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Japanese Study - Virological Characteristics of SARS-CoV-2 BA.2 Variant
Japanese Study - Virological Characteristics of SARS-CoV-2 BA.2 Variant
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bioRxiv preprint doi: https://doi.org/10.1101/2022.02.14.480335; this version posted February 15, 2022. The copyright holder for this preprint
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14
41 Laboratory of Systems Virology, Institute for Frontier Life and Medical
42 Sciences, Kyoto University, Kyoto, Japan.
15
43 Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan.
16
44 Division of Vaccine Science, Department of Microbiology and Immunology,
45 The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
17
46 Division of Infection and immunity, Joint Research Center for Human
47 Retrovirus infection, Kumamoto University, Kumamoto, Japan
18
48 Department of Veterinary Science, Faculty of Agriculture, University of
49 Miyazaki, Miyazaki, Japan.
19
50 International Collaboration Unit, International Institute for Zoonosis Control,
51 Hokkaido University, Sapporo, Japan.
20
52 Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan.
21
53 Tokyo Metropolitan Institute of Public Health, Tokyo, Japan.
22
54 Kuramochi Clinic Interpark, Utsunomiya, Japan.
23
55 Department of Molecular Oncology, Graduate School of Medicine, Chiba
56 University, Chiba, Japan.
24
57 Department of Emergency and Critical Care Medicine, Graduate School of
58 Medicine, Chiba University, Chiba, Japan.
25
59 Department of Respirology, Graduate School of Medicine, Chiba University,
60 Chiba, Japan.
26
61 Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan.
27
62 Graduate School of Medicine and Veterinary Medicine, University of Miyazaki,
63 Miyazaki, Japan.
28
64 Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima,
65 Japan.
29
66 Division of Risk Analysis and Management, International Institute for Zoonosis
67 Control, Hokkaido University, Sapporo, Japan.
30
68 CREST, Japan Science and Technology Agency, Saitama, Japan.
31
69 These authors contributed equally: Izumi Kimura, Daichi Yamasoba, Hesham
70 Nasser, Yuhei Morioka, Naganori Nao, Jumpei Ito, Keiya Uriu, Masumi Tsuda,
71 Jiri Zahradnik.
72
73 *Corresponding authors:
74 [email protected] (Akatsuki Saito);
75 [email protected] (Takashi Irie);
76 [email protected] (Shinya Tanaka);
77 [email protected] (Keita Matsuno);
78 [email protected] (Takasuke Fukuhara);
79 [email protected] (Terumasa Ikeda);
80 [email protected] (Kei Sato)
81
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bioRxiv preprint doi: https://doi.org/10.1101/2022.02.14.480335; this version posted February 15, 2022. The copyright holder for this preprint
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82 Keywords:
83 SARS-CoV-2; COVID-19; Omicron; BA.2; BA.1; B.1.1.529; pathogenicity;
84 fusogenicity; transmissibility
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85 Abstract
86 Soon after the emergence and global spread of a new severe acute respiratory
87 syndrome coronavirus 2 (SARS-CoV-2) Omicron lineage, BA.1 (ref1,2), another
88 Omicron lineage, BA.2, has initiated outcompeting BA.1. Statistical analysis
89 shows that the effective reproduction number of BA.2 is 1.4-fold higher than that
90 of BA.1. Neutralisation experiments show that the vaccine-induced humoral
91 immunity fails to function against BA.2 like BA.1, and notably, the antigenicity of
92 BA.2 is different from BA.1. Cell culture experiments show that BA.2 is more
93 replicative in human nasal epithelial cells and more fusogenic than BA.1.
94 Furthermore, infection experiments using hamsters show that BA.2 is more
95 pathogenic than BA.1. Our multiscale investigations suggest that the risk of BA.2
96 for global health is potentially higher than that of BA.1.
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97 Introduction
98 Virological characteristics of newly emerging SARS-CoV-2 variants, such as
99 transmissibility, pathogenicity and resistance to the vaccine-induced immunity
100 and antiviral drugs, is an urgent global health concern. In February 2022, the
101 Omicron variant (B.1.1.529 and BA lineages) spreads worldwide and represents
102 the most recently recognised variant of concern2. Omicron was first reported
103 from South Africa at the end of November 20211. Then, a variant of Omicron, the
104 BA.1 lineage, has rapidly spread worldwide and outcompeted other variants
105 such as Delta.
106 As of February 2022, another variant of Omicron, the BA.2 lineage, has
107 detected in multiple countries such as Denmark and UK3. Notably, BA.2 has
108 initiated outcompeting BA.13, suggesting that BA.2 is more transmissible than
109 BA.1.
110 In a few months since the emergence of BA.1, we and others revealed
111 the virological characteristics of BA.14-19. For instance, BA.1 is highly resistant to
112 the vaccine-induced humoral immunity and antiviral drugs4-11,16-19. Also, the
113 spike (S) protein of BA.1 is less efficiently cleaved by furin and less fusogenic
114 than those of Delta and an ancestral SARS-CoV-2 belonging to the B.1.1
115 lineage11,12. Further, the pathogenicity of BA.1 is attenuated when compared to
116 Delta and an ancestral B.1.1 virus12-14. However, the virological characteristics of
117 BA.2 remains unaddressed.
118
119 Phylogenetic and epidemic dynamics of BA.2
120 As of February 2022, Omicron is classified into three main lineages, BA.1, BA.2,
121 BA.3, and a sublineage of BA.1, BA1.1, which harbours the R346K substitution
122 in S (Fig. 1a). Although these lineages are monophyletic, their sequences have
123 been greatly diversified. For example, BA.1 differs from BA.2 by 50 amino acids,
124 which is approximately twice as much as the numbers of amino acid differences
125 between four VOCs (Alpha, Beta, Gamma and Delta) and Wuhan-Hu-1, a
126 prototypic SARS-CoV-2 isolate (Fig. 1b). Phylodynamics analysis suggests that
127 BA.1 emerged first, followed by BA.2 and BA.3 (Extended Data Fig. 1). In
128 addition to BA.1, the earlier strains of BA.2, BA.3, and BA.1.1 were isolated from
129 Gauteng Province, South Africa, the place of the earliest Omicron (BA.1)
130 epidemic (Extended Data Fig. 1)20. These results suggest that the remarkable
131 diversification of Omicron occurred in Gauteng Province and all Omicron
132 lineages emerged there.
133 Although BA.1 spread worldwide earlier than BA.2, the lineage
134 frequency of BA.2 increased and exceeded that of BA.1 since January 2022 in
135 multiple countries, such as Philippines, India, Denmark, Singapore, Austria, and
136 South Africa (Fig. 1c and Extended Data Fig. 2). To quantify the growth
137 advantage of BA.2 in the human population, we constructed a Bayesian model
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220 hypothesized that BA.2 S is more efficiently cleaved than BA.1 S. However, an
221 western blotting analysis showed that BA.2 S is less cleaved than BA.1 S (Fig.
222 3e), suggesting that BA.2 S exhibits a higher fusogenicity independently of
223 S1/S2 cleavage.
224 We have recently revealed that BA.1 poorly utilizes TMPRSS2 for the
11
225 infection . To analyse the TMPRSS2 usage by BA.2 S, we performed
226 cell-based fusion assay using 293-ACE2 cells with or without TMPRSS2
227 expression. We verified that 293-ACE2 cells do not express endogenous
228 TMPRSS2 on the cell surface (Extended Data Fig. 6c). As shown in Fig. 3f, the
229 fusogenicity of BA.2 S was significantly higher in both cell lines than that of BA.1.
