key: cord-0703860-ru0lm0pq
authors: Noureddine, F. Y.; Chakkour, M.; El Roz, A.; Reda, J.; Al Sahily, R.; Assi, A.; Joma, M.; Salami, H.; Hashem, S. J.; Harb, B.; Salami, A.; Ghssein, G.
title: The emergence of SARS-CoV-2 variant(s) and its impact on the prevalence of COVID-19 cases in Nabatieh region, Lebanon
date: 2021-04-13
journal: nan
DOI: 10.1101/2021.04.08.21255005
sha: c8c4b57056607e281070fbb09e34a9259b4c0c18
doc_id: 703860
cord_uid: ru0lm0pq

Background: An outbreak of an unknown respiratory illness caused by a novel corona-virus, SARS-CoV-2, emerged in the city of Wuhan in Hubei province, China, in December 2019 and was referred to as coronavirus disease-2019 (COVID-19). Soon after, it was declared as a global pandemic by the World Health Organization (WHO) in March 2020. SARS-CoV-2 mainly infects the respiratory tract with different outcomes ranging from asymptomatic infection to se-vere critical illness leading to death. Different SARS-CoV-2 variants are emerging of which three have raised concerns worldwide due to their high transmissibility among populations. Objec-tive: To study the prevalence of COVID-19 in the region of Nabatieh - South Lebanon during the past year and assess the presence of SARS-CoV-2 variants and their effect on the spread of infec-tion during times of lockdown. Methods: In our study, 37,474 nasopharyngeal swab samples were collected and analyzed for the detection of SARS-CoV-2 virus in suspected patients attend-ing a tertiary health care center in South Lebanon during the period between March 16, 2020 and February 21, 2021. Results: Results demonstrated a variation in the prevalence rates ranging from less than 1% during full lockdown of the country to 8.4% upon easing lockdown re-strictions and reaching 27.5% after the holidays and 2021 New Year celebrations. Interestingly, a new variant(s) appeared starting January 2021 with a significant positive association between the prevalence of positive tests and the percentage of the variant(s). Conclusion: Our results indicate that the lockdown implemented by the Lebanese officials presented an effective intervention to contain COVID-19 spread. Our study also showed that lifting lockdown measures during the holidays, which allowed indoor crowded gatherings to occur, caused a surge in COVID-19 cases and rise in the mortality rates nationwide. More importantly, we confirmed the presence of a highly transmissible SARS-CoV-2 variant(s) circulating in the Lebanese community, at least since January 2021 onwards.

In December 2019, several unidentified pneumonia cases surfaced in Wuhan, China, and 43 were linked to a novel coronavirus (CoV) named 2019-nCoV [1] , and later, severe acute 44 respiratory syndrome coronavirus 2 (SARS-CoV-2) by the International Committee on 45 Taxonomy of Viruses (ICTV) [2] . The respiratory illness caused by this novel coronavirus 46 was referred to as coronavirus disease-2019 [3] . COVID-19 was declared a 47 global pandemic and health problem by the World Health Organization (WHO) in March 48 2020 [4] . 49 Genome-wide phylogenetic analysis of SARS-CoV-2 showed 79.5% sequence identity 50 similarity to severe acute respiratory syndrome coronavirus (SARS-CoV), placing it in the 51 subgenus Sarbecovirus of the genus Betacoronavirus, subfamily Orthocoronavirinae, 52 family Coronaviridae [5, 6] . Coronaviruses are enveloped viruses with positive sense, sin-53 gle-stranded, non-segmented RNA genomes which are, on average, 30 kilobases long [2, 54 7] . SARS-CoV-2 mainly infects the respiratory tract with different outcomes ranging from 55 asymptomatic infections (1.2%), mild to medium cases (80.9%), severe cases (13.8%) , to 56 critical illness (4.7%) and death (2.3%) [8] . According to the daily report of the WHO, as 57 of April 03, 2021, SARS-CoV-2 had affected over 129,619,536 people, and killed more than 58 2,827,610 people all over the world [9] . Also, a total of 547,727,346 vaccine doses have been 59 administered as of March 30, 2021 [9] . 