key: cord-0755949-5fz8ef4f authors: Mutnal, M. B.; Arroliga, A. C.; Walker, K.; Mohammad, A. A.; Brigmon, M. M.; Beaver, R. M.; Midturi, J. K.; Rao, A. title: Early trends for SARS-CoV-2 infection in central and north Texas and impact on other circulating respiratory viruses date: 2020-05-02 journal: nan DOI: 10.1101/2020.04.30.20086116 sha: 83637e1e80489c7cb8453e842a0764c6308871ab doc_id: 755949 cord_uid: 5fz8ef4f Introduction: Rapid diagnosis and isolation are key to containing the rapid spread of a pandemic agent like SARS-CoV-2, which has spread globally since its initial outbreak in Wuhan province in China. SARS-CoV-2 is novel to most parts of the world including USA and the effect on normally prevalent viruses is just becoming apparent. We present our initial data on the prevalence of respiratory viruses in the month of March, 2020. Methods: This is a retrospective cohort study post launching of SARS-CoV-2 testing at BSWH, Temple TX. Testing for SARS-CoV-2 was performed by real-time RT-PCR assay and results were shared with State public health officials for immediate interventions. Results: More than 3500 tests were performed during the first two weeks of testing for SARS-CoV-2 and identified 168 (4.7%) positive patients. Sixty-two (3.2%) of the 1,912 ambulatory patients and 106 (6.3%) of the 1,659 ED/inpatients were tested positive. Higher rate of infection (6.9%) were noted in the patients belonging to age group 25-34 years and least number of positive cases were noted in <25 years old (2%) group. The TX State county specific patient demographic information was shared with respective public health departments for epidemiological interventions. Incidentally, this study showed that there was a sudden decrease in the occurrence of other infections due to seasonal viruses, perhaps due to increased epidemiological awareness, about SARS-CoV-2, among general public. Authors would also like to share a small study on SARS-CoV-2 serological assay for the detection of IgG antibodies. Conclusions: This study was intended to provide an initial experience of dealing with a pandemic and the role of laboratories in crisis management. Epidemiological interventions depend on timely availability of accurate diagnostic tests and throughput capacity of such systems during large outbreaks like SARS-CoV-2. In December 2019, Wuhan city, the capital of Hubei province in China, became the center of an 50 outbreak of pneumonia of unknown cause. By Jan 7, 2020, Chinese scientists had isolated a novel 51 coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; previously known as 2019-52 nCoV), from these patients with virus-infected pneumonia. 1 Cases have now spread to 190 countries. As 53 of March 23, 2020 there were more than 372,000+ confirmed cases and 16,000+ deaths. 2 Although the 54 outbreak is likely to have started from a zoonotic transmission event associated with a large seafood 55 market that also traded in live wild animals, it soon became clear that efficient person-to-person 56 transmission was also occurring. 3 57 The clinical spectrum of SARS-CoV-2 infection appears to be wide, encompassing asymptomatic 58 infection, mild upper respiratory tract illness, and severe viral pneumonia with respiratory failure and 59 even death, with many patients being hospitalized with pneumonia in Wuhan and elsewhere. 4 A global 60 pandemic has erupted due to a high proportion of asymptomatic patients coupled with a high degree of 61 viral shedding, long incubation period, and late clinical manifestations. Prolific testing, therefore, 62 remains one of the most effective epidemiological interventions to stop early community spread. 63 Unfortunately, the novelty of SARS-CoV-2 meant that no testing was immediately available making it 64 difficult for public health officials to stay ahead of the pandemic curve. in Texas State to adopt SARS-Co-V2 testing to assist state public health officials for tracing and tracking 71 patients and their immediate contacts. As the pandemic continues to spread across the nation, goal of this 72 study was to share the early clinical trends for COVID-19 in north and central regions of Texas. The aim 73 All rights reserved. No reuse allowed without permission. was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 2, 2020. . https://doi.org/10.1101/2020.04.30.20086116 doi: medRxiv preprint of this study is to encourage other laboratories to consider an early start to testing during pandemics, share 74 initial trends in this part of the world and possible impact of SARS-CoV-2 on other seasonal respiratory 75 viruses. This report describes the early trends of SARS-CoV-2 infections in the central and north Texas, 76 USA and impact of epidemiological interventions that may have led to the decrease in the incidence of was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. Baylor organization will be referred to as BSW hospitals (BSWH). All adult patients were prescreened 110 according to WHO and BSWH guidelines to be eligible for SARS-CoV-2 testing. Briefly, patients were 111 prescreened on BSWH web portal, phone app and/or through e-visit prior to making appointment for 112 specimen collection at one of the several designated locations. Patients were asked for travel history and 113 any other associated symptoms such as fever, cough and shortness of breath. When clinically indicated, 114 SARS-CoV-2 testing was ordered by the attending physician or by other care providers. 