230 However, although BA.2 S was less fusogenic than B.1.1 S in 293-ACE2 cells,
231 the fusogenicity of BA.2 S and B.1.1 S was comparable in 293-ACE2/TMPRSS2
232 cells (Fig. 3f). These results suggest that the relatively higher fusogenicity of
233 BA.2 is dependent on TMPRSS2 expression on the surface of target cells. To
234 further assess whether the TMPRSS2-dependent infection enhancement was
235 also observed in cell-free virus, we inoculated pseudoviruses into 293-ACE2
236 cells and 293-ACE2/TMPRSS2 cells. Although the infectivity of B.1.1 and Delta
237 was 15.3-fold and 24.6-fold increased by TMPRSS2 expression, respectively,
238 the TMPRSS2 expression on the target cells did not affect the infectivity of both
239 BA.1 and BA.2 (Fig. 3g). These results suggest that TMPRSS2 does not affect
240 the infectivity of cell-free BA.2 virus. However, although the growth of BA.2 and
241 BA.1 was comparable in 293-ACE2 cells, BA.2 was more replicative than BA.1
242 in 293-ACE2/TMPRSS2 cells (Fig. 3h). Overall, our data suggest that BA.2 is
243 more fusogenic and replicative than BA.1 in a TMPRSS2-dependent fashion.
244
245 Virological features of BA.2 in vivo
246 To investigate the dynamics of viral replication of BA.2 in vivo, we conducted
247 hamster infection experiments. Consistent with our recent study12, B.1.1-infected
248 hamsters exhibited decreased body weight and respiratory disorders that are
249 reflected by two surrogate markers for bronchoconstriction or airway obstruction,
250 enhanced pause (Penh) and the ratio of time to peak expiratory follow relative to
251 the total expiratory time (Rpef), and subcutaneous oxygen saturation (SpO2),
252 whereas BA.1-infected hamsters exhibited no or weak disorders (Fig. 4a).
253 Notably, all parameters routinely measured, including body weight, Penh, Rpef
254 and SpO2, of BA.2-infected hamsters were significantly different from uninfected
255 and BA.1-infected hamsters, and these values were comparable to those of
256 B.1.1-infected hamsters (Fig. 4a). These data suggest that BA.2 is more
257 pathogenic than BA.1.
258 To analyse viral spread in the respiratory organs of infected hamsters,
259 viral RNA load and nucleocapside (N) expression were assessed by RT-qPCR
260 of viral RNA and immunohistochemistry (IHC), respectively. As shown in Fig. 4b,
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261 viral RNA loads in the two lung regions, hilum and periphery, of BA.2-infected
262 hamsters were significantly higher than those of BA.1-infected hamsters. In the
263 lung periphery, the viral RNA load of BA.2 was significantly higher than that of
264 B.1.1, and the viral RNA load of BA.2 at 1 d.p.i. was 11-fold and 9.3-fold higher
265 than those of B.1.1 and BA.1 at the same timepoint, respectively (Fig. 4b). To
266 address the possibility that BA.2 more efficiently spreads than BA.1, we
267 investigated the positivity for N protein in the trachea and lung area close to the
268 hilum. At 1 d.p.i., N protein was detectable in the lower tracheal epithelium in all
269 infected hamsters, and particularly, was clearly detectable in the middle part of
270 trachea in BA.2-infected hamsters (Extended Data Fig. 7a). The positivity of N
271 protein was observed in both bronchial and bronchiolar epithelium in all infected
272 lungs (Extended Data Fig. 7b). Notably, alveolar positivities were observed in
273 B.1.1- and BA.2-infected lungs but not in BA.1-infected lungs (Extended Data
274 Fig. 7b). Morphometry showed that the percentage of N-positive cells in
275 BA.2-infected lungs is significantly higher than that of BA.1-infected lungs and
276 peaked at 3 d.p.i. (Fig. 4c and Extended Data Fig. 7c). On the other hand, at 3
277 d.p.i., the percentage of N-positive cells in the bronchus/bronchioles of
278 BA.2-infected hamsters was 5.4-fold lower than that of BA.1-infected hamsters
279 (Fig. 4d). At 5 d.p.i., N protein was almost disappeared in BA.1-infected lungs,
280 whereas alveolar staining was still detectable in B.1.1- and BA.2-infected lungs
281 (Fig. 4c and Extended Data Fig. 7c). These data suggest that BA.2 is more
282 rapidly and efficiently spread in the lung tissues than BA.1.
283
284 Pathogenicity of BA.2
285 To investigate the pathogenicity of BA.2, the right lungs of infected hamsters
286 were collected at 1, 3, and 5 d.p.i. and used them for haematoxylin and eosin
287 (H&E) staining and histopathological analysis12,23. All histopathological
288 parameters including bronchitis/bronchiolitis, haemorrhage, alveolar damage,
289 and the levels of type II pneumocytes, of BA.2-infected hamsters were
290 significantly higher than those in BA.1 (Fig 4e and Extended Data Fig. 8a). The
291 score indicating haemorrhage including congestive edema of BA.2 was
292 significantly higher than that of B.1.1 (Fig. 4e). As shown in our previous
293 studies12,23, hyperplastic large type II pneumocytes suggesting the severity of
294 inflammation were observed in all infected hamsters at 5 d.p.i., and particularly,
295 the area of large type II pneumocytes in BA.2-infected hamsters was
296 significantly larger than those in B.1.1- and BA.1-infected hamsters (Fig. 4e).
297 Total histology score of BA.2 was significantly higher than that of BA.1 (Fig. 4e).
298 Furthermore, in the BA.2- and B.1.1-infected lungs, the inflammation with type II
299 alveolar pneumocyte hyperplasia was found in each lobe especially
300 frontal/upper and accessary lobes (Extended Data Fig. 8b).
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301 Discussion
302 Although BA.2 is considered as an Omicron variant, its genomic sequence is
303 heavily different from BA.1, which suggests that the virological characteristics of
304 BA.2 is different from that of BA.1. Here, we elucidated the virological
305 characteristics of BA.2, such as its higher effective reproduction number, higher
306 fusogenicity, higher pathogenicity when compared to BA.1. Moreover, we
307 demonstrated that BA.2 is resistant to the BA.1-induced humoral immunity. Our
308 data indicate that BA.2 is virologically different from BA.1 and raise a proposal
309 that BA.2 should be given a letter of the Greek alphabet and be distinguished
310 from BA.1, a commonly recognized Omicron variant.
311 We showed evidence suggesting that BA.2 is virologically different and
312 distinguishable from BA.1. First, by using the two different types of antisera that
313 were obtained from experimental animals, convalescent hamsters infected with
314 BA.1 and mice immunized with the BA.1 S protein, we showed that the
315 resistance of BA.2 to the BA.1-induced humoral immunity. Our results indicate
316 that the antigenicity of BA.2 is different from BA.1. Although similar tendency
317 was observed in human samples as well, a statistically significant difference was
318 not observed probably because a relatively lower number of vaccine-naïve
319 individuals who were infected with BA.1 (3 unvaccinated donors and a 1-dose
320 vaccinated donor) were tested in the present study. The effect of BA.1-induced
321 humoral immunity against BA.2 in humans should deeply be verified in the future
322 investigation.