60 The surveillance of the current infection and the implementation of appropriate medical 61 and governmental policies require early and proper diagnosis of the disease. Molecular 62 detection of SARS-CoV-2 nucleic acid in respiratory samples by one step real-time reverse 63 transcriptase-polymerase chain reaction (RT-PCR) is the gold standard for COVID-19 di-64 agnosis [10] . Most commercially available viral nucleic acid detection kits mainly target 65 three conserved regions of the SARS-CoV-2 genome: the RNA-dependent RNA polymer-66 ase (RdRp) gene located in the first open reading frame ORF1ab; the envelope (E) gene; 67 and at a lower rate, the nucleocapsid (N) gene, in addition to the spike glycoprotein (S)-68 encoding gene [11] . S glycoprotein is composed of two subunits; a receptor-binding sub-69 unit S1 and a membrane-fusion subunit S2, both of which allow SARS-CoV-2 to enter the 70 host cells through utilizing membrane-expressed angiotensin-converting enzyme 2 (ACE-71 2) receptors [12] . Nonetheless, viruses mutate, and with SARS-CoV-2, different variants 72 have emerged by the end of 2020, of which three have raised concerns worldwide due to 73 their high transmissibility among populations: B.1.1.7, B.1.351, and B.1.1.28 variants. The 74 accumulation of mutations in the S gene specifically could alter the viral pathogenicity 75 and immunogenicity. In fact, the emerging SARS-CoV-2 B.1.1.7 variant, carrying the 76 N501Y mutation that alters the conformation of receptor-binding domain (RBD) of the S 77 protein, quickly became the dominant circulating SARS-CoV-2 variant in the United King-78 dom in September 2020 [13] . To date, the B.1.1.7 variant has been detected in over 30 coun-79 tries [13] . S protein mutations are also present in the highly transmissible South African 80 variant (B.1.351) with the 501Y.V2 mutation, and the B.1.1.28 variant (P.1) initially identi-81 fied in travellers returning from Brazil [14, 15] . Fortunately, experts are highly confident 82 that the efficacy of the available COVID-19 vaccines, especially mRNA-based vaccines, 83 will not be majorly affected by the SARS-CoV-2 variants of concern [16] [17] [18] . 84 The first case of COVID-19 was documented in Lebanon on February 21st, 2020 [19] . As 85 of April 03, 2021, 474,925 laboratory confirmed cases including 6,346 deaths had been re-86 ported, indicating a rapid spread of the disease across the country [9] . Ten months after 87 the first case was reported, particularly on December 21st, 2020, Lebanon reported the first 88 case of B.1.1.7 SARS-CoV-2 variant infection with growing concerns about the rapid 89 spread of emergent strains and the associated public health implications [20] . Our current 90 study is the first of a kind in Lebanon, since no epidemiological studies have been pub-91 lished, to date, regarding COVID-19 prevalence in Lebanon. The objective of the present 92 study is to assess the prevalence of SARS-CoV-2 and its variant(s) in a Southern Lebanese 93 population and examine whether the new variants are associated with the recent increase 94 in COVID-19 infection rates. 97 In this retrospective cohort study, during the period between March 16, 2020 and February 98 21, 2021, a total of 37,474 nasopharyngeal swab samples were collected and analyzed, by 99 molecular tools, to detect SARS-CoV-2 in suspected patients attending the tertiary health 100 care center "Sheikh Ragheb Harb University Hospital (SRHUH)" in Nabatieh, South Leb-101 anon.

