Epidemiology of the SARS-CoV-2 Omicron Variant Emergence in the Southeast Brazilian Population.

The aim of this study was to describe epidemiological characteristics and perform SARS-CoV-2 genomic surveillance in the southeastern region of São Paulo State. During the first months of 2022, we compared weekly SARS-CoV-2 infection prevalence considering age, Ct value, and variants' lineages. An increase in the number of SARS-CoV-2-positive cases until the fourth epidemiological week of 2022 was observed. From the fourth epidemiological week onwards, the number of tests for SARS-CoV-2 diagnosis began to decrease, but the number of positive samples for SARS-CoV-2 remained high, reaching its most expressive level with a rate of 60% of infected individual cases. In this period, we observed a progressive increase in SARS-CoV-2 infection within the 0-10 age group throughout the epidemiological weeks, from 2.8% in the first epidemiological week to 9.2% in the eighth epidemiological week of 2022. We further observed significantly higher Ct values within younger patient samples compared to other older age groups. According to lineage assignment, SARS-CoV-2 (BA.1) was the most prevalent (74.5%) in the younger group, followed by BA.1.1 (23%), BA.2 (1.7%), and Delta (1%). Phylogenetic analysis showed that BA.2 sequences clustered together, indicating sustained transmission of this Omicron VOC sub-lineage by that time. Our results suggest the initial dissemination steps of the Omicron's sub-linage BA.2 into the younger group, due to specific genomic features of the detected sequences. These data provide interesting results related to the spread, emergence, and evolution of the Omicron variant in the southeast Brazilian population.

Prevalence of Concomitant Distal Suprascapular Nerve Injury in Patients with Root-level Brachial Plexus Palsy: A Clinical Anatomic Study of Injury Pattern.

BACKGROUND: Root-level suprascapular nerve palsy is commonly reconstructed via spinal accessory nerve transfer in brachial plexus injury, yet some patients fail to recover. We hypothesize that this relates to concomitant undetected lesions distal to the nerve transfer coaptation. METHODS: 67 patients with plexus injury and C5/6 root involvement were included in this prospective study between March 2021 and October 2022. During spinal accessory to suprascapular nerve transfer the entire suprascapular nerve was explored, via cresenteric clavicular osteotomy, and anatomic variations and injury patterns categorized. RESULTS: Proximal root involvement was C5-C6 (n=8), C5-C7 (n=13), C5-C8 (n=17), C5-T1(29). Mean time from injury to surgery was 5.6 months. The suprascapular nerve was found to be injured in 16/67 cases (24%). In 9 cases (13%) the lesion was proximal to the suprascapular fossa. In 3 cases (4%) the suprascapular nerve was injured both proximally and within the fossa, and in 4 cases (6%) in the fossa or distal to it. Therefore, in 7 cases (10%), a traditional suprascapular nerve transfer would not successfully bypass the zone of injury of the suprascapular nerve in the fossa. Of the 16 cases of concomitant suprascapular nerve injury, 1/8 in occurred in C5-C6 root injury, 4/13 of C5-C7 root injury, 5/17 of C5-C8 root injury and 6/39 in total paralysis. CONCLUSIONS: Concomitant distal suprascapular nerve injury in brachial plexus stretch palsy occurred in 24% of the cases. This warrants attention from the surgeon to identify distal lesions and to perform the nerve transfer beyond any secondary lesions.

Dynamic clade transitions and the influence of vaccine rollout on the spatiotemporal circulation of SARS-CoV-2 variants in São Paulo, Brazil.

