PMC8594034_01
Timeline: Clinical, epidemiological and laboratory assays of SARS-CoV-2 and CHOV coinfection case. Schematic timeline with events described from top to bottom: molecular and serological laboratory assays for SARS-CoV-2 (light blue) and CHOV (green), type of mechanical ventilation applied to the patient, timeline with the date (year, month, day) and the days of symptoms onset (*) with color coding representing the health institution and clinical management, epidemiological and clinical case description. Abbreviations used in the figure: SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; CHOV, Choclo orthohantavirus; RT-PCR, real time reverse transcription polymerase chain reaction; PCR, polymerase chain reaction; CLIA, chemiluminescent immunoassay; SIA, strip immunoblot assay; PRNT80, 80% plaque reduction neutralization test; Ig, immunoglobulin (A, M and G for this case); ICU, intensive care unit; AMV, advance in mechanical ventilation; COVID-19, coronavirus disease 2019.
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On March 8, 2020, the patient reported gastrointestinal symptoms (vomit and diarrhea) accompanied by unquantified fever of 9 days of evolution ( Figure 1 ). Once in ICU, the patient was managed as a presumptive case of HPS, considering the clinical symptoms and that the patient lived in an endemic region for CHOV ( Supplementary Figure 1 ) and reported possible contact with the reservoir Oligoryzomys costaricensis. The molecular tests confirmed the coinfection by SARS-CoV-2 6 days after symptom onset (first positive RT-PCR on March 14) and then by CHOV (positive Nested PCR on March 17) ( Figure 1 ). The patient took longer to produce antibodies against CHOV; indeed, specific IgG were detected 20 days after its Nested PCR confirmation ( Figure 1  and  Supplementary Table 1 ). Since her admission, antibiotic therapy was given with levofloxacin (750 mg intravenous/day, for 10 days) and piperacillin/tazobactam (4.5 g/six hour, for 17 days), in addition, after SARS-CoV-2 laboratory confirmation, hydroxychloroquine (400mg/day, for 9 days) was started on March 16, according to national the treatment protocol used at that time for COVID-19 ( Figure 1 ). This evolution led to reduced oxygen supply, and it was decided to transfer the patient to the women's COVID-19 ward on April 6 ( Figure 1  and  Table 1 ). Other swabs were repeated on May 7 and 11, both resulted negative, therefore the patient was discharged from the hospital-hotel on May 15, after 62 intra-hospital days ( Figure 1 ). During the one-year follow-up, the patient had no sequelae and still has detectable antibodies against SARS-CoV-2 and CHOV and antibody neutralization activity against SARS-CoV-2 ( Figure 1  and  Supplementary Table 1 ).
Pulmonary images of the patient with HPS and COVID-19. Taken in the intern medicine ward. (A) Posteroanterior chest radiography. Mild peripheral diffuse infiltrate of predominance in both pulmonary bases (black arrows). No cardiomegaly, no pleural effusion. (B) Anteroposterior chest radiography. Increased extent of the radiographic infiltrate in both pulmonary fields (black arrows). No pleural effusion. A rapid progression of the infiltrate is observed in 10 hours of evolution compared to previous radiography. (C) Coronal chest high-resolution simple computed tomography. Scattered multifocal opacities of peripheral predominance in both lungs (white arrows). Isolated consolidated areas (black arrows). (D) Axial chest high-resolution simple computed tomography. Tarnished glass-like opacities in anterior pulmonary location (white arrows) and consolidated areas in posterior pulmonary location (black arrows). Mild bilateral basal posterior pleural effusion (black arrows).
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Table 1 ). The posteroanterior chest radiography showed a mild peripheral diffuse infiltrate with predominance in both pulmonary bases ( Figure 2A ). The same day in the evening, the anteroposterior chest radiography showed an increased extent of the infiltrate in both pulmonary fields ( Figure 2B ), with worsening clinical conditions. A high-resolution chest computed tomography reported scattered multifocal opacities of peripheral bilateral predominance with ground glass images, consolidative foci, and scarce bilateral pleural effusion ( Figures 2C, D ). Even if various clades were co- circulating, most of the initial cases were caused by the 19B clade-related sequences, in contrast with the rest of the world, where the dominant clades were 20A and 20B ( Figure 3A  and  Supplementary Table 2 ).
Phylogenetic trees of the SARS-CoV-2 and CHOV sequences from Panama and worldwide. (A) SARS-CoV-2 phylogenetic tree showing 6610 genomes sampled between December 2019 and April 2020, the analysis grouping the sequences in clades (name indicated at the base of each clade branch) was restricted to samples submitted to GISAID until October 2020 (grey: worldwide, blue: Panama). (B) SARS-CoV-2 subtree showing samples from the 19B clade that forms the cluster of transmission associated to the coinfection case (bigger circle with the sample location in blue). The sample locations at the level of health region within Panama are indicated. For acknowledgment table see 
Supplementary Data
. (C) Phylogenetic tree of the orthohantavirus, including CHOV sequence with GenBank accession number OK393713 (blue) with. Maximum likelihood tree was drawn using worldwide reference sequences of orthohantavirus and rooted to Imji virus reference strain, black circles indicates nodes with ultrabootstrap values greater the 50%. All information about GISAID and Genbank accession numbers for the SARS-Cov-2 and orthohantavirus reference sequences, respectively, are listed in 
Supplementary Data
.
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Even if various clades were co- circulating, most of the initial cases were caused by the 19B clade-related sequences, in contrast with the rest of the world, where the dominant clades were 20A and 20B ( Figure 3A  and  Supplementary Table 2 ). Additionally, the genome obtained from this coinfection case grouped with SARS-CoV-2 samples collected from distant areas of the country, suggesting that the virus was already disseminated through Panama territory ( Figure 3B ). The sequencing of the small segment (S segment) of CHOV (GenBank: OK393713), which encodes the N protein, confirmed that the virus responsible for this case belongs to the same clade of the endemic virus previously reported in Panama ( Figure 3C  and  Supplementary Table 3 ).