103 Swab samples were collected for the extraction of SARS-CoV-2 genome from patients sus-104 pected of having COVID-19. Each collected sample was placed in a specialized transport 105 tube containing a sterile solution of normal saline, then transported to the molecular ge-106 netics unit at the laboratory of the health care center. Upon reception of the samples, RNA extraction was performed either manually using dif-109 ferent spin column viral RNA extraction kits, or automatically using the KingFihser™ Flex 110 Purification System (Thermo Scientific™, Thermo Fisher Scientific, USA) with different 111 magnetic beads viral RNA extraction kits (Table S1) according to the manufacturers' in-112 structions. One-Step Reverse Transcription Real-Time polymerase chain reaction (RT-113 PCR) was used to confirm the presence of the SARS-CoV-2 RNA in the samples, by am-114 plifying different genes specific for SARS-CoV-2. Different COVID-19 diagnostic kits were 115 used (Table S2) . RT-PCR assays were performed through two thermocycler devices: 116 QuantStudio ™ 5 Real-Time PCR System for Human Identification (Applied Biosystem-117 sTM, Thermo Fisher Scientific, USA) and the Rotor-Gene Q Real-Time PCR Cycler (Qi-118 agen, Germany). The reaction mix contained COVID-19 Reaction Mixture, COVID-19 119 Probe Mixture, and the RNA sample. Briefly, the following steps were followed in the RT-120 PCR assays: reverse transcription, 40-45 cycles of denaturation, annealing, extending, and 121 collecting fluorescence signal on different channels. The results were analyzed according 122 to the manufacturers' instructions. 123 

Out of the total number of tests, 6,353 tests were performed using the TaqPath™ COVID-125 19 CE-IVD RT-PCR Kit (Applied Biosystems™, Thermo Fisher Scientific, USA), that de-126 tects the presence of three SARS-CoV-2 genes (ORF1ab, N and S). The results interpreta-127 tion was performed according to the provided instructions (Table S3 ). In case the three 128 genes were detected, SARS-CoV-2 infection by the classic virus was confirmed. However, 129 the detection of two out of three genes, namely the ORF1ab and N genes, and failure to 130 detect the S gene was considered as a finding of possible SARS-CoV-2 mutant strain(s), 131 herein called "S-mutant variant(s)". 132

Descriptive statistics were carried out and reported as frequencies and percentages for 134 categorical variables. Quantitative variables were tested for normality distribution using 135 the Kolmogorov-Smirnov test. When data was not normally distributed, Spearman test 136 was used to study the association between the prevalence of positive tests and the per-137 centage of SARS-CoV-2 S-mutant variants. If not, Pearson test was conducted. All anal-138 yses were performed using SPSS (IBM Corp. Released 2019, SPSS Statistics for Windows 139 Version 26.0, Armonk, NY), and the plots were generated using Origin software 140 (OriginPro, Version 2019b. OriginLab Corporation, Northampton, MA, USA). The level of 141 significance was set at P < 0.05 for all statistical analyses. Over the period of the study, a total of 37,474 RT-PCR detection tests for SARS-CoV-2 145 were performed. As shown in Figure 1 , COVID-19 testing could be divided into three 146 different stages: the first stage (Stage I) extends between March and the week of July 06th, 147 2020 where less than 160 tests had been performed weekly; the second stage (Stage II) 148 extends between the week of July 13th and mid-December 2020 revealing an increase in 149 the number of weekly performed tests reaching a maximum of 1,238 tests per week; and 150 the third stage (Stage III) starts in the week of December 21st, 2020 onwards, and it showed 151 a robust increase in the weekly tests performed (up to 2,047 tests per week). 155 During the period of the study, a total of 6,242 samples (16.6%) rendered positive results 156 for SARS-CoV-2 by RT-PCR, which presents the overall prevalence. However, our results 157 demonstrated a variation in the prevalence rates during the 3 stages previously mentioned 158 ( Figure 2 ). The first stage (Stage I) demonstrated a prevalence rate less than 1% (2/1065), 159 with a weekly percentage fluctuating between 0% and 2.33%. The second stage (Stage II) 160 showed an increase in the prevalence of SARS-CoV-2 positive cases reaching 8.4% 161 (1,670/19,758) with a weekly variation between 0.6% and 16%. In the third stage (Stage III), 162 high prevalence of SARS-CoV-2 positive cases was detected equals to 27.5% (4,570/16,651) 163 with a weekly variation between 19.5% and 33.2% (Figure 2 ). 164 All rights reserved. No reuse allowed without permission.