Since 2021, the emergence of variants of concern (VOC) has led Brazil to experience record numbers of in COVID-19 cases and deaths. The expanded spread of the SARS-CoV-2 combined with a low vaccination rate has contributed to the emergence of new mutations that may enhance viral fitness, leading to the persistence of the disease. Due to limitations in the real-time genomic monitoring of new variants in some Brazilian states, we aimed to investigate whether genomic surveillance, coupled with epidemiological data and SARS-CoV-2 variants spatiotemporal spread in a smaller region, can reflect the pandemic progression at a national level. Our findings revealed three SARS-CoV-2 variant replacements from 2021 to early 2022, corresponding to the introduction and increase in the frequency of Gamma, Delta, and Omicron variants, as indicated by peaks of the Effective Reproductive Number (Reff). These distinct clade replacements triggered two waves of COVID-19 cases, influenced by the increasing vaccine uptake over time. Our results indicated that the effectiveness of vaccination in preventing new cases during the Delta and Omicron circulations was six and eleven times higher, respectively, than during the period when Gamma was predominant, and it was highly efficient in reducing the number of deaths. Furthermore, we demonstrated that genomic monitoring at a local level can reflect the national trends in the spread and evolution of SARS-CoV-2.

Distal nerve transfers for peripheral nerve injuries: indications and outcomes.

Distal nerve transfer is a refined surgical technique involving the redirection of healthy sacrificable nerves from one part of the body to reinstate function in another area afflicted by paralysis or injury. This approach is particularly valuable when the original nerves are extensively damaged and standard repair methods, such as direct suturing or grafting, may be insufficient. As the nerve coaptation is close to the recipient muscles or skin, distal nerve transfers reduce the time to reinnervation. The harvesting of nerves for transfer should usually result in minimal or no donor morbidity, as any anticipated loss of function is compensated for by adjacent muscles or overlapping cutaneous territory. Recent years have witnessed notable progress in nerve transfer procedures, markedly enhancing the outcomes of upper limb reconstruction for conditions encompassing peripheral nerve, brachial plexus and spinal cord injuries.

Anconeus Muscle Transfer to Correct or Prevent Wrist Radial Deviation in Radial and Posterior Interosseous Nerve Injuries.

PURPOSE: Wrist radial deviation is a possible complication of tendon transfer for restoration of wrist extension in cases of radial nerve paralysis. In posterior interosseous nerve (PIN) injury, this is because of the imbalance caused by the intact extensor carpi radialis longus and paralysis of the extensor carpi ulnaris (ECU). This deformity may also occur following transfer of the pronator teres (PT) to the extensor carpi radialis brevis (ECRB) for radial nerve palsy. To address wrist radial deviation, we propose transferring the anconeus muscle, extended by the intermuscular septum between the ECU and the flexor carpi ulnaris (FCU), to the ECU tendon. METHODS: Through an incision over the ulna, the intermuscular septum between the ECU and FCU is harvested at the level of the periosteum and left attached to the anconeus proximally. The anconeus muscle is then released from the ulna, and the intramuscular septum extension is sutured to the ECU tendon under maximal tension. Anconeus muscle transfer was performed on two patients to correct chronic wrist radial deviation following PT to ECRB tendon transfer for radial nerve injury, as well as on two patients with PIN paralysis. In four patients, transfer was performed in addition to standard tendon transfers for radial nerve paralysis to prevent radial wrist deviation deformity. RESULTS: Wrist radial deviation was corrected or prevented in all but one patient at an average follow-up of 10 months. Patients with PIN lesions and those who had anconeus transfer concomitantly with radial nerve tendon transfers were capable of active ulnar deviation. No patient experienced elbow extension weakness, pain, or instability. CONCLUSIONS: Anconeus muscle transfer extended by intermuscular septum presents a viable alternative for addressing radial deviation of the wrist in cases of PIN nerve lesions or following PT to ECRB tendon transfer in radial nerve paralysis. TYPE OF STUDY/LEVEL OF EVIDENCE: Therapeutic V.

Retrograde peripheral nerve regeneration from sensory to motor pathways in rats: a new experimental concept in nerve repair.