323 Second, the higher fusogenicity of BA.2 S is a pronounced
324 characteristics in in vitro experiments. We have demonstrated that Delta S is
325 highly fusogenic than BA.1 S and B.1.1 S, and we considered that the higher
326 fusogenicity is attributed to the higher efficacy of S cleavage11,12,23,27. However,
327 BA.2 S exhibited higher fusogenicity than BA.1 S without the increase of S
328 cleavage efficacy. In recent studies12,23, we have proposed that the fusogenicity
329 of SARS-CoV-2 variant is closely related to its pathogenicity. This hypothesis is
330 further supported by the observations in BA.2 in the present study. However,
331 unlike Delta, the higher fusogenicity of BA.2 appears to be not attributed to the
332 higher efficacy of S cleavage11,12,23,27. Moreover, although TMPRSS2 increased
333 the efficacies of both cell-cell fusion23 and cell-free infection mediated by B.1.1 S
334 and Delta S, TMPRSS2 increased the efficacy of BA.2 S-mediated cell-cell
335 fusion but did not affect that of BA.2 S-mediated cell-free infection. These
336 observations suggest that TMPRSS2 contributes to the cell-cell fusion and
337 cell-free infection mediated by BA.2 S with different mechanisms of action.
338 Third, it would be most critical for global health that BA.2 exhibits higher
339 pathogenicity than BA.1. Although clinical researches on the BA.2 pathogenicity
340 are needed, our investigations using a hamster model showed that the
341 pathogenicity of BA.2 is similar to that of an ancestral B.1.1 and higher than that
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342 of BA.1. More importantly, the viral RNA load in the lung periphery and
343 histopathological disorders of BA.2 were more severe than those of BA.1 and
344 even B.1.1. Together with a higher effective reproduction number and
345 pronounced immune resistance of BA.2, it is evident that the spread of BA.2 can
346 be a serious issue for global health in the near future.
347 In summary, our data suggest the possibility that BA.2 would be the
348 most concerned variant to global health. Currently, both BA.2 and BA.1 are
349 recognised together as Omicron and these are almost undistinguishable. Based
350 on our findings, we propose that BA.2 should be recognised as a unique variant
351 of concern, and this SARS-CoV-2 variant should be monitored in depth.
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352 Methods
353
354 Ethics statement
355 All experiments with hamsters were performed in accordance with the Science
356 Council of Japan’s Guidelines for the Proper Conduct of Animal Experiments.
357 The protocols were approved by the Institutional Animal Care and Use
358 Committee of National University Corporation Hokkaido University (approval ID:
359 20-0123 and 20-0060). All experiments with mice were also performed in
360 accordance with the Science Council of Japan’s Guidelines for the Proper
361 Conduct of Animal Experiments. The protocols were approved by the
362 Institutional Animal Experiment Committee of The Institute of Medical Science,
363 The University of Tokyo (approval ID: PA21-39). All protocols involving
364 specimens from human subjects recruited at Kyoto University, Kuramochi Clinic
365 Interpark and Chiba University were reviewed and approved by the Institutional
366 Review Boards of Kyoto University (approval ID: G1309), Kuramochi Clinic
367 Interpark (approval ID: G2021-004) and Chiba University (approval ID:
368 HS202103-03). All human subjects provided written informed consent. All
369 protocols for the use of human specimens were reviewed and approved by the
370 Institutional Review Boards of The Institute of Medical Science, The University of
371 Tokyo (approval IDs: 2021-1-0416 and 2021-18-0617), Kyoto University
372 (approval ID: G0697), Kumamoto University (approval IDs: 2066 and 2074), and
373 University of Miyazaki (approval ID: O-1021).
374
375 Human sera collection
376 Vaccine sera were collected from sixteen vaccinees four weeks after the second
377 vaccination with mRNA-1273 (Moderna) (average age: 27, range: 20-47, 38%
378 male). The sera obtained from nine vaccinees 10-25 d after the second
379 vaccination with ChAdOx1 (Oxford-AstraZeneca) (average age: 45, range:
380 35-54, 67% male) were purchased from BioIVT. The detail of vaccine sera is
381 summarized in Supplementary Table 1.
382 Convalescent sera were collected from vaccine-naive individuals who
383 had infected with Alpha variant (n=8; average age: 41, range: 21-57, 63% male)
384 and Delta variant (n=15; average age: 51, range: 22-67, 80% male).
385 Convalescent sera of BA.1-infected individuals (n=17; average age: 39, range:
386 20-65, 47% male, 76% received the second vaccination) were also collected. To
387 determine the SARS-CoV-2 variants infected, salivas were collected from
388 COVID-19 patients during onset and RNA was extracted using a QIAamp viral
389 RNA mini kit (Qiagen, Cat# 52906) according to the manufacturer’s protocol. To
390 determine Alpha and Delta variants, viral genome sequencing was performed as
391 previously described11. For the detail, see "Viral genome sequencing" section
392 below. To determine the BA.1 variant, mutation-targeting RT-qPCR was
12
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393 performed. To detect the S E484A substitution (common in all Omicron variants
394 including BA.1 and BA.2), a set of primer/probe E484A (SARS-CoV-2) (Takara,
395 Cat# RC322A) was used. To detect the S R214EPE insertion (specific for
396 B.1.1.529 and BA.1, undetectable in BA.2), a hand-made protocol was used with
397 the following primers and probe: Omi_ins214s-F1, TTC TAA GCA CAC GCC
398 TAT TAT AGT GC; Omi_ins214s-R1, TAA AGC CGA AAA ACC CTG AGG; and
399 Omi_ins214s, FAM-TGA GCC AGA AGA TC-MGB. The twelve convalescent
400 sera during early pandemic (until May 2020) (average age: 71, range: 52-92, 8%
401 male) were purchased from RayBiotech. Sera were inactivated at 56°C for 30
402 min and stored at –80°C until use. The detail of convalescent sera is
403 summarized in Supplementary Table 2.
404
405 Viral genome sequencing
406 Viral genome sequencing was performed as previously described11,12,22,23 with
407 some modifications. Briefly, the sequences of the working viruses were verified
408 by viral RNA-sequencing analysis. Viral RNA was extracted using QIAamp viral
409 RNA mini kit (Qiagen, Cat# 52906). The sequencing library for total
410 RNA-sequencing was prepared using NEB Next Ultra RNA Library Prep Kit for
411 Illumina (New England Biolabs, Cat# E7530). Paired-end, 76-bp sequencing
412 was performed using MiSeq (Illumina) with MiSeq reagent kit v3 (Illumina, Cat#
413 MS-102-3001). Sequencing reads were trimmed using fastp v0.21.028 and
414 subsequently mapped to the viral genome sequences of a lineage A isolate
415 (strain WK-521; GISAID ID: EPI_ISL_408667)29 using BWA-MEM v0.7.1730.
416 Variant calling, filtering, and annotation were performed using SAMtools v1.931
417 and snpEff v5.0e32.
418
419 Phylogenetic and comparative genome analyses
420 To construct a maximum likelihood tree of the Omicron lineages (BA.1, BA.1.1,
421 BA.2, and BA.3) sampled from South Africa, the genome sequence data of
422 SARS-CoV-2 and its metadata were downloaded from the GISAID database
423 (https://www.gisaid.org/) on January 26, 2022. We excluded the data of viral
424 strains with the following features from the analysis: i) lacking the collection date
425 information; ii) sampled from animals other than humans; iii) having the flag of
426 low coverage sequencing; or iv) having >2% of undetermined nucleotide
427 characters. All the BA.2 and BA.3 sequences and 200 randomly sampled BA.1
428 (including 20 BA.1.1) sequences were used for the tree construction in addition
429 to an outgroup sequence, EPI_ISL_466615, the oldest isolate of B.1.1 in the UK.