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The copyright holder for this preprint this version posted April 13, 2021. ;  https://doi.org/10.1101/2021.04.08.21255005 doi: medRxiv preprint (which 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 this version posted April 13, 2021. ;  https://doi.org/10.1101/2021.04.08.21255005 doi: medRxiv preprint Indeed, the results showed a prevalence of COVID-19 positive cases of less than 1% 211 (2/1065) in the studied population during stage I, with a weekly percentage fluctuating 212 between 0% during strict lockdown (March -April) and 2.33% at the end of the first stage 213 where measures started to ease (May -June). This low infection rate can be explained by 214 several reasons including the adherence to the full lockdown measures where people had 215 fear from COVID-19, so they fully abided to the lockdown. In addition, the number of 216 cases in Lebanon during that period was very low [24] which made it easier for health 217 authorities to control the issue. Data from China [25], USA [26] and Indonesia [27] suggest 218 that quarantine and isolation can efficiently reduce the possible peak number of COVID-219 19 and suspend the time of peak infection. The low positivity rate during stage I of our 220 study could be linked to the low number of tests done during that period (1065) subdi-221 vided into less than 160 tests per week. This can be explained by the low number of con-222 firmed COVID-19 cases at the early stages of the outbreak in Southern Lebanon, and by 223 the strict measures taken by municipalities such as early testing for SARS-CoV-2 in indi-224 viduals with symptoms and early isolation practices which showed to effectively inter-225 rupt SARS-CoV-2 transmission [28] . Our results showed less than 1% positivity rate dur-226 ing the strict full lockdown imposed by the health authorities of Lebanon stressing out 227 importance of lockdowns in controlling the spread of the virus. In fact, delaying the lock-228 down could have resulted in a higher number of cases similar to what happened in other 229 countries where, for instance, delaying lockdown for one week resulted in an 8-32% in-230 crease in total COVID-19 cases [29] . Thus, implementing lockdown as early as possible is 231 indispensable to contain the transmission and avoid national outbreaks [21] . 232 The second stage of our study (Stage II) covered the timespan between July and mid-De-233 cember 2020, a stage during which the Lebanese authorities started easing the lockdown 234 restrictions by the end of June 2020 to reach an almost full back-to-normal-life scenario by 235 December 2020. During this stage, the number of weekly tests done in the health care 236 center included in our present study increased to a maximum of 1,238 tests per week, 237 partnered with a significant increase in the prevalence of positive SARS-CoV-2 cases. In 238 stage II, 1,670 confirmed COVID-19 cases were reported out of 19,758 performed tests with 239 a prevalence rate of SARS-CoV-2 infection of approximately 8.4% with a weekly variation 240 between 0.6% during the first weeks (July 2020) -an expected result since it reveals the 241 outcome of the lockdown -and 16% during the rest of the period (September, October, 242 November, and mid-December 2020) during which restrictions were fully-eased and life 243 started shifting towards normal conditions. The increase in positive cases was expected 244 and it was indeed the result of the ease of the national lockdown measures. In fact, lifting 245 lockdown too early had been shown to cause an increase in infection rates and indeed has 246 led to the second COVID-19 pandemic wave worldwide [30] . For instance, a modelling 247 study performed in France showed that the reduced efficiency of lockdown might be 248 caused by the loose lockdown applied. Dolbeault et al. [31] showed that even when allow-249 ing a small margin of the population (2%) to have a higher social interaction level than 250 before lockdown (such as health care workers, supermarket cashiers), the number of in-251 fected cases within the population would be higher than in a complete lockdown situa-252 tion. Rao et al. also demonstrated that if only 50% of the public obeyed lockdown and 253 other precautionary measures implemented by the end of March 2020 in the US, the daily 254 new cases in June would have been 17 times less than the average new COVID-19 cases 255 reported in April (29,000 cases/day). Instead, if a broad, strict lockdown was applied, it 256 could have reduced the daily new cases to 4,300-8,000 cases in May [26] . Moreover, a study 257 performed in England demonstrated that strict lockdown measures imposed by the Brit-258 ish authorities on March 23, 2020 led to a significant decrease in COVID-19 cases, hospital 259 admissions, and deaths, while resurrection of COVID-19 cases started to show in the late 260 summer 2020 after most restrictions had been lifted and lockdown was eased [32] . Those 261 studies support our results in which the 8-fold increase in the prevalence of COVID-19 262 during the second stage (post-lockdown) is highly attributed to the lifting of national lock-263 down accompanied by an ease in restriction measures. On the other hand, our data shows 264 a peak in the number of tests done during this stage, precisely within the week of August 265 03, 2020 in which our center witnessed more than 900 tests. In fact, a massive explosion 266 struck in the middle of Beirut within the port, and destroyed most of the city leaving be-267 hind more than 200 deaths and more than 7000 injuries [33] . During the days following 268 the explosion, our medical center, similar to most of the Lebanese hospitals, witnessed a 269 huge number of income patients. The center's strategy during then was to perform PCR 270 test to all admitted patients, a fact which explains the increase in the number of tests dur-271 ing that week. 272 All rights reserved. No reuse allowed without permission.