BACKGROUND: The polarity of nerve grafts does not interfere with axon growth. Our goal was to investigate whether axons can regenerate in a retrograde fashion within sensory pathways and then extend into motor pathways, leading to muscle reinnervation. METHODS: Fifty-four rats were randomized into four groups. In Group 1, the ulnar nerve was connected end-to-end to the superficial radial nerve after neurectomy of the radial nerve in the axilla. In Group 2, the ulnar nerve was connected end-to-end to the radial nerve distal to the humerus; the radial nerve then was divided in the axilla. In Group 3, the radial nerve was divided in the axilla, but no nerve reconstruction was performed. In Group 4, the radial nerve was crushed in the axilla. Over 6 months, we behaviorally assessed the recovery of toe spread in the right operated-upon forepaw by lifting the rat by its tail and lowering it onto a flat surface. Six months after surgery, rats underwent reoperation, nerve transfers were tested electrophysiologically, and the posterior interosseous nerve (PIN) was removed for histological evaluation. RESULTS: Rats in the crush group recovered toe spread between 5 and 8 days after surgery. Rats with nerve transfers demonstrated electrophysiological and histological findings of nerve regeneration but no behavioral recovery. CONCLUSIONS: Ulnar nerve axons regrew into the superficial radial nerve and then into the PIN to reinnervate the extensor digitorum communis. We were unable to demonstrate behavioral recovery because rats cannot readapt to cross-nerve transfer.

A Fresh Cadaver Study on the Innervation of Brachioradialis and Extensor Carpi Radialis Longus Muscles.

PURPOSE: Distal nerve transfers have revolutionized peripheral nerve surgery by allowing the transfer of healthy motor nerves to paralyzed ones without causing additional morbidity. Radial nerve branches to the brachialis (Ba), brachioradialis (Br), and extensor carpi radialis longus (ECRL) muscles have not been investigated in fresh cadavers. METHODS: The radial nerve and its branches were dissected in 34 upper limbs from 17 fresh cadavers. Measurements were taken to determine the number, origin, length, and diameter of the branches. Myelinated fiber counts were obtained through histological analysis. RESULTS: The first branch of the radial nerve at the elbow was to the Ba muscle, followed by the branches to the Br and ECRL muscles. The Ba and Br muscles consistently received single innervation. The ECRL muscle showed varying innervation patterns, with one, two, or three branches. The branches to the Br muscles originated from the anterior side of the radial nerve, whereas the branches to the Ba and ECRL muscles originated from the posterior side. The average myelinated fiber counts favored the nerve to Br muscle over that to the ECRL muscle, with counts of 542 versus 350 and 568 versus 302 observed in hematoxylin and eosin and neurofilament staining, respectively. CONCLUSIONS: This study provides detailed anatomical insights into the motor branches of the radial nerve to the Ba, Br, and ECRL muscles. CLINICAL RELEVANCE: Understanding the anatomy of the radial nerve branches at the elbow is of utmost importance when devising a reconstructive strategy for upper limb paralysis. These findings can guide surgeons in selecting appropriate donor or recipient nerves for nerve transfer in cases of high tetraplegia and lower-type brachial plexus injuries.

Long-Term Donor-Site Morbidity Following Entire Sural Nerve Harvest for Grafting.

PURPOSE: The sural nerve is the autologous nerve used most commonly for grafting. However, recent studies indicate a high rate of complications and complaints after sural nerve removal. In this prospective study, we evaluated donor-site morbidity following full-length sural nerve harvesting on long-term follow-up. METHODS: Fifty-one legs from 43 patients who underwent complete sural nerve harvesting for brachial plexus reconstruction were included in the study. After an average of 5 years, with a minimum postoperative follow-up of 12 months, sensory deficits in the leg and foot were analyzed using 2.0-g monofilaments. Regions of sensory deficit were marked with a skin marker and photographed. Over these regions of decreased sensation, we tested nociception using an eyebrow tweezer. Patients were also asked about pain, cold intolerance, pruritis, difficulties walking, and foot swelling. RESULTS: Regions most affected (84% of patients) were over the calcaneus and cuboid. However, in these regions, nociception was preserved. Regions of decreased sensation extended to the calf region in 11 of 51 legs. In 13 patients, we also observed regions of decreased sensation on the proximal leg. In five feet, the sensation was entirely preserved. No patient had any complaints about pain, cold intolerance, itchiness, difficulties walking, or foot swelling. CONCLUSION: Decreased sensation with nociception preserved was most common along the lateral side of the foot over the calcaneus and cuboid. Removing the entire sural nerve produced no long-term complaints of pain. Sural nerve use appears safe. TYPE OF STUDY/LEVEL OF EVIDENCE: Therapeutic II.