115 As BSWH laboratory continues testing, this study included data from the day testing began on 116 March 11, 2020 and until March 23, 2020. These two hospital systems within BSWH represent central 117 and north Texas population and are limited to these regions of Texas due to community outreach. Study 118 includes data for SARS-CoV-2 testing from these two regions and seasonal respiratory virus testing data is 119 limited to central Texas region. 120 Epidemiological, demographic, clinical and laboratory data were extracted from electronic 122 medical records and laboratory information system. The SARS-CoV-2 primers were designed by manufacturer of the assay to detect RNA targets from 135 the SARS-CoV-2 in respiratory specimens from patients as recommended for testing by public health 136 authority guidelines. The method employs two primers for amplifying ORF1 gene and N gene from 137 SARS-CoV-2 virus and the assay includes extraction and internal controls built in the same cartridge. 138 Internal sample processing controls to verify sample lysis, nucleic acid extraction, and proper system and 139 reagent performance are built into each Luminex Extraction Cartridge. Human RNAase P was used as an 140 internal control. Luminex Aries offers true random-access testing, however, increased demand for testing 141 necessitated validation of a similar assay on the Luminex NxTAG platform for batched testing, this 142 method includes additional Envelope (E) gene target for SARS-CoV-2 detection. The Luminex NxTAG 143 platform offers high throughput but on a batched processing using similar primers as Luminex Aries. 144 Both assays had received FDA Emergency Use Authorization prior to submission of this manuscript. 145 Other respiratory virus testing 146 BSWH utilizes respiratory virus syndromic panel, also from Luminex, for the diagnosis of upper 147 respiratory infections. This Luminex NxTAG assay was used as previously described 6 was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 2, 2020. was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 2, 2020. The typical turnaround time for specimen collection to verification of test results was less than 15 hours. 183 Individuals were delivered a prescreening questionnaire to be eligible for testing through BSWH Table 1 . More than 75% of the patients presented in emergency department had fever and 192 A total of 3,571 SARS-CoV-2 rRT-PCR tests were performed at BSWH laboratory, 1,912 194 specimens were received from ambulatory and/or drive-through collection sites, and 1,659 from the 195 All rights reserved. No reuse allowed without permission. was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 2, 2020. to 34 years age group (7.4%) followed by 6.9% in 55 years to 64 years age group. Data presented here 199 indicated a lower incidence (2%) among the <25 years old (Figure 4) . was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 2, 2020. . https://doi.org/10.1101/2020.04.30.20086116 doi: medRxiv preprint ( Figure 6) . 221 This study also looked at co-infections rates from SARS-CoV-2 positive patients. We searched for 222 262 patient records that had concurrent testing requests for SARS-CoV-2 and other respiratory virus 223 infections. Contrary to several other reports from other parts of the nation, this study did not notice any 224 co-infection cases with SARS-CoV-2. 225 226 All rights reserved. No reuse allowed without permission. was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The SARS-CoV-2 literature is evolving at breakneck pace, but there is a paucity of literature 228 detailing in-house testing solutions to combat the national delays in turn-around time or the shortages of 229 testing kits available. As real-time rRT-PCR is already widely deployed in diagnostic virology 230 laboratories, this study recommends any institution with molecular testing capabilities consider 231 proactively reaching out to manufacturers to improve testing capabilities and turn-around time. In the race 232 against this pandemic, real-time data empower epidemiologists and public health officials to identify, 233 track, and contain spread as much as possible. Integrating laboratory-based reporting with epidemiologic 234 surveillance registers will only further improve public health outcomes. 