key: cord-0725484-s6p7o125 authors: Chen, Alexander; Wessler, Timothy; Daftari, Katherine; Hinton, Kameryn; Boucher, Richard C.; Pickles, Raymond; Freeman, Ronit; Lai, Samuel K.; Forest, M. Gregory title: Modeling insights into SARS-CoV-2 respiratory tract infections prior to immune protection date: 2022-04-02 journal: Biophys J DOI: 10.1016/j.bpj.2022.04.003 sha: 7632845724cfa0a837752ad0b1c93eefac39c23f doc_id: 725484 cord_uid: s6p7o125 Mechanistic insights into human respiratory tract (RT) infections from SARS-CoV-2 can inform public awareness as well as guide medical prevention and treatment for COVID-19 disease. Yet, complexity of the RT and the inability to access diverse regions pose fundamental roadblocks to evaluate potential mechanisms for onset and progression of infection (and transmission). We present a model that incorporates detailed RT anatomy and physiology, including airway geometry, physical dimensions, thicknesses of airway surface liquids (ASL), and mucus layer transport by cilia. The model further incorporates SARS-CoV-2 diffusivity in ASL and best-known data for epithelial cell infection probabilities, and once infected, duration of eclipse and replication phases, and replication rate of infectious virions. We apply this baseline model in the absence of immune protection to explore immediate, short-term outcomes from novel SARS-CoV-2 depositions onto the air-ASL interface. For each RT location, we compute probability to clear versus infect; per infected cell, we compute dynamics of viral load and cell infection. Results reveal that nasal infections are highly likely within 1-2 days from minimal exposure and alveolar pneumonia occurs only if infectious virions are deposited directly into alveolar ducts and sacs, not via retrograde propagation to the deep lung. Furthermore, to infect just 1% of the 140 m2 of alveolar surface area within one week, either 103 boluses each with 106 infectious virions or 106 aerosols with 1 infectious virion, all physically separated, must be directly deposited. These results strongly suggest COVID-19 disease occurs in stages: a nasal/upper RT infection, followed by self-transmission of infection to the deep lung. Two mechanisms of self-transmission are persistent aspiration of infected nasal boluses that drain to the deep lung and repeated rupture of nasal aerosols from infected mucosal membranes by speaking, singing, cheering that are partially inhaled, exhaled and re-inhaled, to the deep lung. in Supplemental Material) with SARS-CoV-2 mobility in airway 66 surface liquid barriers, epithelial cell infection probabilities, replication rates and duration of virion 67 progeny by infected cells (see Table S2 in hours and days (up to one week) after exposure, we acknowledge that some immune response, especially 84 interferon signaling (see [1, 2] ), is often triggered within these timescales. These effects can be coupled to Our respiratory tract model for pathogen exposure and outcomes starts with the following fact. When 90 presented with a novel viral exposure in the RT, the primary defense mechanism is mucociliary clearance 91 (MCC) [3, 4, 5, 6, 7, 8, 9] . Inhaled particulates deposit onto the air-mucus interface, and the mucus layer 92 is continuously propelled by coordinated, beating cilia in the periciliary liquid (PCL) layer between the 93 epithelium and mucus layer (see Figure 1 ). MCC occurs everywhere in the RT except the alveolar space. [10, 11, 12, 13, 14, 15, 16, 17, 18, 19] and [20, 21, 22] . The computational modeling platform incorporates the following (see Tables S1and S2 in timescale between virion uptake and cell replication of virions, infected cell replication rates, and 108 duration of viable infectious virions (where cell infection probability is a proxy for affinity to, and the 109 density of, angiotensin-converting enzyme (ACE2) or other receptors [23, 24] and the endosomal entry 110 pathway [25] for the virus to enter and hijack cellular machinery) The model, starting from any infectious inoculum or time series of inocula deposited onto the 112 air-mucus or air-alveolar liquid interface, tracks two evolving fronts: the infectious virion front, 113 along with the infectious titer in the ASL in the wake of the front; and, the infected epithelial cell 114 front, along with the total infected cell surface area in the