Identification of Host Factors for Rift Valley Fever Phlebovirus.

Rift Valley fever phlebovirus (RVFV) is a zoonotic pathogen that causes Rift Valley fever (RVF) in livestock and humans. Currently, there is no licensed human vaccine or antiviral drug to control RVF. Although multiple species of animals and humans are vulnerable to RVFV infection, host factors affecting susceptibility are not well understood. To identify the host factors or genes essential for RVFV replication, we conducted CRISPR-Cas9 knockout screening in human A549 cells. We then validated the putative genes using siRNA-mediated knock-downs and CRISPR-Cas9-mediated knock-out studies. The role of a candidate gene in the virus replication cycle was assessed by measuring intracellular viral RNA accumulation, and the virus titers were analyzed using plaque assay or TCID50 assay. We identified approximately 900 genes with potential involvement in RVFV infection and replication. Further evaluation of the effect of six genes on viral replication using siRNA-mediated knock-downs revealed that silencing two genes (WDR7 and LRP1) significantly impaired RVFV replication. For further analysis, we focused on the WDR7 gene since the role of the LRP1 gene in RVFV replication was previously described in detail. WDR7 knockout A549 cell lines were generated and used to dissect the effect of WRD7 on a bunyavirus, RVFV, and an orthobunyavirus, La Crosse encephalitis virus (LACV). We observed significant effects of WDR7 knockout cells on both intracellular RVFV RNA levels and viral titers. At the intracellular RNA level, WRD7 affected RVFV replication at a later phase of its replication cycle (24 h) when compared with the LACV replication, which was affected in an earlier replication phase (12 h). In summary, we identified WDR7 as an essential host factor for the replication of two different viruses, RVFV and LACV, both of which belong to the Bunyavirales order. Future studies will investigate the mechanistic role through which WDR7 facilitates phlebovirus replication.

Identification of host factors for Rift Valley Fever Phlebovirus.

Background: Rift Valley fever phlebovirus (RVFV) is a zoonotic pathogen that causes Rift Valley fever (RVF) in livestock and humans. Currently, there is no licensed human vaccine or antiviral drug to control RVF. Although multiple species of animals and humans are vulnerable to RVFV infection, host factors affecting susceptibility are not well understood. Methodology: To identify the host factors or genes essential for RVFV replication, we conducted a CRISPR-Cas9 knock-out screen in human A549 cells. We then validated the putative genes using siRNA-mediated knockdowns and CRISPR-Cas9-mediated knockout studies, respectively. The role of a candidate gene in the virus replication cycle was assessed by measuring intracellular viral RNA accumulation, and the virus titers by plaque assay or TCID50 assay. Findings: We identified approximately 900 genes with potential involvement in RVFV infection and replication. Further evaluation of the effect of six genes on viral replication using siRNA-mediated knockdowns found that silencing two genes (WDR7 and LRP1) significantly impaired RVFV replication. For further analysis, we focused on the WDR7 gene since the role of LRP1 in RVFV replication was previously described in detail. Knock-out A549 cell lines were generated and used to dissect the effect of WRD7 on RVFV and another bunyavirus, La Crosse encephalitis virus (LACV). We observed significant effects of WDR7 knock-out cells on both intracellular RVFV RNA levels and viral titers. At the intracellular RNA level, WRD7 affected RVFV replication at a later phase of its replication cycle (24h) when compared to LACV which was affected an earlier replication phase (12h). Conclusion: In summary, we have identified WDR7 as an essential host factor for the replication of two relevant bunyaviruses, RVFV and LACV. Future studies will investigate the mechanistic role by which WDR7 facilitates Phlebovirus replication.

