key: cord-0695064-libaqx8g authors: Mutnal, Manohar B.; Arroliga, Alejandro C.; Walker, Kimberly; Mohammad, Amin; Brigmon, Matthew M.; Beaver, Ryan M.; Midturi, John K.; Rao, Arundhati title: Early trends for SARS‐CoV‐2 infection in central and north Texas and impact on other circulating respiratory viruses date: 2020-06-02 journal: J Med Virol DOI: 10.1002/jmv.26010 sha: 2e785c06442d811092b53263c3fca4d66053055e doc_id: 695064 cord_uid: libaqx8g Rapid diagnosis and isolation are key to containing the quick spread of a pandemic agent like severe acute respiratory syndrome‐related coronavirus 2 (SARS‐CoV‐2), which has spread globally since its initial outbreak in Wuhan province in China. SARS‐CoV‐2 is novel and the effect on typically prevalent seasonal viruses is just becoming apparent. We present our initial data on the prevalence of respiratory viruses in the month of March 2020. This is a retrospective cohort study post launching of SARS‐CoV‐2 testing at Baylor Scott and White Hospital (BSWH), Temple, Texas. Testing for SARS‐CoV‐2 was performed by real‐time reverse transcription polymerase chain reaction assay and results were shared with State public health officials for immediate interventions. More than 3500 tests were performed during the first 2 weeks of testing for SARS‐CoV‐2 and identified 168 (4.7%) positive patients. Sixty‐two (3.2%) of the 1912 ambulatory patients and 106 (6.3%) of the 1659 emergency department/inpatients tested were positive. The highest rate of infection (6.9%) was seen in patients aged 25 to 34 years, while the lowest rate of infection was seen among patients aged <25 years old (2%). County‐specific patient demographic information was shared with respective public health departments for epidemiological interventions. Incidentally, this study showed that there was a significant decrease in the occurrence of seasonal respiratory virus infections, perhaps due to increased epidemiological awareness about SARS‐CoV‐2 among the general public, as well as the social distancing measures implemented in response to SARS‐CoV‐2. Data extracted for BSWH from the Centers for Disease Control and Prevention's National Respiratory and Enteric Virus Surveillance System site revealed that Influenza incidence was 8.7% in March 2020, compared with 25% in March 2019. This study was intended to provide an initial experience of dealing with a pandemic and the role of laboratories in crisis management. This study provided SARS‐CoV‐2 testing data from ambulatory and inpatient population. 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 outbreak of pneumonia of unknown cause. By 7th January 2020, Chinese scientists had isolated a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; previously known as 2019-nCoV), from these patients with virus-infected pneumonia. 1 Cases have now spread to 190 countries. As of 23rd March 2020 there were more than 372 000+ confirmed cases and 16 000+ deaths. 2 Although the outbreak is likely to have started from a zoonotic transmission event associated with a large seafood market that also traded in live wild animals, it soon became clear that efficient person-to-person transmission was occurring. 3 The clinical spectrum of SARS-CoV-2 infection appears to be wide, encompassing asymptomatic infection, mild upper respiratory tract illness, and severe viral pneumonia with respiratory failure and even death, with many patients being hospitalized with pneumonia. 4 A global pandemic has erupted due to a high proportion of asymptomatic patients coupled with a high degree of viral shedding, long incubation period, and late clinical manifestations. Prolific testing coupled with case isolation and contact tracing, therefore, remains one of the most effective epidemiological interventions to stop early community spread. Unfortunately, the novelty of SARS-CoV-2 meant that no testing was immediately available, making it difficult for public health officials to get ahead of the pandemic curve. As State public health laboratories became backlogged, Baylor Scott and White Health (BSWH), a large, not-for-profit integrated healthcare delivery system in north and central Texas, collaborated with the Luminex Corporation (Austin, TX) to implement a SARS-CoV-2 realtime reverse transcription polymerase chain reaction (rRT-PCR) assay using the genetic primers previously used in China to help relieve the bottleneck. The BSWH laboratory was one of the first laboratories in Texas to implement SARS-Co-V2 testing to assist state public health officials in their efforts to isolate patients and track their immediate contacts. As the pandemic continues to spread across the nation, goal of this study was to share the early clinical trends for coronavirus disease 2019 (COVID-19) in north and central regions of Texas, to encourage other laboratories to consider early implementation of testing during future pandemics. This study also reports the possible impact of SARS-CoV-2 on other seasonal respiratory viruses in this region, the spread of which may have been affected by epidemiological interventions introduced in response to SARS-CoV-2. This retrospective cohort study included all adult patients (age >18 years) tested for SARS-CoV-2 collected through BSWH testing sites from 11th March 2020 to 23rd March 2020. BSWH is a large, not-for-profit integrated health care delivery system, with 