wake of the front. These fronts are 115 defined by the leading infectious virion and infected cells farthest from the initial site of 116 deposition, while infection and replication continue in the wake. A critical disease metric is the 117 percentage of infected alveolar type 2 (AT2) cells within the 140 m 2 total alveolar surface area 118 [26, 27] , simulated and compiled below versus the number of physically separated, infectious 119 seeds deposited into the alveolar space over a 7-day period. We rely on the rich history of 120 computational modeling and experimental validation of inhaled depositions in the RT [28, 29, 121 30, 31, 32, 33] , including deposition of SARS-CoV-2 in the upper RT [34] . 122 123 Anatomy and Physiology of the Human Respiratory Tract 124 125 126 Once inside the cell, an eclipse phase entails hijacking cellular machinery, viral RNA is then uncoated, 159 replicated, transported to the cell membrane, and shed into the ASL [37, 40] . The eclipse phase, Table S2, 160 for the alpha variant is ~12 hours [37, 40] . Post eclipse, infected cells shed ~ 50K progeny per day into 161 the ASL for ~3 days, of which only ~ 1-2K per day are infectious [37, 40] . Note that virion shedding into Note the total airway surface liquid thickness of these generations is the mucus thickness, Column 3, which varies dramatically, 326 plus the 7 µm periciliary liquid layer which has a uniform thickness throughout the RT. We next present details of infected cell outcomes ( J o u r n a l P r e -p r o o f rupture fluids from the mouth and vocal cords, as a significant mechanism for exhalation of exhaled 497 infectious aerosols into the surrounding air. We make a simple observation that individuals who exhale 498 infectious aerosols --the obvious source of host-to-host transmission --are continuously exposed to their 499 own ambient airspace, creating the potential for individuals with upper respiratory tract infections to exhale 500 and re-inhale massive numbers of aerosols in a poorly ventilated environment when they are actively 501 speaking, eating, singing, or engaging in other vocal activities such as sporting events. This self-502 transmission mechanism has been proposed previously and supported by clinical data from the Deaf 503 community that linked disease severity to the amount of speech activity [65] . We further know from the 504 aerosol modeling community (see [28, 33, 32] ) that a nontrivial percentage of inhaled sub-micron aerosols 505 deposit directly into the deep lung. In work recently posted [41] , we explore the wave of SARS-CoV-2 variants, including the delta and 507 omicron variants [67] , illustrating how to adapt the current baseline model to any novel virus or coronavirus 508 in the early hours and days prior to immune responses, e.g., in the unvaccinated or previously uninfected 509 population. In [41] , we translate three documented mutations on the spikes of SARS-CoV-2 (see [68, 69, rupturing sub-micron aerosols [72, 66, 73, 74, 75] . In poorly ventilated conditions, aerosols are partially 527 inhaled, exhaled, and re-inhaled, as well as inhaled by others, many transporting to the deep lung. A mechanism also exists for direct transport of aerosol seeds from a deep lung infection to the 529 nasal/URT and external airspace: breathing! Scores of authors for decades (see [76, 77, 78, 79, 80, 62, 81, 530 65] , the comprehensive review [82] , and recent article [83] ) have articulated that the small bronchioles 531 (generations just prior to the alveolar ducts, see Figure 1 ) close and open with each breath, rupturing 532 aerosols that then travel, either into the alveolar ducts and sacs during inhalation, or a significant fraction 533 travels all the way up to the nasal passages or ambient air during exhalation. The remaining fraction contact 534 the mucus layers and present a mechanism to self-transmit alveolar infection to the lower RT. We close with comments regarding access to the software used to generate the results presented herein. The code for cylindrical generations can be accessed at https://github.com/mathalexchen/SARS-CoV-537 2_model; we will post analogous code for alveolar generations as well as extensions of the code to achieve 538 optimal performance as they become suited for stable implementation. 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