430 The viral genome sequences were mapped to the reference sequence of
431 Wuhan-Hu-1 (GenBank accession no.: NC_045512.2) using minimap2 v2.1733
432 and subsequently converted to the multiple sequence alignment according to the
433 GISAID phylogenetic analysis pipeline
13
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475 lineage according to the epidemic dynamics calculated on the basis of viral
476 genomic surveillance data. The data were downloaded from the GISAID
477 database (https://www.gisaid.org/) on February 1, 2022. We excluded the data
478 of viral strains with the following features from the analysis: i) lacking the
479 collection date information; ii) sampled from animals other than humans; or iii)
480 sampled by quarantine. We analysed the datasets of the eleven countries with
481 >100 BA.2 sequences (Austria, Denmark, Germany, India, Israel, Philippines,
482 Singapore, South Africa, Sweden, the UK, and the USA) (Fig. 1 and Extended
483 Data Fig. 2). The dynamics of BA.1, BA.1.1, BA.2, and Delta (B.1.617.2 and AY
484 lineages) in each country from October 1, 2021, to January 25, 2022, were
485 analysed. The number of viral sequences of each viral lineage collected on each
486 day in each country was counted. Finally, we constructed the L (lineage) × C
487 (country) × T (time) = 4 × 11 × 117 shaped array, which comprises the count of
488 each viral lineage in each country in each day. This array was used as input data
489 for the statistical model described below.
490 We constructed a Bayesian hierarchical model to represent the relative
491 lineage growth dynamics with a multinomial logistic regression. The
492 mathematical theory underlying the model is described in detail elsewhere38,39,
493 and this model is basically similar to the one used in our previous study12. In the
494 present study, we incorporated a hierarchical structure into the slope parameter
495 over time, which enable us to estimate the global average of the relative
496 effective reproduction number of each viral lineage as well as that in each
497 country. Arrays in the model index over one or more indices: L = 4 viral lineages
498 ; C = 11 countries ; and T = 117 days . The model is:
β Student_t
6, β , σ
µ α β t
499 The explanatory variable is time , and the outcome variable is , which
500 represents the count of viral lineage in country at time . The slope
501 parameter of lineage in country , β , is generated from a student’s t
502 distribution with the hyper parameters of the mean β and the standard
503 deviation σ . As the distribution generating β , we used a student’s t distribution
504 with six degrees of freedom instead of a normal distribution to reduce the effects
505 of outlier values of β . In the model, the linear estimator µ. , consisting of the
506 intercept α. and the slope β. , is converted to the simplex θ. , which
507 represents the probability of occurrence of each viral lineage at time in
508 country , by the softmax link function defined as:
15
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exp
$
softmax
$
∑ exp
$
509 is generated from θ. and the total count of all lineages at in country c
510 according to a multinomial distribution.
511 The relative effective reproduction number of each viral lineage in each
512 county (( ) was calculated according to the slope parameter β as:
r exp
γβ
518 For the parameter estimation, the intercept and slope parameters of the BA.1
519 variant were fixed at 0. Consequently, the relative effective reproduction number
520 of BA.1 was fixed at 1, and those of the respective lineages were estimated
521 relative to that of BA.1.
522 Parameter estimation was performed by MCMC implemented in
523 CmdStan v2.28.1 (https://mc-stan.org) with cmdstanr v0.4.0
524 (https://mc-stan.org/cmdstanr/). Noninformative priors were set for all
525 parameters. Four independent MCMC chains were run with 1,000 and 2,000
526 steps in the warmup and sampling iterations, respectively. We confirmed that all
527 estimated parameters had <1.01 R-hat convergence diagnostic and >200
528 effective sampling size values, indicating that the MCMC runs were successfully
529 convergent. The fitted model closely recapitulated the observed viral lineage
530 dynamics in each country (Extended Data Fig. 2c). The analyses above were
531 performed in R v4.1.2 (https://www.r-project.org/).
532
533 Cell culture
534 HEK293 cells (a human embryonic kidney cell line; ATCC CRL-1573) and
535 HEK293-ACE2 cells [HEK293 cells (ATCC CRL-1573) stably expressing human
536 ACE2]22 were maintained in DMEM (high glucose) (Sigma-Aldrich, Cat#
537 6429-500ML) containing 10% FBS, 1 µg/ml puromycin (InvivoGen, Cat#
538 ant-pr-1) and 1% PS. HEK293-ACE2/TMPRSS2 cells [HEK293 cells (ATCC
539 CRL-1573) stably expressing human ACE2 and TMPRSS2]22 were maintained
540 in Dulbecco’s modified Eagle's medium (DMEM) (high glucose) (Wako, Cat#
541 044-29765) containing 10% foetal bovine serum (FBS) and 1%
542 penicillin-streptomycin (PS). HEK293-C34 cells, IFNAR1 KO HEK293 cells
543 expressing human ACE2 and TMPRSS2 by doxycycline treatment21, were
544 maintained in Dulbecco’s modified Eagle's medium (high glucose)
545 (Sigma-Aldrich, Cat# R8758-500ML) containing 10% FBS, 10 μg/ml blasticidin
16
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(which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
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546 (InvivoGen, Cat# ant-bl-1) and 1% PS. Vero cells [an African green monkey
547 (Chlorocebus sabaeus) kidney cell line; JCRB0111] were maintained in Eagle’s
548 minimum essential medium (EMEM) (Wako, Cat# 051-07615) containing 10%
549 FBS and 1% PS. VeroE6/TMPRSS2 cells (VeroE6 cells stably expressing
550 human TMPRSS2; JCRB1819)29 were maintained in DMEM (low glucose)
551 (Wako, Cat# 041-29775) containing 10% FBS, G418 (1 mg/ml; Nacalai Tesque,
552 Cat# G8168-10ML) and 1% PS. Calu-3 cells (a human lung epithelial cell line;
553 ATCC HTB-55) were maintained in EMEM (Sigma-Aldrich, Cat# M4655-500ML)
554 containing 20% FBS and 1% PS. Calu-3/DSP1-7 cells [Calu-3 cells (ATCC
555 HTB-55) stably expressing DSP1-7]40 were maintained in EMEM (Wako, Cat#
556 056-08385) supplemented with 20% FBS and 1% PS. B16F10 cells (a mouse
557 melanoma cell line; RCB2630) were maintained in DMEM (high glucose)
