Experiences & challenges in making Model Rural Health Research Unit (MRHRU) pandemic ready – Establishing COVID-19 molecular diagnostic facility at MRHRU, Dahanu, Maharashtra

Sir,

The first positive test of COVID-19 in India was recorded on January 27, 2020 from Kerala1. Since then, more than 915.6 million samples have been tested and approximately 44.6 million positive cases identified, as of January 31, 20232. This was made possible by establishing an extensive network of COVID-19 diagnostic laboratories across the country. The Indian Council of Medical Research (ICMR) has worked towards establishing or initiating the COVID-19 diagnostic services in various government and private laboratories, especially ramping up the existing Viral Research and Diagnostic Laboratories setup by the Department of Health Research (DHR), Ministry of Health and Family Welfare, Government of India (GoI) in the first half of 2020. As of February 2023, 3388 laboratories (government - 1456 and private - 1932) were involved in the diagnosis of COVID-19 by using molecular techniques including real-time reverse transcription (RT)-PCR, TruNAT, cartridge-based nucleic acid amplification test, RT-loop-mediated isothermal amplification and CRISPR-Cas93. Most of these laboratories are situated in the urban areas, State headquarters or associated with medical colleges, and a few are in the rural areas. By the end of April 2020, the total number of diagnostic facilities for COVID-19 across the country was 3924. During these initial stages of the pandemic, there was no molecular diagnostic facility in the district of Palghar, Maharashtra, and the samples were being sent to the nearest facilities in Mumbai which were about 100-150 km away from various blocks of Palghar district. Moreover, the results were delayed due to the overburden of samples on the existing facilities in Mumbai.

The GoI conceptualized a central sector scheme of developing infrastructure for the promotion of health research across the country during the 12^th five-year plan (2012-2013 to 2016-2017)5. The establishment of Model Rural Health Research Units (MRHRUs) is a part of that scheme by DHR with 23 MRHRUs spanning across the country, as of June 20225. All MRHRUs have a mentor ICMR institute and a linked medical college to guide the research activities relevant to the local needs. MRHRUs have infrastructure as well as adequate equipment to carry out research activities. MRHRU, Dahanu, has a team of eight staff each including qualified medical (gynaecologist) and non-medical (Ph.D.) scientists; statistical, technical and administrative personnel supported by a nodal officer (public health expert) and a member secretary (medical expert) to conduct various laboratory- and community-based research projects. One of the main objectives of this scheme was to create infrastructure for technology transfer at the periphery to improve the quality of health services delivered to the rural population. In Maharashtra, with the collaboration between ICMR-National Institute for Research in Reproductive and Child Health (ICMR-NIRRCH), Mumbai, as the research mentoring body; Directorate of Health Services, Government of Maharashtra, as the facilitator and Grant Medical College, Mumbai as the linked medical college, MRHRU was established at Dahanu in 2014. This unit is in Palghar district, where the predominant population is tribal and has a hilly terrain with coastal plains. Various community- and laboratory-based research activities addressing the local burden of diseases have been completed or are ongoing6. The district health administration is actively engaged in various research activities of MRHRU.

Considering the non-availability of diagnostic facilities for COVID-19 in Palghar district, public health experts and scientists at ICMR-NIRRCH and the linked medical college planned to initiate a COVID-19 diagnostic laboratory at MRHRU, Dahanu, in the first week of April 20207. Subsequently, they were also approached by the District Collector of Palghar for establishment of this laboratory. Since the available gold standard confirmatory test for COVID-19 was real-time reverse transcription (RT)-PCR assay, a joint proposal was submitted to ICMR for the establishment of a molecular diagnostic facility at MRHRU, Dahanu. The proposal was approved by ICMR on May 10, 2020 leading to the initiation of diagnostic services from May 27, 2020. A brief timeline of the establishment along with the monthly sample load till June 2022 is depicted in Figure.