52 hospitals and more than 1000 care sites, serving patients in 47 counties in north and central Texas. All SARS-CoV-2 tests included in this study were performed at the molecular pathology laboratory located within BSWH, Temple. All ambulatory care patients were prescreened according to World Health Organization and BSWH guidelines to be eligible for SARS-CoV-2 testing via the BSWH web portal, phone app and/or through an e-visit before making an appointment for specimen collection at one of the several designated BSWH locations. Patients were asked about current symptoms, such as fever, cough, and shortness of breath, as well as travel and other exposure history. When clinically indicated, SARS-CoV-2 testing was ordered by the attending physician or other care providers. No prescreening was done for emergency department (ED)/inpatients. In these settings, a nasopharyngeal swab was collected for SARS-CoV-2 testing from all patients showing signs and symptoms of SARS-CoV-2 infection. As BSWH laboratory continues testing, this study included data from the day testing began on 11th March 2020 to 23rd March 2020. These two hospital systems within BSWH represent central and north Texas population and are limited to these regions of Texas due to community outreach. Study includes data for SARS-CoV-2 testing from these two regions and seasonal respiratory virus testing data is limited to central Texas region. The SARS-CoV-2 primers were designed by Luminex to detect RNA targets from the SARS-CoV-2 in respiratory specimens from patients, as recommended for testing by public health authority guidelines. Luminex Aries employs primers for amplifying the ORF1 gene and the N gene from the SARS-CoV-2 virus, and the assay includes extraction and internal controls (Human RNAase P) built into the same cartridge, to verify sample lysis, nucleic acid extraction, and proper system and reagent performance. Luminex Aries offers true random-access testing, unlike the Luminex NxTAG platform, an assay for batched testing (offering high throughput capabilities) on which increased demand for testing necessitated validation. The Luminex NxTAG method also includes an additional Envelope (E) gene target for SARS-CoV-2 detection. F I G U R E 1 Baylor Scott and White Memorial hospital initiated testing on 11th March 2020 following an Emergency Use Authorization submission to Food and Drug Administration (FDA). The data shown represents more than 3500 tests were performed between 11th and 23rd March 2020 for the two different regions of Texas State (Central and North) The typical turnaround time from specimen collection to verification of test results was less than 15 hours. Sars-CoV-2 assays on 27th March and 3rd April 2020, respectively. A total of 3571 SARS-CoV-2 rRT-PCR tests were performed at the BSWH-Temple laboratory, 1912 specimens were received from ambulatory or drive-through collection sites, and 1659 from ED/inpatient settings. Sixty-two (3.2%) ambulatory patients were tested positive, as did 106 (6.3%) ED/inpatient population, noted in Figures 2 and 3 , respectively. BSWH initial data showed that the age group with the highest percentage of positive tests was patients 25 to 34 years (7.4%) followed by 6.9% in 55 years to 64 years age group. Lowest incidence (2%) was seen among those aged <25 years old ( Figure 4) . Clinical symptoms and underlying morbidities for limited number of ED/inpatients are presented in Table 1 . More than 75% of the patients who presented in the ED had fever and cough. An appropriate epidemiological intervention requires identification of patient demographics for public health officials to track and trace positive cases. Therefore, it is prudent that SARS-CoV-2 testing la- The SARS-CoV-2 literature is evolving at breakneck speed, but there is a paucity of literature detailing experiences with the in-house testing solutions implemented to combat the national delays in turnaround time and the shortages of testing kits. Real-time rRT-PCR is already widely deployed in diagnostic virology laboratories; our experience demonstrates that institutions with molecular testing F I G U R E 3 Data shown are daily positives from 11th March 2020 to 23rd March 2020. Nasopharyngeal specimens were collected from patients presented in the emergency department and/or admitted and were tested on Luminex Aries, a true random access instrument for a faster turn-around time F I G U R E 4 Data shown represent positivity rate among various age groups, also shown are number of tests performed and positive results for each group capabilities should consider proactively reaching out to manufacturers to improve testing capabilities and turn-around time should a similar situation recur. In the race against this pandemic, real-time data empower epidemiologists and public health officials to identify, track, and contain spread as much as possible. Integrating laboratorybased reporting with epidemiologic surveillance registers will only improve public health outcomes. The intent of this study was not to assess the performance characteristics of the rRT-PCR assay for the detection of SARS-CoV-2 infection. Accurate determination of test performance characteristics will require appropriate distribution of cohorts among the general population. This is specifically true in the context of virus shedding, transmission dynamics, asymptomatic carriers, and specimen requirements that are still being debated and investigated. SARS-CoV-2 has exhibited a great degree of plasticity in all of the above properties; hence it may take additional time and understanding to determine the performance characteristics of the assay. The evidence available from the literature at the initiation of the public health emergency was sparse for US healthcare systems. The only country with published data and epidemiological or management studies was China. 