558 (Sigma-Aldrich, Cat# D6429-500ML) containing 10% FBS and 1% PS. Expi293
559 cells (Thermo Fisher Scientific, Cat# A14527) were maintained in Expi293
560 expression medium (Thermo Fisher Scientific, Cat# A1435101). Primary human
561 nasal epithelial cells (Cat# EP02, Batch# MP0010) were purchased from
562 Epithelix and maintained according to the manufacturer's procedure.
563
564 Plasmid construction
565 Plasmids expressing the SARS-CoV-2 S proteins of B.1.1 (the parental
566 D614G-bearing variant), Alpha (B.1.1.7), Delta (B.1.617.2) and BA.1 variants
567 were prepared in our previous studies11,12,22,23,41. Plasmids expressing the
568 codon-optimised S proteins of BA.2 and a BA.2 derivative that loses its
569 cytoplasmic tail were generated by site-directed overlap extension PCR using
570 the primers listed in Supplementary Table 3. The resulting PCR fragment was
571 digested with KpnI and NotI and inserted into the corresponding site of the
572 pCAGGS vector. To construct the plasmids expressing anti-SARS-CoV-2
573 monoclonal antibodies (Casirivimab, Imdevimab or Sotrovimab), the sequences
574 of the variable regions of these antibodies were obtained from KEGG Drug
575 Database (https://www.genome.jp/kegg/drug/) and were artificially synthesized
576 (Fasmac). The obtained coding sequences of the variable regions of the heavy
577 and light chains were cloned into the pCAGGS vector containing the sequences
578 of the human immunoglobulin 1 and kappa constant region [kindly provided by
579 Dr. Hisashi Arase (Osaka University, Japan)]. Nucleotide sequences were
580 determined by DNA sequencing services (Eurofins), and the sequence data
581 were analyzed by Sequencher v5.1 software (Gene Codes Corporation).
582
583 Preparation of monoclonal antibodies
584 Casirivimab, Imdevimab and Sotrovimab were prepared as previously
585 described11,42. Briefly, the pCAGGS vectors containing the sequences encoding
586 the immunoglobulin heavy and light chains were cotransfected into HEK293T
17
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(which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
available under aCC-BY-ND 4.0 International license.
587 cells using PEI Max (Polysciences, Cat# 24765-1). At 48 h posttransfection, the
588 cell culture supernatants were harvested, and the antibodies were purified using
589 NAb protein A plus spin kit (Thermo Fisher Scientific, Cat# 89948) according to
590 the manufacturer’s protocol.
591
592 Preparation of mouse sera
593 The SARS-CoV-2 S-immunised mouse sera were prepared as previously
594 described42. To prepare the immunogen, B16F10 cells (2,500,000 cells) were
595 transfected with 5 μg S expression plasmid by PEI Max (Polysciences, Cat#
596 24765-1) according to the manufacturer’s protocol. Two days posttransfection,
597 the transfected cells were washed twice with PBS, and then the cell pellets were
598 stored at –80°C (10,000,000 cells per stock). The expression of transfected S
599 protein was verified by flow cytometry and western blot. BALB/c mice (female, 7
600 weeks old) were purchased from Japan SLC Inc. (Shizuoka, Japan). The mice
601 were maintained under specific pathogen-free conditions. For the immunisation,
602 mice were subcutaneously immunized with the freeze-thawed S-expressing
603 B16F10 cells in complete Freund’s adjuvant (50%) (Sigma-Aldrich, Cat# F5881).
604 Three weeks after immunisation, blood was collected in BD Microtainer blood
605 collection tubes (BD Biosciences, Cat# 365967) and sera were collected by
606 centrifugation.
607
608 Neutralisation assay
609 Pseudoviruses were prepared as previously described11,23,24,41,43. Briefly,
610 lentivirus (HIV-1)-based, luciferase-expressing reporter viruses were
611 pseudotyped with the SARS-CoV-2 spikes. HEK293T cells (1,000,000 cells)
612 were cotransfected with 1 μg psPAX2-IN/HiBiT44, 1 μg pWPI-Luc244, and 500 ng
613 plasmids expressing parental S or its derivatives using PEI Max (Polysciences,
614 Cat# 24765-1) according to the manufacturer's protocol. Two days
615 posttransfection, the culture supernatants were harvested and centrifuged. The
616 pseudoviruses were stored at –80°C until use.
617 For the neutralisation assay, the SARS-CoV-2 S pseudoviruses
618 (counting ~20,000 relative light units) were incubated with serially diluted
619 (40-fold to 29,160-fold dilution at the final concentration) heat-inactivated sera or
620 monoclonal antibodies (Casirivimab, Imdevimab or Sotrovimab) at 37°C for 1 h.
621 Pseudoviruses without sera were included as controls. Then, an 80 μl mixture of
622 pseudovirus and serum/antibody was added to HOS-ACE2/TMPRSS2 cells
623 (10,000 cells/50 μl) in a 96-well white plate. At 2 d.p.i., the infected cells were
624 lysed with a One-Glo luciferase assay system (Promega, Cat# E6130) or a
625 Bright-Glo ™ Luciferase Assay System (Promega, Cat# E2650), and the
20
bioRxiv preprint doi: https://doi.org/10.1101/2022.02.14.480335; this version posted February 15, 2022. The copyright holder for this preprint
(which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
available under aCC-BY-ND 4.0 International license.
708 mutations detected is summarized in Supplementary Table 6, and the raw data
709 are deposited in Gene Expression Omnibus (accession number: GSE196649).
710
711 SARS-CoV-2 infection
712 One day before infection, Vero cells (10,000 cells), VeroE6/TMPRSS2 cells
713 (10,000 cells), Calu-3 cells (20,000 cells), HEK293-ACE2 cells (10,000 cells),
714 HEK293-ACE2/TMPRSS2 cells (10,000 cells), were seeded into a 96-well plate.
715 SARS-CoV-2 [100 TCID50 for VeroE6/TMPRSS2 cells (Fig. 3a), 1,000 TCID50
716 for Vero cells (Fig. 3a), HEK293-ACE2 cells (10,000 cells) (Fig. 3j), and
717 HEK293-ACE2/TMPRSS2 cells (10,000 cells) (Fig. 3j); and 2,000 TCID50 for
718 Calu-3 cells (Fig. 3a)] was inoculated and incubated at 37°C for 1 h. The
719 infected cells were washed, and 180 µl of culture medium was added. The
720 culture supernatant (10 µl) was harvested at the indicated timepoints and used
721 for RT–qPCR to quantify the viral RNA copy number (see “RT–qPCR” section
722 below).
723 The infection experiment primary human nasal epithelial cells (Fig. 3a)
724 was performed as previously described11,23. Briefly, the working viruses were
725 diluted with Opti-MEM (Thermo Fisher Scientific, Cat# 11058021). The diluted
726 viruses (1,000 TCID50 in 100 μl) were inoculated onto the apical side of the
727 culture and incubated at 37°C for 1 h. The inoculated viruses were removed and
728 washed twice with Opti-MEM. To harvest the viruses on the apical side of the
729 culture, 100 μl Opti-MEM was applied onto the apical side of the culture and
730 incubated at 37°C for 10 m. The Opti-MEM applied was harvested and used for
731 RT–qPCR to quantify the viral RNA copy number (see “RT–qPCR” section
732 below).
733
734 RT–qPCR
735 RT–qPCR was performed as previously described11,12,22,23. Briefly, 5 μl of culture
736 supernatant was mixed with 5 μl of 2 × RNA lysis buffer [2% Triton X-100, 50
737 mM KCl, 100 mM Tris-HCl (pH 7.4), 40% glycerol, 0.8 U/μl recombinant RNase
738 inhibitor (Takara, Cat# 2313B)] and incubated at room temperature for 10 min.