Pulp-to-Pulp Pinch Reconstruction in a Tetraplegic Patient Utilizing Nerve and Tendon Transfers: A Case Report.

In tetraplegia, hand reconstruction is of high priority. Key pinch reconstruction has been advocated for tetraplegia hand reconstruction because of the lack of donors for nerve and tendon transfers. We report a patient with mid-cervical tetraplegia who underwent nerve and tendon transfers in the right and left upper limbs seven months post-injury to reconstruct hand function. The particularity of our case resides in the left-hand thumb and index pulp-to-pulp reconstruction. For this, we transferred the nerve to the supinator to the posterior interosseous nerve and the nerve to the extensor carpi radialis brevis to the anterior interosseous nerve. During a second surgery, we relieved clawing by transferring the split flexor digitorum superficialis of the middle and ring fingers, motored by the brachioradialis, to the extensor apparatus of all fingers. Finally, to achieve better thumb palmar abduction, we osteotomized the scaphoid tubercle and fixed it to the distal radius while maintaining thenar muscle attachments. Five years after surgery, the patient was able to grasp and release small objects placed on a table after becoming left-handed. Here, we demonstrated that pinch-to-pinch reconstruction is possible, which increased hand use in daily activities, especially during eating and grabbing small objects over the table.

Pectoralis Major Reinnervation by Retrograde Nerve Regeneration after Complete Paralysis of the Brachial Plexus.

Spontaneous neuronal recovery is an expected phenomenon in brachial plexus palsy patients. However, the spontaneous recovery owing to retrograde regeneration is an evolving phenomenon with dearth of adequate research on it. Pectoralis major contraction on stimulation of median nerve (in the arm) is an unexpected phenomenon, in the absence of any anomalous communication and with distal coaptation site of intraplexal nerve repair. We presumably attribute it to the retrograde regrowth of axons. The case described supports our hypothesis. Level of Evidence: Level V (Therapeutic).

Biotechnological Potential of Microorganisms for Mosquito Population Control and Reduction in Vector Competence.

Mosquitoes transmit pathogens that cause human diseases such as malaria, dengue fever, chikungunya, yellow fever, Zika fever, and filariasis. Biotechnological approaches using microorganisms have a significant potential to control mosquito populations and reduce their vector competence, making them alternatives to synthetic insecticides. Ongoing research has identified many microorganisms that can be used effectively to control mosquito populations and disease transmission. However, the successful implementation of these newly proposed approaches requires a thorough understanding of the multipronged microorganism-mosquito-pathogen-environment interactions. Although much has been achieved in discovering new entomopathogenic microorganisms, antipathogen compounds, and their mechanisms of action, only a few have been turned into viable products for mosquito control. There is a discrepancy between the number of microorganisms with the potential for the development of new insecticides and/or antipathogen products and the actual available products, highlighting the need for investments in the intersection of basic research and biotechnology.

Body yield and quality of fresh and post-freezing filet of Nile tilapia (Oreochromis niloticus) genetic groups.

The aim of this study was to evaluate the body yield and quality of fresh and post-freezing filet of male and female fish of inbred and non-inbred AquaAmérica genetic group and the hybrid between the AquaAmérica and Tilamax varieties. Forty fish (20 males and 20 females) of each genetic group were housed in four 48-m3 hapa net cages, getting 120 fish per cage. The fish were housed at 51 days of age and farmed for 269 days. Pre-slaughter weight was higher (P<0.05) in the AquaAmérica × Tilamax males (0.805±0.204 kg) than in the inbred AquaAmérica male (0.643±0.115 kg). Filet yield percentage was higher (P<0.05) in the AquaAmérica × Tilamax males (32.14±4.72%) than in the inbred AquaAmérica (28.15±2.67%) and non-inbred AquaAmérica (29.06±2.80%) males. Head and viscera yield percentages, pH, color values (L*, a* and b*), shear force, drip loss and cooking loss did not differ significantly between the genetic groups and sexes. Alterations in meat quality were observed after freezing. In conclusion, inbreeding in the AquaAmérica variety resulted in reduced slaughter weight for males; AquaAmérica × Tilamax males have a higher filet yield; and filet quality is not influenced by crossing, inbreeding, or sex, but is changed after freezing.