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The copyright holder for this preprint this version posted April 13, 2021. ; https://doi.org/10.1101 https://doi.org/10. /2021 The third and last stage of our study (stage III) covers the period after mid-December 2020 273 until 21st of February 2021 (the time of termination of data collection) during which the 274 number of PCR tests performed weekly increased to a maximum of 2,047 tests per week. 275 Out of the 16,651 tests performed during this stage, 4,570 tests were positive, indicating a 276 high prevalence rate of COVID-19 (27.5%) with a weekly variation between ~20% during 277 December 2020 and approximately 33% during January -mid-February 2021. This in-278 crease in the prevalence of SARS-CoV-2 infection during the late weeks of December 2020 279 and early weeks of January 2021 can be greatly attributed to the holidays' season during 280 which families and friends gathered in enclosed spaces (houses, restaurants, and even 281 clubs) to celebrate the holidays. Add to that, many clubs and restaurants were fully 282 booked for New Year's Eve parties and celebrations which made the situation even worse. 283 Data from other countries showed a huge increase in both the prevalence of COVID-19 284 daily cases and mortality rates after holidays. For example, 200,000 new cases and 3,000 285 deaths per day were reported in USA alone after thanksgiving celebrations in 2020 [34] . 286 Besides, there was a surge in COVID cases and death rates after 2021 New Year's gather-287 ings and celebrations [35] . A study performed in 11 European countries suggested an in-288 crease in COVID-19 prevalence and mortality rates after holiday vacations during the 289 winter of 2020 [36] . This explains the flood in COVID-19 cases in our study during the 290 early weeks of January as a result of indoor gatherings during the holidays. In fact, viral 291 spread in closed spaces is more likely to occur due to the fact that SARS-CoV-2 is an air-292 borne virus that is transmitted through air, particularly in crowded and poorly-ventilated 293 places [37] . 294 RNA viruses have an intensely high mutation rate that is correlated with virulence varia-295 tion and evolution which contributes to viral adaptation [38] . SARS-CoV-2 is an RNA vi-296 rus, and several testified results indicate that it is rapidly spreading throughout countries 297 and genomes with new mutation hotspots that are emerging, leading to the appearance 298 of new variants that can infect human cells more efficiently, escape neutralizing antibod-299 ies and maximize its genome replication [39] . On December 14, 2020, the health authorities 300 in the United Kingdom reported a new SARS-CoV-2 variant namely B.1.1.7, also called as 301 VOC 202012/01 or 201/501 Y.V. This variant was predicted to have emerged somewhere 302 in September 2020 and has become the most dominant SARS-CoV-2 variant circulating in 303 England [13] . Another variant, the 501Y.V2 emerged during the first wave of the South 304 African COVID-19 epidemic in early October 2020, then it spread rapidly to become the 305 dominant lineage in South Africa by the end of November 2020 [40] . A third variant of 306 concern known as the B.1.1.28 variant, also called P.1 variant, was identified in January 307 2021 and is likely to have originated in Brazil sometime around February 2020 [41] . Nev-308 ertheless, in December 21st, 2020, the Lebanese Ministry of Public Health announced the 309 first case of B.1.1.7 SARS-CoV-2 variant infection in a patient arriving from London [20] . 310 On January 9, 2021, the Lebanese authorities re-established a full lockdown across the 311 country in an attempt to contain the outbreak and the hectic increase in infection rates. By 312 the end of January 2021 and beginning of February 2021, our results showed continuous 313 increase in the positivity rates regardless of the lockdown (even 2 weeks after implement-314 ing the full lockdown measures). During the first week of February 2021, the prevalence 315 of COVID-19 cases was approximately 32% which is considerably high. Out of the total 316 number of samples, 6,353 were analyzed with the TaqPath COVID-19 CE-IVD RT-PCR 317 Kit which identifies three SARS-CoV-2 genes (ORFlab, N and S). Since all the previously 318 described variants comprise mutations in the RNA region coding for the viral spike (S) 319 protein [13, 42] , we considered the absence of the S-gene in these samples an indicator for 320 the presence of certain SARS-CoV-2 variant or variants. Starting January 2021, the absence 321 of S gene in positive samples was detected in our samples. Thus, we postulated the pres-322 ence of 2 types of variants in our samples; the old one that has been circulating since the 323 beginning of the outbreak in Lebanon, herein referred to as the "classic strain", and the 324 newly observed variant or variants causing the failure in detecting the S gene primer by 325 All rights reserved. No reuse allowed without permission.