739 RNase-free water (90 μl) was added, and the diluted sample (2.5 μl) was used
740 as the template for real-time RT-PCR performed according to the manufacturer’s
741 protocol using the One Step TB Green PrimeScript PLUS RT-PCR kit (Takara,
742 Cat# RR096A) and the following primers: Forward N, 5'-AGC CTC TTC TCG
743 TTC CTC ATC AC-3'; and Reverse N, 5'-CCG CCA TTG CCA GCC ATT C-3'.
744 The viral RNA copy number was standardized with a SARS-CoV-2 direct
745 detection RT-qPCR kit (Takara, Cat# RC300A). Fluorescent signals were
746 acquired using QuantStudio 3 Real-Time PCR system (Thermo Fisher Scientific),
747 CFX Connect Real-Time PCR Detection system (Bio-Rad), Eco Real-Time PCR
21
bioRxiv preprint doi: https://doi.org/10.1101/2022.02.14.480335; this version posted February 15, 2022. The copyright holder for this preprint
(which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
available under aCC-BY-ND 4.0 International license.
789 Cat# H3570). The coverslips were mounted on glass slides using
790 Fluoromount-G (Southern Biotechnology, Cat# 0100-01) with Hoechst 33342
791 and observed using an A1Rsi Confocal Microscope (Nikon). The size of
792 syncytium (GFP-positive area) was measured using Fiji software v2.2.0
793 (ImageJ) as previously described12.
794
795 SARS-CoV-2 S-based fusion assay
796 SARS-CoV-2 S-based fusion assay (Fig. 3d and 3f) was performed as
797 previously described12,22,23. This assay utilizes a dual split protein (DSP)
798 encoding Renilla luciferase and GFP genes; the respective split proteins,
799 DSP8-11 and DSP1-7, are expressed in effector and target cells by transfection.
800 Briefly, on day 1, effector cells (i.e., S-expressing cells) and target cells (see
801 below) were prepared at a density of 0.6–0.8 × 106 cells in a 6-well plate. To
802 prepare effector cells, HEK293 cells were cotransfected with the S expression
803 plasmids (400 ng) and pDSP8-11 (400 ng) using TransIT-LT1 (Takara, Cat#
804 MIR2300). To prepare target cells, HEK293 cells were cotransfected with
805 pC-ACE2 (200 ng) and pDSP1-7 (400 ng). Target HEK293 cells in selected wells
806 were cotransfected with pC-TMPRSS2 (40 ng) in addition to the plasmids above.
807 VeroE6/TMPRSS2 cells, Calu-3 cells, HEK293-ACE2 cells and
808 HEK293-ACE2/TMPRSS2 cells were transfected with pDSP1-7 (400ng). On day
809 3 (24 h posttransfection), 16,000 effector cells were detached and reseeded into
810 96-well black plates (PerkinElmer, Cat# 6005225), and target cells (HEK293,
811 VeroE6/TMPRSS2 or Calu-3/DSP1-7 cells) were reseeded at a density of
812 1,000,000 cells/2 ml/well in 6-well plates. On day 4 (48 h posttransfection), target
813 cells were incubated with EnduRen live cell substrate (Promega, Cat# E6481)
814 for 3 h and then detached, and 32,000 target cells were added to a 96-well plate
815 with effector cells. Renilla luciferase activity was measured at the indicated time
816 points using Centro XS3 LB960 (Berthhold Technologies). To measure the
817 surface expression level of S protein, effector cells were stained with rabbit
818 anti-SARS-CoV-2 S S1/S2 polyclonal antibody (Thermo Fisher Scientific, Cat#
819 PA5-112048, 1:100). Normal rabbit IgG (SouthernBiotech, Cat# 0111-01, 1:100)
820 was used as negative controls, and APC-conjugated goat anti-rabbit IgG
821 polyclonal antibody (Jackson ImmunoResearch, Cat# 111-136-144, 1:50) was
822 used as a secondary antibody. Surface expression level of S proteins
823 (Extended Data Fig. 6a) was measured using FACS Canto II (BD Biosciences)
824 and the data were analysed using FlowJo software v10.7.1 (BD Biosciences).
825 Gating strategy for flow cytometry is shown in Supplementary Fig. 1. To
826 calculate fusion activity, Renilla luciferase activity was normalized to the MFI of
827 surface S proteins. The normalized value (i.e., Renilla luciferase activity per the
828 surface S MFI) is shown as fusion activity.
829
23
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(which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
available under aCC-BY-ND 4.0 International license.
871 Western blot (Fig. 3e) was performed as previously described12,22,23. The
872 HEK293 cells cotransfected with the S expression plasmids and pDSP8-11 (see
873 “SARS-CoV-2 S-based fusion assay” section above) were used. To quantify the
874 level of the cleaved S2 protein in the cells, the harvested cells were washed and
875 lysed in lysis buffer [25 mM HEPES (pH 7.2), 20% glycerol, 125 mM NaCl, 1%
876 Nonidet P40 substitute (Nacalai Tesque, Cat# 18558-54), protease inhibitor
877 cocktail (Nacalai Tesque, Cat# 03969-21)]. After quantification of total protein by
878 protein assay dye (Bio-Rad, Cat# 5000006), lysates were diluted with 2 ×
879 sample buffer [100 mM Tris-HCl (pH 6.8), 4% SDS, 12% β-mercaptoethanol,
880 20% glycerol, 0.05% bromophenol blue] and boiled for 10 m. Then, 10 μl
881 samples (50 μg of total protein) were subjected to Western blot. For protein
882 detection, the following antibodies were used: mouse anti-SARS-CoV-2 S
883 monoclonal antibody (clone 1A9, GeneTex, Cat# GTX632604, 1:10,000), rabbit
884 anti-beta actin (ACTB) monoclonal antibody (clone 13E5, Cell Signalling, Cat#
885 4970, 1:5,000), horseradish peroxidase (HRP)-conjugated donkey anti-rabbit
886 IgG polyclonal antibody (Jackson ImmunoResearch, Cat# 711-035-152,
887 1:10,000) and HRP-conjugated donkey anti-mouse IgG polyclonal antibody
888 (Jackson ImmunoResearch, Cat# 715-035-150, 1:10,000). Chemiluminescence
889 was detected using SuperSignal West Femto Maximum Sensitivity Substrate
890 (Thermo Fisher Scientific, Cat# 34095) according to the manufacturer’s
891 instruction. Bands were visualized using an Amersham Imager 600 (GE
892 Healthcare), and the band intensity was quantified using Image Studio Lite v5.2
893 (LI-COR Biosciences) or Fiji software v2.2.0 (ImageJ). Uncropped blots are
894 shown in Supplementary Fig. 2.
895
896 Pseudovirus infection
897 Pseudovirus infection was (Fig. 3g) performed as previously
898 described11,12,22-24,43. Briefly, the same amount of pseudoviruses (normalized to
899 the HiBiT value, which indicates the amount of p24 HIV-1 antigen) was
900 inoculated into HEK293-ACE2 cells or HEK293-ACE2/TMPRSS2 and viral
901 infectivity was measured as described above (see “Neutralisation assay”
902 section). To analyse the effect of TMPRSS2 for pseudovirus infectivity, the fold
903 change of the values of HEK293-ACE2/TMPRSS2 to HEK293-ACE2 was
904 calculated.
905
906 Animal experiments
907 Animal experiments (Fig. 4) were performed as previously described12,23. Syrian
908 hamsters (male, 4 weeks old) were purchased from Japan SLC Inc. (Shizuoka,
909 Japan). Baseline body weights were measured before infection. For the virus
910 infection experiments, hamsters were euthanized by intramuscular injection of a
911 mixture of either 0.15 mg/kg medetomidine hydrochloride (Domitor®, Nippon
25
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(which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
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28
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(which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
available under aCC-BY-ND 4.0 International license.