Base of the Third Metacarpal as a Palpable and Reliable Landmark for Identifying the Median Nerve's Thenar Branch.

PURPOSE: The objective of this study was to investigate whether the base of the third metacarpal can predict the location of the thenar branch (TB) of the median nerve and the accuracy of palpating the base of the third metacarpal. METHODS: In 15 patients with ulnar nerve lesions around the elbow, we transferred the opponens motor branch to repair the deep terminal division of the ulnar nerve (DTDUN). Before surgery, we located the TB by palpating the base of the third metacarpal volarly. During surgery, we placed three needles at the following places: one at the entrance of the TB into the abductor pollicis brevis, another at the point where the TB contacted the thenar muscles, and third at the DTDUN's trajectory over the third metacarpal. We obtained fluoroscopic images and measured distances between the needles and structures with image software. We also examined the relationship between the TB, DTDUN, and the volar tubercle of the base of the third metacarpal in cadaver hands. Finally, we invited 22 surgeons to palpate the base of the third metacarpal on volunteer hands and verified their accuracy using fluoroscopy. RESULTS: During surgery, after dissection and palpation of the TB, under fluoroscopy, we confirmed that the palpable bone prominence was the base of the third metacarpal. In cadaver dissections, we observed the TB crossing the volar tubercle of the base of the third metacarpal superficially from proximal to distal and from ulnar to radial. The DTDUN was, on average, 14 mm distal to the base of the third metacarpal distal limit. In total, 19 of the 22 surgeons correctly identified the base of the third metacarpal and consequently the trajectory of the TB. CONCLUSIONS: The palpable base of the third metacarpal can be used to determine the trajectory of both the TB and DTDUN. TYPE OF STUDY/LEVEL OF EVIDENCE: Diagnostic II.

Comparative cohort analysis of pressure ulcer/injury in intensive care unit patients before and during the COVID-19 pandemic.

COVID-19 has emerged as a global pandemic leading to an increase in hospitalization and intensive care unit (ICU) admissions worldwide. Due to severe acute respiratory distress syndrome (ARDS), many patients require prone positioning, which is associated with increased pressure ulcer/injury (PU/PI) incidence. COVID-19 pathophysiology may favor the occurrence of PU/PI due to hypoxemia, inflammatory status, and vasculopathy. This study aimed to compare the incidence of PU/PI in ICU patients before and during the COVID-19 pandemic. A retrospective cohort study was conducted at a university hospital in Brazil. Data from the medical charts of every adult patient admitted to ICU from March to July 2019 and the same period in 2020 were collected. The group from 2019 included 408 patients admitted due to multiple causes, and the group from 2020 included 229 patients admitted due to COVID-19 infection. The incidence of PU/PI was significantly higher in patients admitted in 2020 compared to 2019 (62,5 vs. 33,8%, respectively). Also, PU/PI location and severity have been different between groups, with the patients with COVID-19 (2020 group) more exposed to stage 3, 4, and non-stageable lesions, as well as more PU/PI on face skin and other less common locations. In conclusion, the COVID-19 pandemic has highlighted a higher PU/PI incidence. ICU patients were older during the pandemic, had higher body mass index and comorbidities, and needed more invasive medical devices and pronation. The occurrence of PU/PI was also associated with prolonged hospitalization and mortality.

Bacterial Microbiota from Lab-Reared and Field-Captured Anopheles darlingi Midgut and Salivary Gland.