235 The intent of this study was not to assess the performance characters of the rRT-PCR assay for 236 the detection of SARS-CoV-2 infection. Authors are of the opinion that accurate determination of test 237 performance characters will require appropriate distribution of cohorts among the general population 238 especially in the context of virus shedding, transmission dynamics, asymptomatic carriage and specimen 239 requirements are still being debated and investigated. SARS-CoV-2 has exhibited great degree of plasticity 240 in all of the above characters hence it may take additional time and understanding to determine the 241 performance characters of the assay. 242 The literature data available at the time of the emergency were few for most USA healthcare 243 systems and above all stemming from the only experience available on the outbreak from COVID 2019. 244 The only country with published data and epidemiological or management studies was represented by the 245 Chinese outbreak. 7 However, the health system and the Chinese government represent a very different 246 model from the USA reality where healthcare is regional and private for most part, which enjoys 247 significant autonomy such as the possibilities available to try to improve and optimize diagnosis, 248 management and partnership with public health officials. In this context, BSWH ramped up efforts in 249 laboratory diagnosis and collegial collaboration with public health officials for effective epidemiological 250 All rights reserved. No reuse allowed without permission. was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 2, 2020. To best of authors' knowledge, this is the first report on SARS-CoV-2 testing from this part of the 272 world. BSWH laboratory would like to share this information with our readers and other laboratories that 273 early adoption of testing for pandemic diseases like COVD-19 has long-term implications in management 274 and control measures. BSWH laboratory provided test results data on both ambulatory and inpatient 275 population, and shared patient demographics with local public health officials. 276 All rights reserved. No reuse allowed without permission. was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 2, 2020. . https://doi.org/10.1101/2020.04.30.20086116 doi: medRxiv preprint emergency department or admitted for further evaluations. Major symptoms included were fever and 278 cough, more than 75% of the patients reported to have these symptoms. Khuwara et al 12 reported similar 279 findings in Wuhan outbreak, reporting greater than 90% and 75% of the patients exhibiting fever and 280 cough, respectively. 281 Interestingly, data mining did not yield any co-infections with SARS-CoV-2 unlike Stanford 282 Medicine data 13 . This study attributes the initial trend of not finding co-infections with SARS-CoV-2 to was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 2, 2020. This study was intended to provide an initial experience of dealing with a pandemic and how 302 laboratories are required to be part of the crisis management. This study demonstrated that proactive 303 collaboration with assay manufacturers would enable laboratories to be prepared for emerging diseases 304 like COVID-19. Epidemiological interventions depend on availability of accurate diagnostic tests and 305 throughput capacity of such system during large outbreaks like SARS-CoV-2. It is also important to have a 306 well-organized plan to report the test results to public health officials to initiate counter measures to 307 control the infections. It is also imperative to build a diagnostic algorithm to include testing for other 308 seasonal respiratory viruses, especially most common viruses like Influenza and RSV, which may require 309 medical attention. 310 was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 2, 2020. The Novel Coronavirus Originating in Wuhan, China: Challenges for 324 Global Health Governance Clinical Features of 69 Cases with Coronavirus Disease Clinical course and risk factors for mortality of adult inpatients with 331 COVID-19 in Wuhan, China: a retrospective cohort study Clinical Evaluation of the Luminex NxTAG Respiratory 336 Pathogen Panel The Novel Coronavirus: A Bird's Eye View Rapid viral diagnosis and ambulatory management of 340 suspected COVID-19 cases presenting at the infectious diseases referral hospital The European Virus Archive goes global: A growing resource 344 for research Detection of 2019 novel coronavirus (2019-nCoV) by real-346 time RT-PCR Molecular Diagnosis of a Novel Coronavirus Causing an Outbreak of Pneumonia COVID-19: Active measures to support community-dwelling older adults. Travel 350 Med Infect Dis Rates of Co-infection Between SARS-CoV-2 and 352 Other Respiratory Pathogens Closure of schools during an influenza pandemic Priorities for the US Health Community Responding to COVID-356 19 Authors would like to thank Jeffry Hunt for help with data extraction and Courtney