1012 References
1013 1 WHO. "Classification of Omicron (B.1.1.529): SARS-CoV-2 variant of
1014 concern (November 26, 2021)”
1015 https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.
1016 1.529)-sars-cov-2-variant-of-concern. (2021).
1017 2 WHO. “Tracking SARS-CoV-2 variants (February 3, 2022)”.
1018 https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/.
1019 (2022).
1020 3 UKHSA. "SARS-CoV-2 variants of concern and variants under
1021 investigation in England. Technical briefing 35 (January 28, 2022)".
1022 https://assets.publishing.service.gov.uk/government/uploads/system/uplo
1023 ads/attachment_data/file/1050999/Technical-Briefing-35-28January2022.
1024 pdf. (2022).
1025 4 Cele, S. et al. Omicron extensively but incompletely escapes Pfizer
1026 BNT162b2 neutralization. Nature, doi:
1027 https://doi.org/10.1038/d41586-41021-03824-41585 (2021).
1028 5 Cao, Y. et al. Omicron escapes the majority of existing SARS-CoV-2
1029 neutralizing antibodies. Nature, doi:
1030 https://doi.org/10.1038/d41586-41021-03796-41586 (2021).
1031 6 Dejnirattisai, W. et al. Reduced neutralisation of SARS-CoV-2 omicron
1032 B.1.1.529 variant by post-immunisation serum. Lancet,
1033 doi:https://doi.org/10.1016/S0140-6736(1021)02844-02840 (2021).
1034 7 Cameroni, E. et al. Broadly neutralizing antibodies overcome
1035 SARS-CoV-2 Omicron antigenic shift. Nature, doi:
1036 https://doi.org/10.1038/d41586-41021-03825-41584 (2021).
1037 8 Garcia-Beltran, W. F. et al. mRNA-based COVID-19 vaccine boosters
1038 induce neutralizing immunity against SARS-CoV-2 Omicron variant. Cell,
1039 doi: https://doi.org/10.1016/j.cell.2021.1012.1033 (2021).
1040 9 Planas, D. et al. Considerable escape of SARS-CoV-2 Omicron to
1041 antibody neutralization. Nature, doi:
1042 https://doi.org/10.1038/d41586-41021-03827-41582 (2021).
1043 10 Liu, L. et al. Striking antibody evasion manifested by the Omicron variant
1044 of SARS-CoV-2. Nature, doi:
1045 https://doi.org/10.1038/d41586-41021-03826-41583 (2021).
1046 11 Meng, B. et al. Altered TMPRSS2 usage by SARS-CoV-2 Omicron
1047 impacts tropism and fusogenicity. Nature,
1048 doi:10.1038/s41586-022-04474-x (2022).
1049 12 Suzuki, R. et al. Attenuated fusogenicity and pathogenicity of
1050 SARS-CoV-2 Omicron variant. Nature, doi:10.1038/s41586-022-04462-1
1051 (2022).
1052 13 Shuai, H. et al. Attenuated replication and pathogenicity of SARS-CoV-2
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(which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
available under aCC-BY-ND 4.0 International license.
32
bioRxiv preprint doi: https://doi.org/10.1101/2022.02.14.480335; this version posted February 15, 2022. The copyright holder for this preprint
(which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
available under aCC-BY-ND 4.0 International license.
1202 20fk0108413, to Atsushi Kaneda, Terumasa Ikeda and Kei Sato) and
1203 (20fk0108451, to G2P-Japan Consortium, Akatsuki Saito, Takashi Irie, Keita
1204 Matsuno, Takasuke Fukuhara, Terumasa Ikeda, and Kei Sato); AMED Research
1205 Program on HIV/AIDS (21fk0410034, to Akifumi Takaori-Kondo; 21fk0410033,
1206 to Akatsuki Saito; and 21fk0410039, to Kei Sato); AMED CRDF Global Grant
1207 (21jk0210039 to Akatsuki Saito); AMED Japan Program for Infectious Diseases
1208 Research and Infrastructure (21wm0325009, to Akatsuki Saito; 21wm0125008,
1209 to Hirofumi Sawa and 21wm0225003, to Hirofumi Sawa); JST A-STEP
1210 (JPMJTM20SL, to Terumasa Ikeda); JST SICORP (e-ASIA) (JPMJSC20U1, to
1211 Kei Sato); JST SICORP (JPMJSC21U5, to Kei Sato), JST CREST
1212 (JPMJCR20H4, to Kei Sato); JSPS KAKENHI Grant-in-Aid for Scientific
1213 Research C (19K06382, to Akatsuki Saito); JSPS KAKENHI Grant-in-Aid for
1214 Scientific Research B (21H02736, to Takasuke Fukuhara; 18H02662, to Kei
1215 Sato; and 21H02737, to Kei Sato); JSPS Fund for the Promotion of Joint
1216 International Research (Fostering Joint International Research) (18KK0447, to
1217 Kei Sato); JSPS Core-to-Core Program (A. Advanced Research Networks)
1218 (JPJSCCA20190008, to Kei Sato); JSPS Research Fellow DC1 (19J20488, to
1219 Izumi Kimura); JSPS Leading Initiative for Excellent Young Researchers
1220 (LEADER) (to Terumasa Ikeda); World-leading Innovative and Smart Education
1221 (WISE) Program 1801 from the Ministry of Education, Culture, Sports, Science
1222 and Technology (MEXT) (to Naganori Nao); The Tokyo Biochemical Research
1223 Foundation (to Kei Sato); Mitsubishi Foundation (to Terumasa Ikeda);
1224 Shin-Nihon Foundation of Advanced Medical Research (to Mako Toyoda and
1225 Terumasa Ikeda); Tsuchiya Foundation (to Takashi Irie); a Grant for Joint
1226 Research Projects of the Research Institute for Microbial Diseases, Osaka
1227 University (to Akatsuki Saito); an intramural grant from Kumamoto University
1228 COVID-19 Research Projects (AMABIE) (to Terumasa Ikeda); Intercontinental
1229 Research and Educational Platform Aiming for Eradication of HIV/AIDS (to
1230 Terumasa Ikeda); and Joint Usage/Research Center program of Institute for
1231 Frontier Life and Medical Sciences, Kyoto University (to Kei Sato).
1232
1233 Consortia
1234 The Genotype to Phenotype Japan (G2P-Japan) Consortium
1235 Mai Suganami1, Akiko Oide1, Mika Chiba1, Tomokazu Tamura5, Kana Tsushima5,
1236 Haruko Kubo5, Zannatul Ferdous9, Hiromi Mouri9, Miki Iida9, Keiko Kasahara9,
1237 Koshiro Tabata9, Mariko Ishizuka9, Asako Shigeno29, Kenzo Tokunaga32, Seiya
1238 Ozono32, Isao Yoshida21, So Nakagawa33, Jiaqi Wu33, Miyoko Takahashi33,
1239 Bahityar Rahmutulla Nawai23, Yutaka Suzuki34, Yukie Kashima34, Kazumi Abe34,
1240 Kiyomi Imamura34, Ryoko Kawabata28, Otowa Takahashi3, Kimiko Ichihara3,
1241 Kazuko Kitazato3, Haruyo Hasebe3, Chihiro Motozono17, Toong Seng Tan17,
1242 Isaac Ngare17
34
bioRxiv preprint doi: https://doi.org/10.1101/2022.02.14.480335; this version posted February 15, 2022. The copyright holder for this preprint
(which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
available under aCC-BY-ND 4.0 International license.