(which 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 this version posted April 13, 2021. ;  the kits used in our study, herein referred to as the "S-mutant variant(s)". Our results 326 showed a rapid increase in the prevalence of the "S-mutant variant(s)" starting January 327 2021 where the percentage of its prevalence sharply surged from 72.3% at the end of Jan-328 uary 2021, to 96.5% in the week of February 15th, 2021. The prevalence of positive cases 329 during that same period jumped from approximately 20% to 31%. This suggests that the 330 "S-mutant variant(s)" variants are indeed highly transmissible and might be responsible 331 for the rapid surge in cases during the end of the third stage in our study. Taking into 332 consideration that all of the aforementioned variants are characterized by being more in-333 fectious due to their mutations in the spike (S) protein that gave them an infectious ad-334 vantage [13, 42] , this may explain the rapid increase in COVID-19 positive cases in our 335 samples in correlation with the appearance of the new variants. Also, a significant positive 336 correlation was noted between the prevalence of positive COVID-19 cases and the per-337 centage of "S-mutant variant(s)" during Stage III (r = 0. 828, P = 0. 006). Similarly, a study 338 conducted in the UK showed that the SARS-CoV-2 B.1.17 lineage is linked with consider-339 ably higher infection and mortality rates among adults [43] . To the best of our knowledge, 340 our results represent the first epidemiological study in Lebanon to demonstrate the pres-341 ence of new "S-mutant variant(s)" within our population, which may be similar to those 342 previously identified in the UK, South Africa and Brazil, or a new one, that is responsible 343 for the surge in COVID-19 cases during the third stage of the study. 344 Whether the above variant(s) is one of the internationally identified lineages or is a new 345 variant that has emerged within the Lebanese population remains to be deciphered. More 346 studies are needed to investigate the nature of the present variant(s). The lack of appro-347 priate sequencing techniques in our country is a limitation implementing further studies 348 regarding identifying the nature of the new variant(s) due to the financial and economic 349 crisis that the country is currently experiencing. This crisis also prompted the use of dif-350 ferent PCR kits to analyse the samples where the market availability of certain kits in Leb-351 anon is indeed challenging. The missing data during the week of January 4 th , 2021, regard-352 ing the percentages of SARS-CoV-2 strains, was due to the unavailability of the TaqPath™ 353 COVID-19 CE-IVD RT-PCR Kit. Finally, a correlation study between demographic and 354 clinical data of the whole 37,474 patients included in the present study will follow in a 355 future study to further explore the effect of SARS-CoV-2 variants in our population. 356 

Our study emphasizes the importance of strict lockdown measures to control the COVID-358 19 outbreak and any similar pandemics in the future. It shows how lifting restrictions and 359 allowing indoor gatherings can dramatically influence COVID-19 spread within the pop-360 ulation. In addition, our results revealed the presence of novel SARS-CoV-2 variant(s) 361 among the Lebanese population which is likely correlated to the rapid increase in the 362 prevalence rates of COVID-19 positive cases starting of January 2021. 

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We would like to express our gratitude to the healthcare center "Sheikh Ragheb 377 Harb University Hospital" for their support in the conduction of this study. 378 We thank Dr. Hisham F. Bahmad for taking the time and effort necessary to review the manuscript. 379 380 Conflicts of Interest: The authors declare no conflict of interest. 381