Anopheles darlingi is a major malaria vector in the Amazon region and, like other vectors, harbors a community of microorganisms with which it shares a network of interactions. Here, we describe the diversity and bacterial composition from the midguts and salivary glands of lab-reared and field-captured An. darlingi using metagenome sequencing of the 16S rRNA gene. The libraries were built using the amplification of the region V3-V4 16S rRNA gene. The bacterial community from the salivary glands was more diverse and richer than the community from the midguts. However, the salivary glands and midguts only showed dissimilarities in beta diversity between lab-reared mosquitoes. Despite that, intra-variability was observed in the samples. Acinetobacter and Pseudomonas were dominant in the tissues of lab-reared mosquitoes. Sequences of Wolbachia and Asaia were both found in the tissue of lab-reared mosquitoes; however, only Asaia was found in field-captured An. darlingi, but in low abundance. This is the first report on the characterization of microbiota composition from the salivary glands of An. darlingi from lab-reared and field-captured individuals. This study can provide invaluable insights for future investigations regarding mosquito development and interaction between mosquito microbiota and Plasmodium sp.

Rapid Identification of ASFV, CSFV and FMDV from Mongolian Outbreaks with MinION Short Amplicon Sequencing.

African swine fever virus (ASFV), classical swine fever virus (CSFV), and foot-and-mouth disease virus (FMDV) cause important transboundary animal diseases (TADs) that have a significant economic impact. The rapid and unequivocal identification of these pathogens and distinction from other animal diseases based on clinical symptoms in the field is difficult. Nevertheless, early pathogen detection is critical in limiting their spread and impact as is the availability of a reliable, rapid, and cost-effective diagnostic test. The purpose of this study was to evaluate the feasibility to identify ASFV, CSFV, and FMDV in field samples using next generation sequencing of short PCR products as a point-of-care diagnostic. We isolated nucleic acids from tissue samples of animals in Mongolia that were infected with ASFV (2019), CSFV (2015), or FMDV (2018), and performed conventional (RT-) PCR using primers recommended by the Terrestrial Animal Health Code of the World Organization for Animal Health (WOAH). The (RT-) PCR products were then sequenced in Mongolia using the MinION nanopore portable sequencer. The resulting sequencing reads successfully identified the respective pathogens that exhibited 91-100% nucleic acid similarity to the reference strains. Phylogenetic analyses suggest that the Mongolian virus isolates are closely related to other isolates circulating in the same geographic region. Based on our results, sequencing short fragments derived by conventional (RT-) PCR is a reliable approach for rapid point-of-care diagnostics for ASFV, CSFV, and FMDV even in low-resource countries.

Retrospective Insights of the COVID-19 Epidemic in the Major Latin American City, São Paulo, Southeastern Brazil.

São Paulo is the financial center of Brazil, with a population of over 12 million, that receives travelers from all over the world for business and tourism. It was the first city in Brazil to report a case of COVID-19 that rapidly spread across the city despite the implementation of the restriction measures. Despite many reports, much is still unknown regarding the genomic diversity and transmission dynamics of this virus in the city of São Paulo. Thus, in this study, we provide a retrospective overview of the COVID-19 epidemic in São Paulo City, Southeastern, Brazil, by generating a total of 9995 near-complete genome sequences from all the city's different macro-regions (North, West, Central, East, South, and Southeast). Our analysis revealed that multiple independent introduction events of different variants (mainly Gamma, Delta, and Omicron) occurred throughout time. Additionally, our estimates of viral movement within the different macro-regions further suggested that the East and the Southeast regions were the largest contributors to the Gamma and Delta viral exchanges to other regions. Meanwhile, the North region had a higher contribution to the dispersion of the Omicron variant. Together, our results reinforce the importance of increasing SARS-CoV-2 genomic monitoring within the city and the country to track the real-time evolution of the virus and to detect earlier any eventual emergency of new variants of concern that could undermine the fight against COVID-19 in Brazil and worldwide.