1243
32
1244 National Institute of Infectious Diseases, Tokyo, Japan
33
1245 Tokai University, Isehara, Japan
34
1246 The University of Tokyo, Kashiwa, Japan
1247
35
bioRxiv preprint doi: https://doi.org/10.1101/2022.02.14.480335; this version posted February 15, 2022. The copyright holder for this preprint
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1289 the panel indicate the number of GFP-positive cells counted. c, Plaque assay.
1290 Diameter of plaques (20 plaques per virus) are summarized. d,f, S-based fusion
1291 assay. The fusion activity (arbitrary units) is shown. e, Western blot. Left,
1292 representative blots of S-expressing cells. ACTB is an internal control. Right, the
1293 ratio of S2 to the full-length S plus S2 proteins. g, Fold increase of pseudovirus
1294 infectivity by TMPRSS2 expression. Assays were performed in quadruplicate
1295 (a,g,h), octuplicate (a, most left) or triplicate (d–f) and data are the average ± s.d.
1296 Each dot indicates the result from an individual plaque (c) and an individual
1297 replicate (e,g). In b and c, raw data are shown in Extended Data Fig. 5 and 6.
1298 Statistically significant differences between BA.2 and other variants through
1299 timepoints were determined by multiple regression (a,d,f,h). Familywise error
1300 rates (FWERs) calculated using the Holm method are indicated in the figures.
1301 Statistically significant differences between BA.1 and BA.2 were determined by
1302 two-sided Mann–Whitney U-tests (b,d) or two-sided paired Student’s t-tests (e).
1303
1304 Fig. 4 | Virological features of BA.2 in vivo.
1305 Syrian hamsters were intranasally inoculated with B.1.1, BA.1 and BA.2. a, Body
1306 weight, Penh, Rpef, SpO2 values routinely measured. Hamsters of the same age
1307 were intranasally inoculated with PBS (uninfected). b, Viral RNA load in the lung
1308 hilum (left) and periphery (right). c,d, Percentage of N-positive cells in the whole
1309 lobes of lung (c) and bronchiole in the frontal/upper lobe of lung (d) measured by
1310 IHC. e, Histopathological scoring of lung lesions. Representative pathological
1311 features are shown in our previous studies12,23. Data are the average (a, 6
1312 hamsters per each group; b–e, 4 hamsters per each group) ± s.e.m. In a–c,e,
1313 statistically significant differences between BA.2 and other variants or uninfected
1314 hamsters through timepoints were determined by multiple regression. The data
1315 at 0 d.p.i. was excluded from the analyses. FWERs calculated using the Holm
1316 method are indicated in the figures. In d, each dot indicates the result from an
1317 individual hamster. In c–e, raw data are shown in Extended Data Fig. 7 and 8.
37
bioRxiv preprint doi: https://doi.org/10.1101/2022.02.14.480335; this version posted February 15, 2022. The copyright holder for this preprint
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1359 S genes were swapped with respective lineage/strain (GISAID IDs are indicated
1360 in the figure). Additionally, the ORF7b was swapped with sfGFP gene.
1361
1362 Extended Data Fig. 5. Syncytia and plaque formations by BA.2.
1363 a, Fluorescence microscopy. GFP area of infected VeroE6/TMPRSS2 cells
1364 (m.o.i. 0.01) at 24, 48, and 72 h.p.i were measured. Higher-magnification views
1365 of the regions indicated by squares are shown at bottom. b, Plaque assay. c,
1366 Coculture of S-expressing cells with HEK293-ACE2/TMPRSS2 cells. Left,
1367 representative images of S-expressing cells cocultured with HEK293 cells (top)
1368 or HEK293-ACE2/TMPRSS2 cells (bottom). Nuclei were stained with Hoechst
1369 33342 (blue). Right, the size distribution of syncytia (green). Numbers in the
1370 panel indicate the numbers of GFP-positive syncytia counted. Data are the
1371 average ± s.d. A statistically significant difference between BA.1 an BA.2 was
1372 determined by two-sided Mann–Whitney U-test. In a and b, summarized data
1373 are shown in Fig. 3b and 3c. Scale bars, 500 μm (a) or 200 μm (c).
1374
1375 Extended Data Fig. 6. Expression and binding properties of BA.2 S.
1376 a, S expression on the cell surface. Representative histograms stained with
1377 anti-S1/S2 polyclonal antibody (left) and the summarised data (right) are
1378 respectively shown. The number in the histogram indicates MFI. Grey
1379 histograms indicate isotype controls. b, Binding affinity of SARS-CoV-2 S RBD
1380 to ACE2 by yeast surface display. Left, The percentage of the binding of the
1381 SARS-CoV-2 S RBD expressed on yeast to soluble ACE2 (left) and the
1382 summarised data (right) are respectively shown. c, TMPRSS2 expression on the
1383 cell surface. Left, representative histograms stained with anti-TMPRSS2
1384 polyclonal antibody are shown. The number in the histogram indicates MFI. Grey
1385 histograms indicate isotype controls. Right, summarized data. Assays were
1386 performed in triplicate, and data are the average ± s.d. Each dot indicates the
1387 result from an individual replicate. A statistically significant difference between
1388 BA.1 an BA.2 was determined by two-sided unpaired Student’s t-test (a) or
1389 two-sided Mann–Whitney U-test (b).
1390
1391 Extended Data Fig. 7. IHC of SARS-CoV-2 N protein.
1392 a,b, IHC of viral N protein in the middle part of trachea of all infected hamsters (n
1393 = 4 per each viral strain) at 1 d.p.i. (a) and the lung at 1, 3 and 5 d.p.i (b). Each
1394 panel indicates the representative result from an individual infected hamster. c,
1395 Lung lobes of the hamsters infected with B.1.1, BA.1 or BA.2 (n = 4 for each
1396 virus) at 1, 3 and 5 d.p.i. were immunohistochemically stained with
1397 anti-SARS-CoV-2 N monoclonal antibody. In each panel, IHC staining (top) and
1398 the digitalized N-positive area (bottom, indicated in red) are shown. The number
39
bioRxiv preprint doi: https://doi.org/10.1101/2022.02.14.480335; this version posted February 15, 2022. The copyright holder for this preprint
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1399 in the bottom panel indicates the percentage of N-positive area. Summarized
1400 data is shown in Fig. 4c. Scale bars, 1 mm (a); 500 μm (b); or 5 mm (c).
1401
1402 Extended Data Fig. 8. Pathological features of BA.2.
1403 a, H&E staining of the lungs of infected hamsters. Uninfected lung alveolar
1404 space and bronchioles are also shown. b, Type II pneumocytes in the lungs of
1405 infected hamsters. Left, lung lobes of the hamsters infected with B.1.1 (n = 4),
1406 BA.1 (n = 4), and BA.2 (n = 4) at 5 d.p.i. In each panel, H&E staining (top) and
1407 the digitalized inflammation area (bottom, indicated in red) are shown. The
1408 number in the bottom panel indicates the percentage of the section represented
1409 by the indicated area (i.e., the area indicated with red colour per the total area of
1410 the lung lobes). Right, summarized data. Each dot indicates the result from an
1411 individual hamster.
1412 Scale bars, 250 μm (a) or 5 mm (b).
40
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