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Figure

Timeline of the establishment of COVID-19 diagnostic facility at MRHRU, Dahanu, along with monthly sample size and positivity rate. Source: https://www.mohfw.gov.in/and https://ourworldindata.org/coronavirus/country/india (Data on the total test performed was available till July 2022). MRHRU, Model Rural Health Research Unit

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MRHRU technical team underwent training for two days on COVID-19 diagnosis at ICMR-National Institute of Virology Unit, Mumbai, and ICMR-NIRRCH. Existing biosafety level II cabinets were upgraded as per the ICMR guidelines, and one real-time PCR instrument was relocated from ICMR-NIRRCH to MRHRU. Although MRHRU had a core team, the number of personnel was not adequate to cope with the sample load. The district health administration supported MRHRU diagnostic facility by recruiting qualified technical and data entry teams (one microbiologist, two technicians and two data entry operators). The technical team appointed by the district was trained to perform RNA extraction and RT-PCR by MRHRU scientists. MRHRU was provided with an automated nucleic acid extraction machine by district administration and the consumables required to carry out the RT-PCR test by the State government of Maharashtra. A nodal officer of the COVID-19 laboratory attended virtual meetings with State health authorities on a daily basis. Various challenges related to the development of infrastructure, capacity building with qualified local staff, validation of equipment, power outages, demand for increase in the testing capacity of the facility, arranging logistics for kits, etc. were faced to establish the COVID-19 diagnostic facility at MRHRU (Table). Timely guidance from the scientists at mentoring institute has been valuable in overcoming various challenges. To the best of our knowledge, MRHRU, Dahanu, is the first and only MRHRU to get approval and function as a COVID-19 diagnostic centre across India3.

During the pandemic’s first wave, routine work at MRHRU came to a halt especially affected were the research involving field visits and sample collection. Subsequently, this issue was resolved with the additional staff provided by the district health authorities for COVID-19 diagnosis.

By the end of June 2022, a total of 56,394 clinical samples were tested for the presence of SARS-CoV-2, of which 5536 tested positive, giving a cumulative positivity of 9.82 per cent. Coordinating with the district health facilities to maintain the stable inflow of the samples, batch-wise rotation of the available human resources, upfront stocking of the consumables and maintaining complete records of the samples helped the facility to provide the reports within the ICMR’s time limit of 24 h from the time of sample receipt. This further helped the health authorities to check the infection spread. From the inception of the diagnostic facility, three peak stages of COVID-19 positivity were observed similar to the national trend of COVID-19 waves (Figure)8. The highest positivity rate during the first wave was recorded in August and September 2020 with a positivity rate of 24.65 and 25.61 per cent, respectively. While the second wave of COVID-19 in the region started in February 2021, the highest positivity was recorded between April and May 2021 with a positivity rate of 27.63 and 19.98 per cent, respectively. The most recent rise in positivity was observed in the month of January 2022 with a positivity of 22.9 per cent, which was the shortest of the three waves. During the peak stages, samples were pooled as per the guidelines of ICMR, to increase the testing capacity9. At this time MRHRU, Dahanu, also served as the district coordinating centre for sending samples to the Indian SARS-CoV-2 Genomics Consortium (INSACOG), where samples were sequenced to identify the circulating variant of SARS-CoV-210. In July 2021, INSACOG reported a case from Palghar district with Delta Plus variant, a variant of concern11.

Establishment of COVID-19 diagnostic facility at MRHRU, Dahanu, is an example depicting a successful partnership between District Health System and ICMR Research Institute. As the existing MRHRUs have the infrastructure and trained personnel to establish such diagnostic facilities, and with support from District Health System (additional manpower), they can be geared up in times of outbreaks, epidemics or pandemics in future to serve the local rural population. MRHRUs can also help in establishing the district-level sentinel sero-surveillance centre for various infectious diseases across the rural areas of India. The service delivery model developed at Dahanu, Maharashtra, can be replicated at MRHRUs located in other States.