7 However, the structure of both the political and the health care system in China is very different from the United States, where healthcare is regional and private for most part, and much of the public health authority is decentralized and vested in state and local governments. While these structures create challenges for the coordinated, authoritarian type of response China implemented to control and mitigate its. SARS-CoV-2 outbreak, the substantial autonomy they provide creates opportunities to try to improve and optimize diagnosis, management and partnership with public health officials. In this context, BSWH ramped up efforts in laboratory diagnosis and collegial collaboration with public health officials to support effective epidemiological interventions. Because SARS-CoV-2 infection symptoms range from nonspecific mild respiratory symptoms to acute respiratory distress, 4 and because these symptoms are very similar to those of many seasonal viruses, 8 BSWH implemented outpatient screening protocols hosted on the BSWH web portal, phone app, and e-visit sites to ensure appropriate prescreening of individuals for targeted laboratory testing. Real-time RT-PCR testing for various other infections is widely deployed in most diagnostic laboratories. In the case of a public health emergency, proficient diagnostic laboratories can rely on this robust technology and infrastructure to establish new diagnostic tests within their routine services before pre-formulated assays become available. In addition to information on reagents, oligonucleotides, and positive controls, laboratories working under quality control programs need to rely on documentation of technical qualification of the assay formulation as well as data from external clinical evaluation tests. 8, 9 Everything listed above can be true for a laboratory-developed test; however, if commercial manufacturers design assays under FDA oversight, all of the above requirements can be mitigated. The available genome sequence of SARS-CoV-2 has T A B L E 1 Demographic, comorbidity, symptoms, other social, and past medical history of BSWH inpatient population Baseline characteristics (total n = 14) Sex, % (n) We provide results from a molecular diagnostic laboratory's initial experience with dealing with a pandemic, and an example of how laboratories can contribute to management of public health crises. We demonstrate that proactive collaboration with assay manufacturers can enable laboratories to be prepared for-or respond rapidly to-emerging diseases like COVID-19. Epidemiological interventions depend on availability of accurate diagnostic tests and high throughput capacity during large outbreaks like SARS-CoV-2. It is also important to have a well-organized plan to report the test results to public health officials to initiate counter measures to control the infections, and to build a diagnostic algorithm to include testing for other seasonal respiratory viruses, especially most common viruses like influenza and RSV, which may require medical attention. The novel coronavirus originating in Wuhan, China: challenges for global health governance Clinical features of 69 cases with coronavirus disease Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study Clinical evaluation of the Luminex NxTAG respiratory pathogen panel The novel coronavirus: a bird's eye view Rapid viral diagnosis and ambulatory management of suspected COVID-19 cases presenting at the infectious diseases referral hospital in Marseille, France-31st The European virus archive goes global: a growing resource for research Molecular diagnosis of a novel coronavirus (2019-nCoV) causing an outbreak of pneumonia COVID-19: active measures to support community-dwelling older adults Rates of co-infection between SARS-CoV-2 and other respiratory pathogens Closure of schools during an influenza pandemic Priorities for the US health community responding to COVID-19 Early trends for SARS-CoV-2 infection in central and north Texas and impact on other circulating respiratory viruses The authors would like to thank Jeffry Hunt for help with data extraction and Courtney Shaver for help with statistics. Asthma, % (n) 36 (5) COPD, % (n) 21 (3) CHF, % (n) 14 (2) HTN, % (n) 50 (7) Medications, % (n) (11) Headache % (n) 36 (5) Rhinorrhea % (n) 28 (4) Cough % (n) 79 (11) Otalgia/pressure % (n) 21 (3) Odynophagia % (n) 7 (1) Mild dyspnea % (n) 64 (9) Severe dyspnea % (n) 21 (3) Diarrhea % (n) 7 (1) Clinical characteristics, % (n)Abnormal chest x-ray 50 (7) Peripheral pulse oximetry <94 28 (4) Temperature 38°C/100.4°F 50 (7) Abbreviations: ACE, angiotensin-converting enzyme; BMI, body mass index; BSWH, Baylor Scott and White Health; CHF, congestive heart failure; COPD, chronic obstructive pulmonary disease; HTN, hypertension. All authors declare that there are no conflict of interests.