

Sahajpal NS, Mondal AK, Ananth S, Njau A, Ahluwalia P, Newnam G, Lozoya-Colinas A, Hud NV, Kota V, Ross TM, Reid MD, Fulzele S, Chaubey A, Hegde M, Rojiani AM, Kolhe R. SalivaSTAT: Direct-PCR and Pooling of Saliva Samples Collected in Healthcare and Community Setting for SARS-CoV-2 Mass Surveillance. Diagnostics (Basel). 2021 May 19;11(5):904. doi: 10.3390/diagnostics11050904. PMID: 34069462

The Georgia State COVID-19 Lab Surge Task Force

In anticipation of the spread of the virus in the US, the Georgia State Task Force COVID-19 response was formed on March 13, 2020, to discuss challenges and implement solutions in a coordinated manner that would enable a robust response throughout the state. The task force brought together a diverse set of expertise when everyone worked beyond their institutional silos as a cohesive team to fight the pandemic. Key institutional leaders met almost immediately to discuss the pandemic, and several of the individuals were already communicating within the task force to discuss the challenges as a cohesive unit.

Our first call identified key lab leaders at three major universities, Georgia Department of Public Health, and the Georgia Public Health Lab to help guide the development of the methods and processes needed to ensure quality and repeatable results across many labs. To add some structure to this initiative, we set up a project management and resource-sharing platform on Basecamp. As we assigned personnel to tasks, teams, based on their expertise, were identified in these critical areas (1) Laboratory Methods, (2) Data Management and Reporting, (3) Logistics and Supplies, and (4) New Technology & Testing Innovations. The initiative was executed in three phases with the following objectives identified by the team within the first 24hrs.

Developed CLIA LDT assay for COVID-19, influenza A and B, and RSV screening and testing on saliva and NSP samples "all-in-one"

Sahajpal, N. S., Mondal, A. K., Ananth, S., Njau, A., Jones, K., Ahluwalia, P., ... & Kolhe, R. (2022). Clinical validation of a multiplex PCR-based detection assay using saliva or nasopharyngeal samples for SARS-Cov-2, influenza A and B. Scientific reports, 12(1), 1-7. https://doi.org/10.1038/s41598-022-07152-0 PMID: 35241679

Exploring the human genome to identify susceptibility loci for COVID-19 severity

https://www.covid19hostgenomesv.org/index.html

Sahajpal NS, Jill Lai CY, Hastie A, Mondal AK, &… Hoischen A, Chaubey A, Kolhe R; COVID19hostgenomesv Consortium. Optical genome mapping identifies rare structural variations as predisposition factors associated with severe COVID-19. iScience. 2022 Feb 18;25(2):103760. PMID: 35036860; https://doi.org/10.1016/j.isci.2022.103760

Developed CLIA LDT assay for sequencing SARS-CoV-2 genome + 39 other viruses; along with UGA, we mapped these mutations, associating phylogenetic structure with demographics

Sahajpal NS, Mondal AK, Njau A, Petty Z, Chen J, Ananth S, Ahluwalia P, Williams C, Ross TM, Chaubey A, DeSantis G, Schroth GP, Bahl J, Kolhe R. High-Throughput Next-Generation Sequencing Respiratory Viral Panel: A Diagnostic and Epidemiologic Tool for SARS-CoV-2 and Other Viruses. Viruses. 2021 Oct 14;13(10):2063. https://doi.org/10.3390/v13102063 PMID: 34696495

Studying the human nasal microbiome in elderly patients with COVID-19

Kolhe R, Sahajpal NS, Vyavahare S, Dhanani AS, Adusumilli S, Ananth S, Mondal AK, Patterson GT, Kumar S, Rojiani AM, Isales CM, Fulzele S. Alteration in Nasopharyngeal Microbiota Profile in Aged Patients with COVID-19. Diagnostics (Basel). 2021 Sep 5;11(9):1622. doi: 10.3390/diagnostics11091622. PMID: 34573964

Community Outreach and Adapting CLIA laboratories

During the Pandemic Response

Meeting people where they are: Addressing health disparities in minority and rural populations

A substantial percentage of the GA population is from rural communities, often with a high percentage of minorities. These communities are often poorly represented in federally funded clinical studies and are historically difficult to engage in such work. Unfortunately, these same populations are at high risk for severe COVID-19. To mitigate the burden of COVID-19 within underserved AA communities, we decided to engage and “meet people where they are” by intervening at local AA churches and barbershops.

Moore JX, Gilbert KL, Lively KL, Laurent C, Chawla R, Li C, Johnson R, Petcu R, Mehra M, Spooner A, Kolhe R, Ledford CJW. Correlates of COVID-19 Vaccine Hesitancy among a Community Sample of African Americans Living in the Southern United States. Vaccines (Basel). 2021 Aug 8;9(8):879. doi: 10.3390/vaccines9080879. PMID: 34452004

Emergency preparedness for the next pandemic or next wave/variant

Sahahjpal NS, Mondal AK, Ananth S, Jones K, Chaubey A, Kolhe R. COVID-19 diagnostic assay sensitivity: lessons for the upcoming wave or next pandemic. Future Med Chem. 2021 Oct;13(20):1713-1715. doi: 10.4155/fmc-2021-0209. Epub 2021 Sep 2. PMID: 34472366

Adaptation of the clinical laboratory in response to the rapidly evolving COVID-19 pandemic

Sahajpal NS, Mondal AK, Ananth S, Njau A, Fulzele S, Ahaluwalia P, Chaubey A, Hegde M, Rojiani AM, Kolhe R. Making a Difference: Adaptation of the Clinical Laboratory in Response to the Rapidly Evolving COVID-19 Pandemic. Acad Pathol. 2021 Jun 9;8:23742895211023948. doi: 10.1177/23742895211023948. PMID: 34263025

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